A linear array of nucleosomes generated by unfolding from the natural condition of chromatin.
The consensus sequence centered about 10 bp before the start point of a bacterial gene. It is involved in melting DNA during the initiation reaction.
A family of seven evolutionarily conserved and highly homologous adaptors that form homo- or heterodimers and/or tetramers and that bind a multitude of protein and DNA ligands through either the amphipathic groove or the outer surface. They regulate diverse cell homeostasis events, such as signal transduction, survival, cell cycle progression, and DNA replication, as well as cell differentiation processes, such as class switch recombination (CSR).
The hypothesis that the early vertebrate genome underwent two rounds of duplication.
The region in an mRNA between the termination codon and the end of the message.
A coil of nucleosomes. It is the basic level of organization of nucleosomes in chromatin.
The consensus sequence centered about 35 bp before the start point of a bacterial gene. It is involved in initial recognition by RNA polymerase.
Repeats that recur at a high frequency in Ig switch regions, but not in the genome at large. They are specifically bound by 14-3-3 adaptors and other class switch recombination (CSR) elements. They are important for CSR targeting.
The generation of 3′ overhanging single-stranded regions that occurs via exonucleolytic digestion of the 5′ ends at a double-strand break.
The region in an mRNA between the start of the message and the first codon.
The second splicing complex; it is formed by the binding of U2 snRNP to the E complex.
The conserved 11-bp sequence of A-T base pairs in the yeast ARS element that comprises the replication origin.
The site of the ribosome that an aminoacyl-tRNA enters to base pair with the codon.
Describes a process in which RNA polymerase starts transcription but terminates before it has left the promoter. It then reinitiates. Several cycles may occur before the elongation stage begins.
The average number of mRNA molecules per cell.
Consists of a small number of individual molecular species, each present in a large number of copies per cell.
An autonomous transposable element in maize.
A fragment of a chromosome (generated by breakage) that lacks a centromere and is lost at cell division.
Mutagens that act on DNA to cause the insertion or deletion of a single base pair. They were useful in defining the triplet nature of the genetic code.
An enzyme that removes the amino group from the cytidine base in DNA; mediates DNA damage that leads to the initiation of immunoglobulin (Ig) diversification.
A protein that stimulates the expression of a gene, typically by interacting with a promoter to stimulate RNA polymerase. In eukaryotes, the sequence to which it binds in the promoter is called an enhancer.
An autonomous transposable element in maize.
The response mediated by lymphocytes that are activated by their specific interaction with antigen. The response develops over several days as lymphocytes with antigen-specific receptors are stimulated to proliferate and become effector cells. It is responsible for immunological memory.
A survival mechanism used by plasmids. The mechanism kills the bacterium upon loss of the plasmid.
Plasmids that carry genes coding for the synthesis of opines of the agropine type. The tumors usually die early.
See activation-induced (cytidine) deaminase (AID).
One of several alternative forms of a gene occupying a given locus on a chromosome.
The expression in any particular lymphocyte of only one allele coding for the expressed immunoglobulin heavy or light chain. This is caused by feedback from the first immunoglobulin allele to be expressed that prevents activation of the allele on the other chromosome.
A by-product of β-galactosidase (encoded by LacZ), the true inducer of the lac operon.
Polyploidization resulting from hybridization between two different but reproductively compatible species.
The ability of a protein to change its conformation (and therefore activity) at one site as the result of binding a small molecule to a second site located elsewhere on the protein.
The production of different RNA products from a single product by changes in the usage of splicing junctions.
One of a set of dispersed, related sequences, each approximately 300 bp long, in the human genome (members of the SINE family). The individual members have Alu cleavage sites at each end.
The triplet UAG, one of the three termination codons that end polypeptide translation.
The precise, primer-to-primer, double-stranded nucleic acid product of a PCR or RT-PCR reaction.
Insoluble fibrous protein polymers with a cross β-sheet structure generated by prions or other dysfunctional protein aggregations (such as in Alzheimer’s disease).
The renaturation of a duplex structure from single strands that were obtained by denaturing duplex DNA.
An autoimmune antiserum that defines the Sm domain that is common to a group of proteins found in snRNPs that are involved in RNA splicing.
A protein that is produced by B lymphocytes and that binds a particular antigen. Consists of two identical light chains disulfide bond–linked to two identical heavy chains. They are synthesized in membrane-bound and secreted forms. Those produced during an immune response recruit effector functions to help neutralize and eliminate the pathogen.
A molecule that can bind specifically to an antigen receptor, such as a B cell receptor or an antibody, and can induce a specific immune response.
Cells of the immune system that are very efficient at internalizing antigen either by phagocytosis or by receptor-mediated endocytosis, and then displaying a fragment of the antigen, bound to a class II MHC molecule, on their membrane. Examples include dendritic cells, macrophages, and B cells.
The site or region on the surface of a macromolecular antigen that induces an antibody response.
Strands of the double helix are organized in opposite orientation so that the 5′ end of one strand is aligned with the 3′ end of the other strand.
A positive regulator that functions in opening chromatin.
RNA that has a complementary sequence to an RNA that is its target.
See template strand.
A mechanism of transcriptional control in which termination is prevented at a specific terminator site, allowing RNA polymerase to read into the genes beyond it.
Proteins that allow RNA polymerase to transcribe through certain terminator sites.
Bacteria that lack a nucleoid but are of similar shape to wild-type bacteria.
Programmed cell death triggered by a cellular stimulus through a signal transduction pathway.
An RNA domain that binds a small molecule; this can result in a conformation change in the RNA.
A DNA base excision repair (BER) pathway enzyme that nicks the phosphodiester backbone of an abasic site generated by DNA glycosylase. Nicks generated in proximity on opposite DNA strands are critical for the generation of double-strand breaks in switch regions of the immunoglobulin locus.
A protein that, when bound to DNA, can alter the structure of the DNA (e.g., introduce a bend). These proteins appear to have no other function.
See AU-rich element (ARE).
An origin for replication in yeast. The common feature among different examples of these sequences is a conserved 11-bp sequence called the A domain.
Proteins that are required for formation of a macromolecular structure but are not themselves part of that structure.
A complex of one or more proteins associated with an ATPase of the SWI2/SNF2 superfamily that uses the energy of ATP hydrolysis to alter or displace nucleosomes.
The loci on a lambda phage and the bacterial chromosome at which recombination integrates the phage into, or excises it from, the bacterial chromosome.
The regulation of bacterial operons by controlling termination of transcription at a site located before the first structural gene.
A terminator sequence at which attenuation occurs.
A eukaryotic mRNA cis sequence consisting largely of A and U ribonucleotides that acts as a destabilizing element.
An active transposon with the ability to transpose (i.e., encode a functional transposase).
A DNA sequence element that contains an origin of replication.
Polyploidization resulting from mitotic or meiotic errors within a species.
A method of capturing an image of radioactive materials on film.
A site or mutation that affects only the properties of its own molecule of DNA, often indicating that a site does not code for a diffusible product.
The ability of an intron to excise itself from an RNA by a catalytic action that depends only on the sequence of RNA in the intron.
A proteinaceous structure around which the chromosomes condense at the start of synapsis.
A lymphocyte that produces antibodies. Developed primarily in the bone marrow. Those lymphocytes emerging from the marrow undergo further differentiation in the bloodstream and peripheral lymphoid organs.
Receptor composed of the antigen-binding membrane immunoglobulin and the Igα and Igβ signaling coreceptors. It has the same structure and specificity of the antibody that will be produced by the same B cell after its activation by antigen.
A mutation that reverses the effect of a mutation that had inactivated a gene; thus, it restores the original sequence or function of the gene product.
A bacterial virus.
Exceptionally large puffs on polytene chromosomes that are the sites of RNA transcription. They are useful in studying the structure of active genes and synthesis and transport of RNA molecules.
A series of short, repeated sequences found in the nontranscribed spacer of Xenopus rDNA genes.
Portions of polytene chromosomes visible as dense regions that contain the majority of DNA; they include active genes.
The complex of transcription factors that assembles at the promoter before RNA polymerase is bound.
Transcription factors required by RNA polymerase II to form the initiation complex at all RNA polymerase II promoters. Factors are identified as TFIIX, where X is a letter.
DNA repair systems that directly remove the damaged base and replace it with the correct base within the DNA.
Binding of nucleotide bases such that each base pair consists of a purine and pyrimidine held together by one or more hydrogen bonds. In DNA, the purine adenine (A) binds to the pyrimidine thymine (T) and the purine guanine (G) binds to the pyrimidine cytosine (C). In RNA, the pyrimidine uracil (U) is substituted for thymine.
Curves in DNA often associated with poly(A) stretches on the same side of the double helix that are thought to assist with both activation and repression of transcription.
A system in which an origin generates two replication forks that proceed away from the origin in opposite directions.
The structure containing all four chromatids (two representing each homologue) at the start of meiosis.
See closed (blocked) reading frame.
Technique used to transfer proteins, DNA, or RNA onto a carrier such as nitrocellulose or nylon. Following the blotting, the molecules can be visualized through a number of different techniques (e.g., staining).
A DNA sequence element bound by proteins that prevents the spread of open or closed chromatin.
The ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous.
A short sequence just before the end of an intron at which the lariat intermediate is formed in splicing by joining the 5′ nucleotide of the intron to the 2′ position of an adenosine.
The mode of genetic recombination in which two DNA duplex molecules are broken at corresponding points and then rejoined crosswise (involving formation of a length of heteroduplex DNA around the site of joining).
A domain of 110 amino acids that binds to acetylated lysines (often in histones).
Stochastic fluctuations that can be locked into a productive structure.
A protein with a basic DNA-binding region adjacent to a leucine zipper dimerization motif.
The total amount of DNA in the genome (per haploid set of chromosomes).
The lack of relationship between the DNA content of an organism and its coding potential.
See cyclic AMP (cAMP).
The structure at the 5′ end of eukaryotic mRNA; it is introduced after transcription by linking the terminal phosphate of 5′ guanosine triphosphate (GTP) to the terminal base of the mRNA.
The external protein coat of a virus particle.
The domain of eukaryotic RNA polymerase II that is phosphorylated at initiation and is involved in coordinating several activities with transcription.
A sequence of events, each of which is stimulated by the previous one. In transcriptional regulation, as seen in sporulation and phage lytic development, it means that regulation is divided into stages and that at each stage one of the genes that is expressed codes for a regulator needed to express the genes of the next stage.
The ability of glucose to prevent the expression of a number of genes. In bacteria this is a positive control system; in eukaryotes, it is completely different.
A mechanism that enables bacteria to utilize a preferred carbon source first even in the presence of high levels of a non-preferred carbon source; for example, the presence of glucose results in repression of the lac operon even in the presence of lactose.
A positive regulator protein activated by cyclic AMP. It is needed for RNA polymerase to initiate transcription of many operons of Escherichia coli.
To link together two circular molecules, as in a chain.
A transcription factor involved in regulation of chromatin architecture, V(D)J recombination, insulator activity, and transcription regulation. It binds together DNA strands, thus forming chromatin loops, and anchors DNA to cellular structures such as the nuclear lamina. It also defines the boundaries between active and heterochromatic DNA.
A single-stranded DNA complementary to an RNA, synthesized from it by reverse transcription in vitro.
Information cannot be transferred from protein to protein or protein to nucleic acid but can be transferred between nucleic acids and from nucleic acid to protein.
A structure that lies in the middle of the synaptonemal complex, along which the lateral elements of homologous chromosomes align; it is formed from Zip proteins.
A constricted region of a chromosome that includes the site of attachment (the kinetochore) to the mitotic or meiotic spindle. It consists of unique DNA sequences and proteins not found anywhere else in the chromosome.
A biochemical control mechanism that prevents the cell from progressing from one stage to the next unless specific goals and requirements have been met.
A proofreading mechanism in which the correction event occurs after the addition of an incorrect subunit to a polymeric chain by means of reversing the addition reaction.
A site at which two homologous chromosomes synapse during meiosis.
Either of the two threadlike strands formed when a chromosome duplicates during the early stages of cell division. The two strands are held together at the centromere and separate into daughter chromosomes during anaphase.
The combination of DNA and proteins that make up the contents of the nucleus of a cell. Its primary functions are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene expression and DNA replication and repair. The primary protein components are histones that compact the DNA.
The energy-dependent displacement or reorganization of nucleosomes that occurs in conjunction with activation of genes for transcription.
Nucleosomes that contain linker histones.
An aggregate in the nucleus of heterochromatin from different chromosomes.
Domains of approximately 60 amino acids that recognize various methylated states of lysines in histones and other proteins; some have other functions, such as RNA binding.
Densely staining granules visible in chromosomes under certain conditions, especially early in meiosis, when a chromosome may appear to consist of a series of such granules.
A region of altered chromosome structure that includes at least one active transcription unit.
A discrete unit of the genome carrying many genes. Each consists of a very long molecule of duplex DNA and an approximately equal mass of proteins (in eukaryotes). It is visible as a morphological entity only during cell division.
The coupling of the homologous chromosomes at the start of meiosis.
A proteinaceous structure in the shape of a sister chromatid pair, generated when chromosomes are depleted of histones.
The discrete three-dimensional spaces occupied by individual chromosomes in the interphase nucleus.
Multigene complex in eukaryotes that brings together various genes from distant loci into close proximity.
A site that affects the activity only of sequences on its own molecule of DNA (or RNA); this property usually implies that the site does not code for protein.
A site or mutation that affects the properties only of its own molecule of DNA, often indicating that a site does not code for a diffusible product.
The genetic unit defined by the complementation test; it is equivalent to a gene.
A protein complex that forms a circle around the DNA. By connecting to DNA polymerase, it ensures that the enzyme action is processive.
A five-subunit protein complex that is responsible for loading the β clamp onto DNA at the replication fork.
A somatic change in the Ig gene locus organization in which the constant region of the heavy chain is changed but the variable region (and therefore antigen specificity) remains the same. This allows different progeny B cells from the same activated B cell to produce antibodies of different classes or isotypes. Naïve mature B cells express IgM and IgD. After activation by antigen, they undergo class switching to IgG, IgA, or IgE. Class switching is effected by DNA recombination between the switch regions lying upstream of different C heavy chain gene clusters.
See class switch recombination.
The process by which only lymphocyte(s) that bind a given antigen through their surface B cell receptor are stimulated to proliferate and differentiate to produce antibodies that specifically bind the same antigen. Requires that each lymphocyte expresses on its surface B cell receptors of a single, typically unique specificity. Thus, the antigen “selects” the lymphocytes to be activated. Originally a theory, but now an established principle in immunology.
An exact replica or copy, whether it is Dolly the sheep or a fragment of DNA.
Propagation of a DNA sequence by incorporating it into a hybrid construct that can be replicated in a host cell.
DNA (often derived from a plasmid or a bacteriophage genome) that can be used to propagate an incorporated DNA sequence in a host cell; vectors contain selectable markers and replication origins to allow identification and maintenance of the vector in the host.
A reading frame that cannot be translated into protein because of the occurrence of termination codons.
The stage of initiation of transcription before RNA polymerase causes the two strands of DNA to separate to form the “transcription bubble.” The DNA is double stranded.
Rule discovered by Erwin Chargaff that purines tend to cluster on one DNA strand and pyrimidines tend to cluster on the other. As applied to exons, the purines, A and G, tend to be clustered in one DNA strand of the DNA duplex (usually the nontemplate strand) and these are complemented by clusters of the pyrimindines, T and C, in the template strand.
Factors required for transcription that do not bind DNA but are required for (DNA-binding) activators to interact with the basal transcription factors.
Constitutes an intermediate during recombination of immunoglobulin and T cell receptor V(D)J gene segments. It identifies with the termini of the cleaved V, D, and J DNA regions. The subsequent joining yields coding joint(s).
A part of a gene that codes for a polypeptide sequence.
The DNA strand that has the same sequence as the mRNA and is related by the genetic code to the protein sequence that it represents.
(1) A triplet of nucleotides that codes for an amino acid. (2) A termination signal.
A higher usage of one codon in genes to encode amino acids for which there are several synonymous codons.
A description of the relative abundance of tRNAs for each codon.
tRNAs recognized by a particular aminoacyl-tRNA synthetase. All are charged with the same amino acid.
Proteins that regulate the separation of sister chromatids during cell division. They hold the sister chromatids together after DNA replication until anaphase, at which point their removal leads to the separation of the sister chromatids.
See concerted (coincidental) evolution.
A structure that is produced by fusion of two replicons, one originally possessing a transposon and the other lacking it; the product has copies of the transposon present at both junctions of the replicons, oriented as direct repeats.
The relationship that describes the 1:1 correspondence of a sequence of triplet nucleotides to a sequence of amino acids.
Field of study that examines similarities and differences among DNA sequences, genes, gene order, regulatory sequences, and other genomic landmarks to determine how organisms are related to each other.
A group of plasmids that contains members unable to coexist in the same bacterial cell.
A set of approximately 20 proteins that function through a cascade of proteolytic actions that lead to generation of intermediates (membrane attack complex) that lyse target cells and/or chemotactic fragments that attract macrophages, neutrophils, or lymphocytes.
Base pairs that match up in the pairing reactions in double helical nucleic acids (A with T in DNA or with U in RNA, and C with G).
The double-stranded DNA that is synthesized from a single-stranded RNA template through a reaction catalyzed by reverse transcriptase.
Mutant genes that do not complement each other, thus indicating that the mutations occur on the same gene. Complementation tests are used to determine whether two mutations are in the same or different genes.
A test that determines whether two mutations are alleles of the same gene. It is accomplished by crossing two different recessive mutations that have the same phenotype and determining whether the wild-type phenotype can be produced. If so, the mutations are said to complement each other and are probably not mutations in the same gene.
mRNA that consists of a large number of individual mRNA species, each present in very few copies per cell. This accounts for most of the sequence complexity in RNA.
Segments of DNA that have similar function as simple transposons and IS elements in that they have protein-coding DNA segments flanked by inverted, repeated sequences that can be recognized by transposase enzymes.
The ability of two or more related genes to evolve together as though constituting a single locus.
Class of ATPases that are involved in the control of the condensation of genetic material into compact chromosomes at mitosis. They form complexes that have a core of the heterodimer SMC2–SMC4 associated with other (non-SMC) proteins.
A mutation that is lethal under one set of conditions but not lethal under a second set of conditions, such as temperature.
A process in which two cells come in contact and transfer genetic material. In bacteria, DNA is transferred from a donor to a recipient cell. In protozoa, DNA passes from each cell to the other.
An idealized sequence in which each position represents the base most often found when many actual sequences are compared.
Sequences in which many examples of a particular nucleic acid or protein are compared and the same individual bases or amino acids are always found at particular locations.
Genes that encode the constant regions of immunoglobulin heavy or light chain.
The part of an immunoglobulin or T cell receptor that varies least in amino acid sequence between different molecules. C regions are encoded by C gene segments. In antibodies, the heavy chain regions identify the class or subclass of immunoglobulin and mediate effector functions. Humans have five Ig classes, or isotypes: IgM, IgD, IgG (IgG1, IgG2, IgG3, and IgG4), IgA, and IgE.
Describes a state in which a gene is expressed continuously.
A gene that is (theoretically) expressed in all cells because it provides basic functions needed for sustenance of all cell types.
The inert state of particular (often repetitive) DNA sequences, such as satellite DNA.
The fact that neighboring sequences may change the efficiency with which a codon is recognized by its aminoacyl-tRNA or is used to terminate polypeptide translation.
Transposable units in maize originally identified solely by their genetic properties. They may be autonomous (able to transpose independently) or nonautonomous (able to transpose only in the presence of an autonomous element).
The effect of a single gene on the organism carrying it, usually as a result of the polypeptide it encodes.
The number of copies of a plasmid that is maintained in a bacterium (relative to the number of copies of the origin of the bacterial chromosome).
Region of nucleosomal DNA that has an invariant length of 146 bp, the minimum length of DNA needed to form a stable monomeric nucleosome, and is relatively resistant to digestion by nucleases.
The complex of RNA polymerase subunits needed for elongation. It does not include additional subunits or factors that may be needed for initiation or termination.
One of the four types of histone (H2A, H2B, H3, and H4 and their variants) found in the core particle derived from the nucleosome. (This excludes linker histones.)
The shortest sequence at which an RNA polymerase can initiate transcription (typically at a much lower level than that displayed by a promoter containing additional elements). For RNA polymerase II, it is the minimal sequence at which the basal transcription apparatus can assemble, and it includes three sequence elements: the Inr, the TATA box, and the downstream promoter element (DPE). It is typically approximately 40 bp long.
The segment of DNA that is common to the attachment sites on both the phage lambda and bacterial genomes. It is the location of the recombination event that allows phage lambda to integrate.
A molecule that triggers repression of transcription by binding to a regulator protein.
Cloning vector derived from a bacterial plasmid by incorporating the cos sites of phage lambda, which make the plasmid DNA a substrate for the lambda packaging system.
An RNA molecule that prevents an RNA primer from initiating transcription by base pairing with the primer.
The process in bacteria where a message is simultaneously being translated while it is still being transcribed.
The DNA found in the chloroplast.
Stretches of 1 to 2 kb in mammalian genomes that are enriched in CpG dinucleotides; frequently found in promoter regions of genes.
Clusters of regularly interspersed short palindromic repeats in prokaryotes that are transcribed and processed into short RNAs that function in RNA interference.
A possible consequence of unequal crossing over that allows a mutation in one member of a tandem cluster to spread through the whole cluster (or to be eliminated).
A tumor that can be induced in many plants by infection with the bacterium Agrobacterium tumefaciens.
See catabolite repressor protein (CRP).
A satellite DNA sequence not identified as such by a separate peak on a density gradient; that is, it remains present in main band DNA.
Non-protein-coding RNAs transcribed by RNA Pol II, frequently generated from the 3′ ends of genes (resulting in antisense transcripts) and rapidly degraded after synthesis.
The domain of RNA polymerase that is involved in stimulating transcription by contact with regulatory proteins.
The DNA found in the chloroplast.
See cryptic unstable transcripts (CUTs).
The coregulator of catabolite repressor protein (CRP); it has an internal 3′–5′ phosphodiester bond. Its concentration is inverse to the concentration of glucose.
Serine-threonine protein kinases that are synthesized in an inactive form and activated by binding a cyclin protein subunit.
Cell cycle–dependent proteins that have no intrinsic enzymatic activity but when bound to an inactive cyclin-dependent kinase can activate it.
A schematic representation of chromosomes that indicates the arrangement of individual genes. Created by analyzing the banding patterns of chromosomes that have undergone changes such as deletions and mutations.
The part of a transmembrane protein that is exposed to the cytosol.
A T lymphocyte, usually CD8+, that can kill target cells expressing specifically recognized antigens, such as virus-encoded glycoproteins expressed on the surface of virus-infected cells.
A cytoplasmic condition that affects P element activity; it results from the presence or absence of a repressor of transposition, which is provided by the mother to the egg.
(1) A region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region. (2) The displacement of a region of one strand of duplex DNA by a complementary single-stranded invader.
Coding sequences in the Ig heavy chain and TCRβ and TCRδ loci. They lie in cluster between the variable (V) and joining (J) gene segment clusters. Not present in Iδ, Igλ, and TCRα and TCRγ loci.
An enzyme that adds a methyl group to an unmethylated target sequence on DNA.
tRNA that has no amino acid or polypeptide chain attached because it has completed its role in protein synthesis and is ready to be released from the ribosome.
An exoribonuclease that is specific for digesting poly(A) tails.
An enzyme that catalyzes the removal of the 7-methyl guanosine cap at the 5′ end of eukaryotic mRNAs.
A complex of bacterial enzymes, including RNAase and helicase activities, that is involved in degrading mRNA.
Genes in phage lambda that are equivalent to the middle genes of other phages. They cannot be transcribed until regulator protein(s) coded by the immediate early genes have been synthesized.
A casual name for an enzyme that removes a methyl group, typically from DNA, RNA, or protein.
A molecule’s conversion from the physiological conformation to some other (inactive) conformation. In DNA, this involves the separation of the two strands due to breaking of hydrogen bonds between bases.
The most powerful antigen-presenting cell. Its main function is to process antigen material and present it to T cells to initiate an immune response. They account for less than 1% of blood mononuclear cells and are present in small quantities in tissues that are in contact with the external environment. In the skin, they are called Langerhans cells.
Any one of many different cis sequences, present in some mRNAs, that stimulates rapid decay of that mRNA.
An endonuclease that processes double-stranded precursor RNA to 21- to 23-nucleotide RNAi molecules.
A popular DNA sequencing method that relies on synthetic primers. It is also called the Sanger technique. DNA polymerases are used to copy a single-stranded DNA template by adding nucleotides to the growing chain. The chain elongates at the 3′ end of a primer, which is an oligonucleotide that anneals to the template. The deoxynucleotides added to the extension are determined by base-pair matching to the template.
A chain-terminating nucleotide that lacks a 3′–OH group and therefore is not a substrate for DNA polymerization. Used in DNA sequencing and as an antiviral drug.
Identical (or closely related) sequences present in two or more copies in the same orientation in the same molecule of DNA.
Method of directing the orientation of inserts into vectors by digesting a DNA insert or vector molecule with two restriction endonuclease enzymes to create either blunt or noncomplementary sticky ends at both ends of each restriction fragment. The insert can then be ligated to the vector (plasmid or bacteriophage) in a specific, fixed orientation.
A region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region. The same term is also used to describe the displacement of a region of one strand of duplex DNA by a complementary single-stranded invader.
A nonautonomous transposable element in maize, related to the autonomous Activator (Ac) element.
An enzyme that catalyzes the removal of only one or a few nucleotides before dissociating from the substrate.
The corrected percent difference in nucleotide sequence between two related DNA sequences or in amino acid sequences between two proteins.
Technique used to identify individuals by characteristics of their DNA for the purposes of paternity testing or criminal investigations. Although approximately 99.9% of human DNA sequences are the same in every person, there are enough differences in a person’s DNA that it is possible to distinguish one individual from another (unless they are monozygotic twins). Identification is based on the small set of DNA variations that is likely to differ between unrelated individuals.
The enzyme that makes a bond between an adjacent 3′–OH and 5′–phosphate end where there is a nick in one strand of duplex DNA.
An enzyme that adds a methyl group to a DNA substrate.
Temperature-sensitive replication mutants in Escherichia coli that identify a set of loci called the dna genes.
An enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). Any particular enzyme may be involved in repair or replication (or both).
Technique used to identify individuals by characteristics of their DNA for the purposes of paternity testing or criminal investigations. Although approximately 99.9% of human DNA sequences are the same in every person, there are enough differences in a person’s DNA that it is possible to distinguish one individual from another (unless they are monozygotic twins). Identification is based on the small set of DNA variations that is likely to differ between unrelated individuals.
The removal and replacement of damaged DNA by the correct sequence.
See DNA polymerase.
An enzyme that degrades DNA.
In reference to a chromosome, it may refer either to a discrete structural entity defined as a region within which supercoiling is independent of other regions or to an extensive region including an expressed gene that has heightened sensitivity to degradation by the enzyme DNase I. In a protein, it is a discrete continuous part of the amino acid sequence that can be equated with a particular function.
A type of mutation in which the altered product possesses a new molecular function or pattern of gene expression.
A mutation that results in a mutant gene product that prevents the function of the wild-type gene product, causing loss or reduction of gene activity in cells containing both the mutant and wild-type alleles. The most common cause is that the gene codes for a homomultimeric protein whose function is lost if only one of the subunits is a mutant.
Mechanisms employed to compensate for the discrepancy between the presence of two X chromosomes in one sex but only one X chromosome in the other sex.
Breaks that occur when both strands of a DNA duplex are cleaved at the same site. Genetic recombination is initiated by such breaks. The cell also has repair systems that act on breaks that are created at other times.
The period (usually measured in minutes) that it takes for a bacterial cell to reproduce.
A mutation in a promoter that decreases the rate of transcription.
Sequences proceeding farther in the direction of expression within the transcription unit.
A common component of RNA polymerase II promoters that do not contain a TATA box.
An endonuclease that processes double-stranded primary RNAs into short (approximately 70-bp) precursors for Dicer processing.
A nonautonomous transposable element in maize, related to the autonomous Activator (Ac) element.
The first complex to form at a splice site, consisting of U1 snRNP bound at the splice site together with factor ASF/SF2, U2AF bound at the branch site, and the bridging protein SF1/BBP.
The site of the ribosome that briefly holds deacylated tRNAs before their release.
Genes that are transcribed before the replication of phage DNA. They code for regulators and other proteins needed for later stages of infection.
The part of the phage lytic cycle between entry and replication of the phage DNA. During this time, the phage synthesizes the enzymes needed to replicate its DNA.
The elongation factor that binds aminoacyl-tRNA and places it into the A site of a bacterial ribosome.
A member of the erbB family of receptors that binds Epidermal Growth Factor (EGF).
See exon junction complex (EJC).
Technique whereby an electric pulse is applied to a cell to create temporary pores in the cell membrane, increasing the membrane’s permeability to chemicals, drugs, or DNA. Can be used to transform bacteria and yeast or to introduce new DNA into tissue cultures, especially of mammalian cells.
The stage in a macromolecular synthesis reaction (replication, transcription, or translation) when the nucleotide or polypeptide chain is extended by the addition of individual subunits.
Proteins that associate with ribosomes cyclically during the addition of each amino acid to the polypeptide chain.
An enzyme that cleaves bonds within a nucleic acid chain; it may be specific for RNA or for single- or double-stranded DNA.
Successive replications of a synapsed diploid pair of chromosomes that do not separate, thus remaining attached in their extended state. Results in production of giant chromosomes.
A ribonuclease that cleaves an RNA at internal site(s).
A cis-acting sequence that increases the utilization of (most) eukaryotic promoters and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
Peptide hormone that binds to EGFR in a lock-and-key type mechanism.
Changes that influence the phenotype without altering the genotype. They consist of changes in the properties of a cell that are inherited but that do not represent a change in genetic information.
A plasmid able to integrate into bacterial DNA.
The site or region on the surface of a macromolecular antigen that induces an antibody response.
A polypeptide that has been added to a protein that allows its identification by an antibody.
Relatively short noncoding RNA molecules transcribed from the DNA sequence of enhancer regions. Evidence suggests that they play a role in regulation of transcription.
A DNA polymerase that incorporates noncomplementary bases into the daughter strand.
A repair process in which noncomplementary bases are incorporated into the daughter strand.
Regions that comprise most of the genome in the interphase nucleus, are less tightly coiled than heterochromatin, and contain most of the active or potentially active single-copy genes.
Release of phage or episome or other sequence from the host chromosome as an autonomous DNA molecule.
A type of repair system in which one strand of DNA is directly excised and then replaced by resynthesis using the complementary strand as a template.
Any segment of an interrupted gene that is represented in the mature RNA product.
The process in which a pair of splicing sites are recognized by interactions involving the 5′ site of the intron and also the 5′ site of the next intron downstream.
A protein complex that assembles at exon–exon junctions during splicing and assists in RNA transport, localization, and degradation.
The hypothesis that genes have evolved by the recombination of various exons coding for functional protein domains.
Inserting a genomic fragment into a vector whose function depends on the provision of splicing junctions by the fragment.
An enzyme that cleaves nucleotides one at a time from the end of a polynucleotide chain; it may be specific for either the 5′ or 3′ end of DNA or RNA.
A ribonuclease that removes terminal ribonucleotides from RNA.
An exonuclease complex involved in nuclear processing and nuclear/cytoplasmic RNA degradation.
A short-sequenced fragment of a cDNA sequence that can be used to identify an actively expressed gene.
A cloning vehicle containing a promoter that can drive expression of an attached gene.
A sequence that remains in the mature protein that is produced by processing a precursor via protein splicing.
Genes that reside outside the nucleus in organelles such as mitochondria and chloroplasts.
An episome that can be free or integrated in Escherichia coli, and that can sponsor conjugation in either form.
The inert state of sequences that also exist in active copies (e.g., one mammalian X chromosome in females).
Rule discovered by Erwin Chargaff that applies to most regions of DNA whereby base A in one strand of the duplex is matched by a complementary base (T) in the other strand, and base G in one strand of the duplex is matched by a complementary base (C) in the other strand. Rule applies to single bases as well as to dinucleotides, trinucleotides, and oligonucleotides.
The process by which a new allele replaces the allele that was previously predominant in a population.
A process whereby the emission from an excited fluorophore is captured and reemitted at a longer wavelength by a nearby second fluorophore whose excitation spectrum matches the emission frequency of the first fluorophore.
The genome-wide pressure for single-stranded nucleic acid, whether in free form or extruded from duplex forms, to adopt secondary and higher order stem-loop structures.
A technique for identifying the site on DNA bound by some protein by virtue of the protection of bonds in this region against attack by nucleases.
A mutation that inactivates a functional gene.
The strand of DNA that is synthesized continuously in the 5′ to 3′ direction.
A genetic mutation formed through the addition or deletion of nucleotide bases such that the reading frame is thrown off. The resulting polypeptide formed is usually abnormally short or abnormally long and most likely nonfunctional.
A site that is a palindromic sequence that is methylated on both strands of DNA.
Chimeric proteins that are produced due to the joining of two or more genes that originally coded for separate proteins.
Denotes the form of the histone variant H2AX when it is phosphorylated on a SQEL/Y motif at the site of a double-strand break.
Bands generated on eukaryotic chromosomes by staining techniques that appear as a series of lateral striations. They are used for karyotyping (i.e., identifying chromosomes and chromosomal regions by the banding pattern).
Nucleic acids that are rich in guanine and can fold into a four-strand structure stabilized by hydrogen bonds that can be stacked.
A mutation that causes an increase in the normal gene activity. It sometimes represents acquisition of certain abnormal properties. It is often, but not always, dominant.
A type of DNA repair in which one DNA duplex may act as a donor of genetic information that directly replaces the corresponding sequences in the recipient duplex by a process of gap generation, strand exchange, and gap filling.
The tendency of a species’ genome to conform to its optimal GC content.
Rule discovered by Erwin Chargaff that the overall proportion of guanine (G) and cytosine (C) in a genome tends to be a species-specific character and that the GC content tends to be greater in exons than in introns.
A group of adjacent genes that are identical or related.
The alteration of one strand of a heteroduplex DNA to make it complementary with the other strand at any position(s) where there were mispaired bases or the complete replacement of genetic material at one locus by a homologous sequence.
Process whereby the guanine (G) and cytosine (C) content of DNA increases due to gene conversion during recombination.
The process by which the information in a sequence of DNA in a gene is used to produce an RNA or polypeptide, involving transcription and (for polypeptides) translation.
A set of genes within a genome that code for related or identical proteins or RNAs. The members were derived by duplication of an ancestral gene followed by accumulation of changes in sequence between the copies. Most often the members are related but not identical.
The correspondence between triplets in DNA (or RNA) and amino acids in polypeptide.
The chance fluctuation (without selective pressure) of the frequencies of alleles in a population.
Direct manipulation of an organism’s genome through the use of biotechnology to insert or delete genes. Often involves production and use of recombinant DNA to transfer genes between organisms.
The change in frequency of a genetic variant due to its linkage to a selected variant at another locus.
See linkage map.
A process by which separate DNA molecules are joined into a single molecule due to such processes as crossing over or transposition.
The complete set of sequences in the genetic material of an organism. It includes the sequence of each chromosome plus any DNA in organelles.
The structure of the genome as influenced by factors other than the effects of products of its genes.
Examination of a genome-wide set of genetic variants in different individuals to determine whether a particular variant is associated with a trait.
A repair enzyme that removes damaged bases by cleaving the bond between the base and the sugar.
An analog of guanosine triphosphate (GTP) that cannot be hydrolyzed. It is used to test which stage in a reaction requires hydrolysis of GTP.
Inducers that resemble authentic inducers of transcription but that are not substrates for the induced enzymes.
See replication fork.
Recruits the exchange factor SOS to the cell membrane to activate the RAS protein as part of the signal transduction pathway that ultimately cases the cell to begin replication and growth.
The rule that describes the presence of these constant dinucleotides at the first two and last two positions of introns of nuclear genes.
A small RNA whose sequence is complementary to the sequence of an RNA that has been edited. It is used as a template for changing the sequence of the pre-edited RNA by inserting or deleting nucleotides.
An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other. It does this by cutting the DNA, passing DNA through the break, and then resealing the DNA.
An RNA sequence that can fold back on itself, forming double-stranded RNA.
The time taken for the concentration of a given population of RNA molecules to decrease by half, in the absence of new synthesis.
The particular combination of alleles in a defined region of some chromosome—in effect, the genotype in miniature. Originally used to describe combinations of major histocompatibility complex (MHC) alleles, it now may be used to describe particular combinations of restriction fragment length polymorphisms (RFLPs), single nucleotide polymorphisms (SNPs), or other markers.
A small molecule that can elicit an immune response only when conjugated with a carrier, such as a large protein or a microbe-associated molecular pattern (MAMP).
Histone acetylase transferase, an enzyme that adds an acetate group to histone proteins.
A fusion gene produced by unequal crossing over that has the N-terminal part of β globin and the C-terminal part of δ globin.
A fusion gene produced by unequal crossing over between the γ and β globin genes.
An unusual globin protein that results from unequal crossing over between the β and δ genes. The genes become fused together to produce a single β-like chain that consists of the N-terminal sequence of δ joined to the C-terminal sequence of β.
A condition in which there is a disproportionate amount of the abnormal tetramer β4 relative to the amount of normal hemoglobin (α2β2).
Histone deacetylase, an enzyme that removes acetate groups from acetylated lysine amino acids in histone proteins.
A set of loci activated in response to an increase in temperature (and other stresses to the cell). All organisms have them. Their products usually include chaperones that act on denatured proteins.
See heat-shock genes.
An enzyme that uses energy provided by ATP hydrolysis to separate the strands of a nucleic acid duplex.
The motif that is responsible for dimerization of a class of transcription factors called HLH proteins. A bHLH protein has a basic DNA-binding sequence close to the dimerization motif.
The motif that describes an arrangement of two α-helices that form a site that binds to DNA, one fitting into the major groove of DNA and the other lying across it.
A virus that provides functions absent from a defective virus, enabling the latter to complete the infective cycle during a mixed infection with the helper virus.
DNA that is methylated on one strand of a target sequence that has a cytosine on each strand.
Regions of the genome that are highly condensed, are not transcribed, and are late replicating. It is divided into two types: constitutive and facultative.
DNA that is generated by base pairing between complementary single strands derived from the different parental duplex molecules; it occurs during genetic recombination.
RNA that comprises nuclear transcripts made primarily by RNA polymerase II; it has a wide size distribution and variable stability.
A protein composed of two or more different polypeptide chains.
Having more than one mitochondrial allelic variant in a cell.
An Esherichia coli gene that controls the stability of the bacteriophage CII protein during an infection which determines whether the phage will enter the lytic or lysogenic cycle.
A bacterium that has an integrated F plasmid within its chromosome. Hfr stands for high frequency recombination, referring to the fact that chromosomal genes are transferred from an Hfr cell to an F− cell much more frequently than from an F+ cell.
Very short DNA sequences (typically < 100 bp) that are present many thousands of times in the genome, often organized as long regions of tandem repeats.
An enzyme that modifies histones by addition of acetyl groups; some transcriptional coactivators have this activity. Also known as lysine acetyltransferase (KAT).
The hypothesis that combinations of specific modifications on specific histone residues act cooperatively to define chromatin function.
Enzyme that removes acetyl groups from histones; may be associated with repressors of transcription.
A motif found in all four core histones in which three α-helices are connected by two loops.
The complex of two copies each of the four different core histones (H2A, H2B, H3, and H4); DNA wraps around this complex to form the nucleosome.
Flexible amino- or carboxy-terminal regions of the core histones that extend beyond the surface of the nucleosome; they are sites of extensive posttranslational modification.
Any of a number of histones closely related to one of the core histones (H2A, H2B, H3, or H4) that can assemble into a nucleosome in the place of the related core histone; many have specialized functions or localization. There are also numerous linker variants.
Conserved DNA-binding proteins that form the basic subunit of chromatin in eukaryotes. H2A, H2B, H3, and H4 form an octameric core around which DNA coils to form a nucleosome. Linker histones are external to the nucleosome.
The ribonucleoprotein form of hnRNA (heterogeneous nuclear RNA) in which the hnRNA is complexed with proteins. Pre-mRNAs are not exported until processing is complete; thus, they are found only in the nucleus.
An intermediate structure in homologous recombination in which the two duplexes of DNA are connected by the genetic material exchanged between two of the four strands, one from each duplex. A joint molecule is said to be resolved when nicks in the structure restore two separate DNA duplexes.
Type of chromosome in some species whereby the centromeres are diffuse and spread out along the entire length of the chromosome. Species with these chromosomes still make spindle fiber attachments for mitotic chromosome separation, but do not require one and only one regional or point centromere per chromosome.
(1) The DNA polymerase complex that is competent to initiate replication. (2) The RNA polymerase form that is competent to initiate transcription. It consists of the five subunits of the core enzyme (α2ββ′ω) and sigma factor.
A DNA-binding motif that typifies a class of transcription factors.
See homologous genes (homologs).
Related genes in the same species, such as alleles on homologous chromosomes or multiple genes in the same genome sharing common ancestry.
Recombination involving a reciprocal exchange of sequences of DNA, for example, between two chromosomes that carry the same genetic loci.
A molecular complex (such as a protein) in which the subunits are identical.
The transfer of DNA from one cell to another by a process other than cell division, such as bacterial conjugation.
A site in the genome at which the frequency of mutation (or recombination) is very much increased, usually by at least an order of magnitude relative to neighboring sites.
A gene that is (theoretically) expressed in all cells because it provides basic functions needed for sustenance of all cell types.
An engineered mini-chromosome that can act as a new chromosome in a human cell. The new chromosome has the potential to act as a gene delivery vector in humans.
Gene complex that encodes the major histocompatibility complex (MHC) proteins in humans.
The inability of certain strains of Drosophila melanogaster to interbreed, because the hybrids are sterile (although otherwise they may be phenotypically normal).
The pairing of complementary RNA and DNA strands to give an RNA–DNA hybrid.
A fatal disease resulting from the absence of the hemoglobin α gene.
A short region of chromatin detected by its extreme sensitivity to cleavage by DNase I and other nucleases; it comprises an area from which nucleosomes are excluded.
A bacterial initiation factor that stabilizes the initiation complex for polypeptide translation.
A bacterial initiation factor that binds the initiator tRNA to the initiation complex for polypeptide translation.
A bacterial initiation factor required for 30S ribosomal subunits to bind to initiation sites in mRNA. It also prevents 30S subunits from binding to 50S ribosomal subunits.
One of the five classes of immunoglobulin that are defined by the type of CH region. These immunoglobulins are abundant on mucosal surfaces and on secretions in the respiratory tract and the intestine.
One of the five classes of immunoglobulin that are defined by the type of CH region. These immunoglobulins are associated with the allergic response and with defense against parasites.
One of the five classes of immunoglobulin that are defined by the type of CH region. These immunoglobulins are the most abundant immunoglobulins in circulation and are able to pass into extravascular spaces.
Genes in phage lambda that are equivalent to the early class of other phages. They are transcribed immediately upon infection by the host RNA polymerase.
In phages, the ability of a prophage to prevent another phage of the same type from infecting a cell. In plasmids, the ability of a plasmid to prevent another of the same type from becoming established in a cell. It can also refer to the ability of certain transposons to prevent others of the same type from transposing to the same DNA molecule.
A segment of the phage genome that enables a prophage to inhibit additional phage of the same type from infecting the bacterium. This region has a gene that encodes for the repressor, as well as the sites to which the repressor binds.
A protein (antibody) that is produced by B cells and in large amounts by plasma cells and that binds to a particular antigen.
One of two types of identical subunits in an antibody tetramer. Each antibody contains two of them. The –NH2 end forms part of the antigen recognition site, whereas the –COOH end determines the class or isotype.
One of two types of identical subunits in an antibody tetramer. Each antibody contains two of them. The –H2 end forms part of the antigen recognition site, whereas the –COOH end determines the class, κ or λ.
Occurs when the transposon removes itself from the original insertion site but leaves behind some of its sequence.
A change in a gene that occurs during passage through the sperm or egg with the result that the paternal and maternal alleles have different properties in the very early embryo. This is caused by methylation of DNA.
Hybridization performed by denaturing the DNA of cells squashed on a microscope slide so that reaction is possible with an added single-stranded RNA or DNA; the added preparation is radioactively labeled and its hybridization is followed by autoradiography.
A functional assay used to identify components of a process. The reaction is reconstructed using extracts from a mutant cell. Fractions from wild-type cells are then tested for restoration of activity.
A technique for examining the organization of DNA by making a cut at a specific site and identifying all fragments containing the sequence adjacent to one side of the cut; it reveals the distance from the cut to the next break(s) in DNA.
Mutations that result from the action of a mutagen. The mutagen may act directly on the bases in DNA or it may act indirectly to trigger a pathway that leads to a change in DNA sequence.
A molecule that triggers gene transcription by binding to a regulator protein.
A gene that is turned on by the presence of its substrate.
The ability to synthesize certain enzymes only when their substrates are present; applied to gene expression, it refers to switching on transcription as a result of interaction of the inducer with the regulator protein.
A phage’s entry into the lytic (infective) cycle as a result of destruction of the lysogenic repressor, which leads to excision of free phage DNA from the bacterial chromosome.
The stages of transcription up to synthesis of the first bond in RNA. This includes binding of RNA polymerase to the promoter and melting a short region of DNA into single strands.
A special codon (usually AUG) used to start synthesis of a polypeptide.
Proteins that associate with the small subunit of the ribosome specifically at the stage of initiation of polypeptide translation.
The sequence at the start point of transcription of a pol II promoter between −3 and +5 that has the general sequence Py2CAPy5.
A response triggered by receptors whose specificity is predefined for certain common motifs found in bacteria and other infectious agents. The receptor that triggers the response is typically a member of the Toll-like receptor (TLR) family, and the pathway resembles the signaling pathway triggered by the Toll receptor of Drosophila. The pathway culminates in activation of transcription factors that induce the expression of genes, whose products inactivate the infective agent, typically by permeabilizing its membrane.
A piece of DNA inserted into a larger DNA vector, such as a plasmid, through recombinant DNA techniques.
A small bacterial transposon that carries only the genes needed for its own transposition.
A sequence that prevents an activating or inactivating effect from passing from one side to the other.
An enzyme that is responsible for a site-specific recombination that inserts one molecule of DNA into another.
Insertion of a viral or another DNA sequence into a host genome as a region covalently linked on either side to the host sequences.
The part that is removed from a protein that is processed by protein splicing.
The complete set of protein complexes/protein–protein interactions present in a cell, tissue, or organism.
The change in the properties of a heteromultimeric protein brought about by the interaction of subunits coded by two different mutant alleles; the mixed protein may be more or less active than the protein consisting of subunits of only one or the other type.
The relatively dispersed regions of polytene chromosomes that lie between the bands.
The distance between the termination codon of one gene and the initiation codon of the next gene.
An insulator element characterized by two CTCF binding sites that is located between the VH and DHJH regions. Helps to equalize antibody repertoires by suppressing transcription of proximal VH regions and their recombination with DH elements that have not yet joined with JH regions.
A eukaryotic messenger RNA sequence that allows a ribosome to initiate polypeptide translation without migrating from the 5′ end.
A gene in which the coding sequence is not continuous due to the presence of introns.
Terminators that are able to terminate transcription by bacterial RNA polymerase in the absence of any additional factors.
A segment of DNA that is transcribed but later removed from within the transcript by splicing together the sequences (exons) on either side of it.
The process in which a pair of splicing sites are recognized by interactions involving only the 5′ site and the branchpoint/3′ site.
The ability of certain introns to insert themselves into a target DNA. The reaction is specific for a single target sequence.
The hypothesis that the earliest genes contained introns and some genes subsequently lost them.
The hypothesis that the earliest genes did not contain introns, and that introns were subsequently added to some genes.
Two different segments of the double helix that read the same but in opposite directions; that is, a sequence of nucleotides is followed downstream by its reverse complement.
The short, related or identical sequences present in reverse orientation at the ends of some transposons.
See internal ribosome entry site (IRES).
A cis sequence found in certain mRNAs whose stability or translation is regulated by cellular iron concentration.
See cognate tRNAs.
Technique that separates molecules based on their isoelectric point, which is the pH at which a protein has no net charge. Often performed on proteins in gels.
The formation of one or more bands of molecules of the same density during isopycnic centrifugation.
Different restriction enzymes that share the same recognition sequence.
Gene segments that code sequences in the immunoglobulin and T cell receptor loci. They lie as the only element or in clusters between the variable (V) and constant (C) gene segment clusters.
A pair of DNA duplexes that are connected together through a reciprocal exchange of genetic material.
Term used to describe the excess of DNA in some genomes that lack any apparent function.
Lysine acetyltransferase; an enzyme that transfers an acetate group to a lysine amino acid.
A proofreading mechanism that depends on incorrect events proceeding more slowly than correct events, so that incorrect events are reversed before a subunit is added to a polymeric chain.
A small organelle associated with the surface of the centromere that attaches a chromosome to the microtubules of the mitotic spindle. Each mitotic chromosome contains two “sisters” that are positioned on opposite sides of its centromere and face in opposite directions.
An antibiotic that inhibits protein synthesis by acting on EF-Tu.
A large protein fragment (68 kD) produced when DNA polymerase I is cleaved by a protease. It is used in synthetic reactions in vitro. It retains polymerase and proofreading 3′–5′ exonuclease activities.
A process by which a gene is downregulated by introducing a silencing vector or molecule to reduce the expression (usually translation) of the target gene.
A process similar to a knockout, in which new genes or genes containing more subtle mutations are inserted into the genome.
A process in which a functional gene is eliminated, usually by replacing most of the coding sequence with a selectable marker in vitro and transferring the altered gene to the genome by homologous recombination.
A human neurological disease caused by prions. It may be caused by eating infected brains.
A negative gene regulator encoded by the lacI gene that turns off the lac operon.
The strand of DNA that must grow overall in the 3′ to 5′ direction and that is synthesized discontinuously in the form of short fragments (5′–3′) that are later connected covalently.
The extremely extended meiotic bivalents of certain amphibian oocytes.
An intermediate in RNA splicing in which a circular structure with a tail is created by a 5′ to 2′ bond.
Genes transcribed when phage DNA is being replicated. They encode components of the phage particle.
The part of the phage lytic cycle from DNA replication to lysis of the cell. During this time, the DNA is replicated and structural components of the phage particle are synthesized.
A structure in the synaptonemal complex that forms when a pair of sister chromatids condenses on to an axial element.
See locus control region (LCR).
The untranslated sequence at the 5′ end of mRNA that precedes the initiation codon.
The product that would result from translation of a short coding sequence used to regulate transcription of an operon by controlling ribosome movement.
The strand of DNA that is synthesized continuously in the 5′ to 3′ direction.
A less severe type of mutation where the amino acid substitution does not completely deactivate a certain function of the protein, but rather decreases its function or makes it less effective.
A hemoprotein that acts as an oxygen carrier in the nitrogen-fixing root nodules of leguminous plants. Facilitates the diffusion of oxygen in order to promote nitrogen fixation.
Replication by an error-prone DNA polymerase on a template that contains a damaged base. The polymerase can incorporate a noncomplementary base into the daughter strand.
A motif found in the extracellular domains of some surface receptors in animal and plant cells that consists of repeating stretches of 20 to 30 amino acids that are unusually rich in the hydrophobic amino acid leucine. These repeats are frequently involved in the formation of protein–protein interactions.
A dimerization motif that is found in a class of transcription factors.
A factor located in the nucleus and necessary for replication; it is inactivated or destroyed after one round of replication. New factors must be provided for further rounds of replication to occur.
A type of hnRNA; long intergenic noncoding RNA.
See long-interspersed nuclear elements (LINEs).
The tendency of genes to be inherited together as a result of their location on the same chromosome; measured by percent recombination between loci.
A nonrandom association between alleles at two different loci, often as a result of linkage.
A map of the positions of loci or other genetic markers on a chromosome obtained by measuring recombination frequencies between markers.
Nonnucleosomal DNA present between nucleosomes.
A family of histones (such as histone H1) that are not components of the nucleosome core; linker histones bind nucleosomes and/or linker DNA and promote 30-nm fiber formation.
In a closed molecule of DNA, the number of times one strand crosses over another in space.
The discrepancy between the existence of –1.67 supercoils in the path of DNA on the nucleosome compared with the measurement of –1 supercoil released when the restraining protein is removed.
Large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins, and elicit strong immune responses in animals. Also known as lipoglycans.
A spherical vesicle with at least one lipid bilayer that can be used to introduce nucleic acids into targeted cells.
The position on a chromosome at which the gene for a particular trait resides; it may be occupied by any one of the alleles for the gene.
The region that is required for the expression of several genes in a domain.
A major class of retrotransposons that occupy approximately 21% of the human genome (see also retrotransposon).
Evolutionarily conserved noncoding RNA molecules that are longer than 200 nucleotides and are located within the intergenic loci or regions overlapping antisense transcripts of protein coding genes. They are involved in numerous cellular functions, including transcriptional regulation, RNA processing, RNA modification, and epigenetic silencing. They have recently been shown to play an important role in the targeting of the class switch recombination machinery.
The sequence that is repeated at each end of the provirus (integrated retroviral sequence).
A mutation that eliminates or reduces the activity of a gene. It is often, but not always, recessive.
See long terminal repeat (LTR).
A gene encoding a specialized function, synthesized (usually) in large amounts in particular cell types.
A repair enzyme (usually also a glycosylase) that opens the sugar ring at the site of a damaged base.
An enzyme (typically present in large complexes) that acetylates lysine residues in histones (or other proteins). Previously known as histone acetyltransferase (HAT).
The death of bacteria at the end of a phage infective cycle when they burst open to release the progeny of an infecting phage (because phage enzymes disrupt the bacterium’s cytoplasmic membrane or cell wall). The same term also applies to eukaryotic cells (e.g., when infected cells are attacked by the immune system).
The ability of a phage to survive in a bacterium as a stable prophage component of the bacterial genome.
Infection of a bacterium by a phage that ends in the destruction of the bacterium with release of progeny phage.
An enzyme that adds a methyl group to a target site that is already hemimethylated.
Large contiguous regions on chromosomes that appear to act as independent units. Four such regions have been identified in Escherichia coli.
A fissure running the length of the DNA double helix that is 22 Å across.
A chromosomal region containing genes that are involved in the immune response. The genes encode proteins for antigen presentation, cytokines, and complement, as well as other functions. It is highly polymorphic. Its genes and proteins are divided into three classes.
Region on the Y chromosome that does not undergo crossing over with the X chromosome. Contains three types of sequences: X-transposed sequences, X-degenerate segments, and ampliconic segments.
The preferential survival in the progeny of genetic markers provided by one parent.
Oocyte particles containing translationally repressed mRNAs awaiting activation later in development.
Yeast mating type is determined by a single active locus (the active cassette) and two inactive copies of the locus (the silent cassettes). Mating type is changed when an active cassette of one type is replaced by a silent cassette of the other type.
A region of DNA that attaches to the nuclear matrix. It is also known as a scaffold attachment site (SAR).
A protein encoded by a group I or group II intron that is needed to assist the RNA to form the active conformation that is required for self-splicing.
A modified RNA transcript. Modification may include the removal of intron sequences and alterations to the 5′ and 3′ ends.
See multiple cloning site (MCS).
A large protein complex associated with yeast RNA polymerase II. It contains factors that are necessary for transcription from many or most promoters.
The midpoint of the temperature range over which the strands of DNA separate.
The intermediate that represents one strand of a gene coding for polypeptide. Its coding region is related to the polypeptide sequence by the triplet genetic code.
See major histocompatibility complex (MHC).
An arrayed series of thousands of tiny DNA oligonucleotide samples imprinted on a small chip. mRNAs can be hybridized to microarrays to assess the amount and level of gene expression.
Broadly conserved microbial components, including bacterial flagellin and lipopolysaccharides, that are recognized by pattern-recognition receptors, which critically initiate innate immune responses.
An endonuclease that cleaves DNA; in chromatin, DNA is cleaved preferentially between nucleosomes.
Technique that uses a small glass micropipette to insert genetic material, proteins, or macromolecules directly into cell cytoplasm, an embryo, or a nucleus.
Small (21 to 23 nucleotides), evolutionarily conserved noncoding RNAs that function in RNA silencing and posttranscriptional regulation of gene expression. Bind to complementary sequences within the 3′ untranslated region (UTR) of their target mRNAs and negatively regulate protein expression by accelerating mRNA degradation and inhibiting mRNA translation.
DNAs consisting of tandem repetitions of very short (typically less than 10 bp) units repeated a small number of times.
The structure in eukaryotic cells from which the microtubules emerge. It organizes flagella/cilia and the mitotic and meiotic spindle apparatus.
Phage genes that are regulated by the proteins encoded by early genes. Some proteins coded by them catalyze replication of the phage DNA; others regulate the expression of a later set of genes.
An anucleate bacterial (Escherichia coli) cell produced by a division that generates a cytoplasm without a nucleus.
DNAs consisting of tandemly repeated copies of a short, repeating sequence, with more repeat copies than a microsatellite but fewer than a satellite. The length of the repeating unit is measured in tens of base pairs. The number of repeats varies between individual genomes.
A fissure running the length of the DNA double helix that is 12 Å across.
The single-stranded DNA sequence that is complementary to the viral RNA genome of a plus-strand virus.
Repair that corrects recently inserted bases that do not pair properly. The process preferentially corrects the sequence of the daughter strand by distinguishing the daughter strand and parental strand, sometimes on the basis of their states of methylation.
A suppressor that codes for a tRNA that has been mutated to recognize a different codon. By inserting a different amino acid at a mutant codon, the tRNA suppresses the effect of the original mutation.
Sequences of DNA that are repeated 10 to 1,000 times throughout the genome and interspersed with other sequences.
An approximately constant rate of evolution that occurs in DNA sequences, such as by the genetic drift of neutral mutations.
mRNA that codes for one polypeptide.
mRNA degradation, assuming that the degradation process is stochastic.
Mitochondrial DNA.
Occurs when the control system allows the plasmid to exist in more than one copy per individual bacterial cell.
A bacterial chromosome that has more than one set of replication forks, because a second initiation has occurred before the first cycle of replication has been completed.
A non-Mendelian pattern of inheritance where more than two alleles code for a trait. In most cases, the result is that more than two phenotypes are possible based on the dominance pattern of the individual alleles.
A sequence of DNA containing a series of tandem restriction endonuclease sites that can be used in cloning vectors for creating recombinant molecules.
Substances that increase the rate of mutation by inducing changes in DNA sequence, directly or indirectly.
A site in the genome at which the frequency of mutation (or recombination) is very much increased, usually by at least an order of magnitude relative to neighboring sites.
A mutation or a mutated gene that increases the basal level of mutation. Such genes often code for proteins that are involved in repairing damaged DNA.
A small hemoprotein found in muscle cells that binds to oxygen. Highly conserved protein, containing 153 amino acids and the iron cofactor heme.
A short, nontemplated sequence that is added randomly by the enzyme TdT at coding joints during rearrangement of immunoglobulin and T cell receptor genes. They increase the degree of diversity of the antigen receptors’ V(D)J sequences.
The rule that states that only one X chromosome is active in female mammalian cells; any others are inactivated.
The aminoacyl-tRNA that initiates bacterial polypeptide translation. The amino group of the methionine is formylated.
A ribonucleotide chain that is still being synthesized so that its 3′ end is paired with DNA where RNA polymerase is elongating.
See noncoding RNAs (ncRNAs).
Occurs when interallelic complementation allows a mutant subunit to suppress the activity of a wild-type subunit in a multimeric protein.
A mechanism of gene regulation in which a regulator is required to turn the gene off.
A control circuit in which an active repressor is inactivated by the substrate of the operon.
A control circuit in which an inactive repressor is activated by the product of the operon.
Type of selection whereby an individual with a disadvantageous mutation is less able to survive and produce fertile progeny relative to those without the mutation. Results in selective removal of rare, deleterious alleles from the population.
The left-handed, double-helical form of DNA. Creates tension in the DNA that is relieved by the unwinding of the double helix. The result is the generation of a region in which the two strands of DNA have separated.
A gene located within an intron of another gene.
Particles containing translationally repressed mRNAs in transit to final cell destinations.
A mutation that has no significant effect on evolutionary fitness and usually has no effect on the phenotype.
Substitutions in a protein that cause changes in amino acids that do not affect activity.
A protein complex that functions as a transcription factor. Is found in most cells and mediates signaling in response to a variety of immunological, inflammatory, and microbial stimuli or viral antigens. Dysregulation of its expression has been associated with cancer, inflammatory and autoimmune diseases, and abnormal immune system development.
The ability of Escherichia coli DNA polymerase I to use a nick as a starting point from which one strand of a duplex DNA can be degraded and replaced by resynthesis of new material; it is used to introduce radioactively labeled nucleotides into DNA in vitro.
A pathway that rapidly degrades an mRNA with ribosomes stalled in its coding region.
A pattern of inheritance that does not follow that expected by Mendelian principles (each parent contributing a single allele to offspring). This pattern of inheritance is exhibited by extranuclear genes.
Two (or more) copies of the same gene that are present at different locations in the genome (contrasted with alleles, which are copies of the same gene derived from different parents and present at the same location on the homologous chromosomes).
A transposon that encodes a nonfunctional transposase; it can transpose only in the presence of a trans-acting autonomous member of the same family.
RNA that does not contain an open reading frame.
Any structural protein found in a chromosome except one of the histones.
The process that ligates blunt ends. It is common to many repair pathways and to certain recombination pathways (such as immunoglobulin recombination).
An inactive gene copy that arises by incomplete gene duplication or duplication followed by inactivating mutations.
Occurs as a result of the recombination of V(D)J gene segments if the rearranged gene segments are not in the correct reading frame. It occurs when nucleotide addition or subtraction disrupts the reading frame or when a functional protein is not produced.
DNA that is unique (present only once) in a genome.
The movement of a transposon that leaves a donor site (usually generating a double-strand break) and moves to a new site.
A pathway that degrades an mRNA that has a nonsense mutation prior to the last exon.
A gene coding for a mutant tRNA that is able to respond to one or more of the termination codons and insert an amino acid at that site.
A pathway that rapidly degrades an mRNA that lacks an in-frame termination codon.
Mutations have altered the amino acid that is encoded.
See coding strand.
The region between transcription units in a tandem gene cluster.
Ti plasmids of Agrobacterium tumefaciens that carry genes for the synthesis of the opine nopaline. They retain the ability to differentiate into early embryonic structures.
Technique used to detect the presence of particular mRNA in a sample. RNA are separated by size and detected on a membrane using a hybridization probe with a base sequence complementary to the sequence of the target mRNA.
An enzyme that can break a phosphodiester bond.
A duplex hairpin in TMV (tobacco mosaic virus) in which assembly of coat protein with RNA is initiated.
The structure in a prokaryotic cell that contains the genome. The DNA is bound to proteins and is not enclosed by a membrane.
The region of a chromosome carrying genes coding for rRNA.
A discrete region of the nucleus where ribosomes are produced.
A molecule consisting of a purine or pyrimidine base linked to the 1′ carbon of a pentose sugar.
The basic structural subunit of chromatin, consisting of approximately 200 bp of DNA and an octamer of histone proteins.
The placement of nucleosomes at defined sequences of DNA instead of at random locations with regard to sequence.
A molecule consisting of a purine or pyrimidine base linked to the 1′ carbon of a pentose sugar and a phosphate group linked to either the 5′ or 3′ (or, rarely, 2′) carbon of the sugar.
A repair pathway that entails excision of a large region of DNA containing a site of (typically helix-distorting) damage such as ultraviolet-induced photoproducts. In humans, defects in XP genes involved in this repair process result in the disease xeroderma pigmentosum.
A mutation that completely eliminates the function of a gene.
The sequence of DNA that is recognized by the N antitermination actor.
The triplet UAA, one of the three termination codons that end polypeptide translation.
Plasmids of Agrobacterium tumefaciens that carry genes coding the synthesis of opines of the octopine type. The tumors are undifferentiated.
Short stretches of 1,000 to 2,000 bases produced during discontinuous replication; they are later joined into a covalently intact strand.
A short poly(A) tail, generally referring to a stretch of less than 15 adenylates.
A gene that when mutated may cause cancer. The mutation is a dominant gain of function mutation.
Beadle and Tatum’s hypothesis that a gene is responsible for the production of a single enzyme.
A modified version of the not generally correct one gene–one enzyme hypothesis; the hypothesis that a gene is responsible for the production of a single polypeptide.
The triplet UGA, one of the three termination codons that end polypeptide translation. It has evolved to code for an amino acid in a small number of organisms or organelles.
The stage of initiation of transcription when RNA polymerase causes the two strands of DNA to separate to form the “transcription bubble.”
A sequence of DNA consisting of triplets that can be translated into amino acids starting with an initiation codon and ending with a termination codon.
The site on DNA at which a repressor protein binds to prevent transcription from initiating at the adjacent promoter.
A unit of bacterial gene expression and regulation, including structural genes and control elements in DNA recognized by regulator gene product(s).
A derivative of arginine that is synthesized by plant cells infected with crown gall disease.
A sequence of DNA at which replication is initiated.
A sequence of DNA at which replication is initiated.
Found in eukaryotes, a multiprotein complex that binds to the replication origin, the autonomously replicating sequence (ARS), and remains associated with it throughout the cell cycle.
Related genes in different species.
In comparative genomics, a species that is less closely related to the species being investigated, but close enough to show substantial similarity.
A gene in which part of the sequence is found within part of the sequence of another gene.
B-form DNA that has more than 10.5 base pairs per turn of the helix.
A type of transposon in Drosophila melanogaster.
A short palindromic (inverted repeat) sequence that is generated during rearrangement of immunoglobulin and T cell receptor V(D)J gene segments. They are produced at coding joints when RAG proteins cleave the hairpin ends generated during V(D)J rearrangement.
The site in the ribosome that is occupied by peptidyl-tRNA, the tRNA carrying the nascent polypeptide chain, still paired with the codon to which it is bound in the A site.
The ratio of the length of DNA to the unit length of the fiber containing it.
A symmetrical sequence that reads the same forward and backward.
Genes that share a common ancestry due to gene duplication.
Genes that share a common ancestry due to gene duplication.
The complex of ParB (and IHF in some cases) with parS in some plasmids, such as P1. Its formation enables further molecules of ParB to bind cooperatively, resulting in the formation of a very large protein–DNA complex.
DNA that results from a Holliday junction being resolved by cutting the exchanged strands. The duplex is largely unchanged, except for a DNA sequence on one strand that came from the homologous chromosome.
DNA segments that are present in pathogenic bacterial genomes but absent in their nonpathogenic relatives.
Receptors that recognize highly conserved microbe-associated molecular patterns (MAMPs) found in bacteria, viruses, and other infectious agents. They are found on innate immune cells such as neutrophils, macrophages, and dendritic cells (DCs) and cause the pathogen to be phagocytosed and killed. Some are also expressed in cells important for adaptive immune responses, such as all B lymphocytes and some T lymphocyte subsets.
The activity of the large ribosomal subunit that synthesizes a peptide bond when an amino acid is added to a growing polypeptide chain. The actual catalytic activity is a property of the rRNA.
The tRNA to which the nascent polypeptide chain has been transferred following peptide bond synthesis during polypeptide translation.
An abbreviation of bacteriophage or bacterial virus.
An enzyme that can break a phosphomonoester bond, cleaving a terminal phosphate.
A pathway in which a phosphate group is passed along a series of proteins.
A repair mechanism that uses a white light–dependent enzyme to split cyclobutane pyrimidine dimers formed by ultraviolet light.
A surface appendage on a bacterium that allows the bacterium to attach to other bacterial cells. It appears as a short, thin, flexible rod. During conjugation, it is used to transfer DNA from one bacterium to another.
The subunit that is polymerized into the pilus in bacteria.
The first translation event for a newly synthesized and exported mRNA.
Piwi RNA, a special form of miRNA found in germ cells.
Domain of approximately 50 to 80 amino acids. Many of these domains bind various methylation states of lysines in histones. Also called the PHD finger.
Circular, extrachromosomal DNA. It is autonomous and can replicate itself.
The strand of the duplex sequence representing a retrovirus that has the same sequence as that of the RNA.
A virus with a single-stranded nucleic acid genome whose sequence directly codes for the protein products.
A mutation within a gene in which only one nucleotide base is altered through substitution, insertion, or deletion.
The effect of a mutation in one gene in influencing the expression (at transcription or translation) of subsequent genes in the same transcription unit.
A stretch of adenylic acid that is added to the 3′ end of mRNA following its synthesis.
The protein that binds to the 3′ stretch of poly(A) on a eukaryotic mRNA.
An exoribonuclease that is specific for digesting poly(A) tails.
The enzyme that adds the stretch of polyadenylic acid to the 3′ end of eukaryotic mRNA. It does not use a template.
mRNA that includes coding regions representing more than one gene.
A process for the amplification of a defined nucleic acid section through repeated thermal cycles of denaturation, annealing, and polymerase extension.
The transition from initiation to elongation of DNA replication by substitution of an enzyme that will extend the chain. On the leading strand, this is DNA polymerase ε; on the lagging strand this is DNA polymerase δ.
The simultaneous occurrence in the population of alleles showing variations at a given position.
A chain of nucleotides, such as DNA or RNA.
An event that results in an increase in the number of haploid chromosome sets in the cell, typically from diploid to tetraploid, and usually as a result of fertilization of unreduced gametes.
An mRNA that is simultaneously being translated by multiple ribosomes.
See polyribosome.
Chromosomes that are generated by successive replications of a chromosome set without separation of the replicas.
Silencing of gene expression that occurs as the result of proximity to heterochromatin.
The localization of certain cell structures in specific places.
This describes a system in which a gene is not expressed unless some action turns it on.
A control circuit in which an inactive positive regulator is converted into an active regulator by the substrate of the operon.
A control circuit in which an active positive regulator is inactivated by the product of the operon.
Type of selection whereby an individual with an advantageous mutation survives (i.e., is able to produce more fertile progeny) relative to those without the mutation.
The right-handed, double-helical form of DNA. Both strands of the double helix coil together in the same direction as the coiling of the strands.
A protein–DNA complex in Saccharomyces cerevisiae that consists of the ORC complex bound to the origin.
All changes made to the nucleotides of RNA after their initial incorporation into the polynucleotide chain.
Guanosine tetraphosphate, a signaling molecule in bacteria to reduce transcription of rRNA (and some other) genes when the amount of acylated tRNA is reduced.
The nuclear transcript that is processed by modification and splicing to give an mRNA.
The removal of a transposon plus one of the duplicated target sequences from the chromosome. Such an event can restore function at the site where the transposon inserted.
In eurkaryotic transcription, the assembly of transcription factors at the promoter before binding of RNA polymerase.
The termination of protein or of RNA synthesis before the chain has been completed. In translation it can be caused by mutations that create stop codons within the coding region. In RNA synthesis it is caused by various events that act on RNA polymerase.
A protein–DNA complex at the origin in Saccharomyces cerevisiae that is required for DNA replication. The complex contains the ORC complex, Cdc6, and the MCM proteins.
Single-stranded DNA bound in a helical nucleoprotein filament with a strand transfer protein such as Rad51 or RecA.
The initial product of transcription that consists of an RNA extending from the promoter to the terminator and possesses the original 3′ and 5′ ends.
A type of RNA polymerase that synthesizes short segments of RNA that will be used as primers for DNA replication.
A short sequence (often of RNA) that is paired with one strand of DNA and that provides a free 3′–OH end at which a DNA polymerase starts synthesis of a deoxyribonucleotide chain.
A protein complex required to synthesize an RNA primer during replication.
A proteinaceous infectious agent that behaves as an inheritable trait, although it contains no nucleic acid. Examples are PrPSc, the agent of scrapie in sheep and bovine spongiform encephalopathy, and Psi, which confers an inherited state in yeast.
Promoter upstream transcripts, short RNAs produced from both strands of DNA from active promoters.
A radioactive nucleic acid, DNA or RNA, used to identify a complementary fragment.
An inactive gene copy that lacks introns, contrasted with the interrupted structure of the active gene. Such genes originate by reverse transcription of mRNA and insertion of a duplex copy into the genome.
A particle containing multiple mRNAs and proteins involved in mRNA degradation and translational repression, occurring in many copies in the cytoplasm of eukaryotes.
An enzyme that remains associated with the substrate while catalyzing the sequential removal of nucleotides.
The ability of an enzyme to perform multiple catalytic cycles with a single template instead of dissociating after each cycle.
Occurs as a result of the recombination of V(D)J gene segments if all the rearranged gene segments are in the correct reading frame.
Apoptosis triggered by a cellular stimulus through a signal transduction pathway.
Frameshifting that is required for expression of the polypeptide sequences encoded beyond a specific site at which a +1 or −1 frameshift occurs at some typical frequency.
A region of DNA where RNA polymerase binds to initiate transcription.
Promoter upstream transcripts, short RNAs produced from both strands of DNA from active promoters.
A mechanism for correcting errors in DNA synthesis that involves scrutiny of individual units after they have been added to the chain.
A phage genome covalently integrated as a linear part of the bacterial chromosome.
The autocatalytic process by which an intein is removed from a protein and the exteins on either side become connected by a standard peptide bond.
The complete set of proteins that is expressed by the entire genome. Sometimes the term is used to describe the complement of proteins expressed by a cell at any one time.
Genes that code for elements of the signal transduction pathway that when altered may cause cancer.
A duplex sequence of DNA integrated into a eukaryotic genome that represents the sequence of the RNA genome of a retrovirus.
Regions on the Y chromosome that frequently exchange with the X chromosome during male meiosis.
Inactive but stable components of the genome derived by mutation of an ancestral active gene. Usually they are inactive because of mutations that block transcription or translation or both.
An expansion of a band of a polytene chromosome associated with the synthesis of RNA at some locus in the band.
A double-ringed nitrogenous base, such as adenine or guanine.
The tendency of a species’ AG (purine) content at the first, second, and third positions of the codons of its genes to conform to an optimal value.
An antibiotic that terminates protein synthesis by mimicking a tRNA and becoming linked to the nascent protein chain.
A single-ringed nitrogenous base, such as cytosine, thymine, or uracil.
A dimer that forms when ultraviolet irradiation generates a covalent link directly between two adjacent pyrimidine bases in DNA. It blocks DNA replication and transcription.
DNA sequencing technique based on the detection of the release of pyrophosophate when nucleotides are incorporated into a single-stranded DNA. A chemoluminescent enzyme is used to detect the activity of DNA polymerase. The method allows for the sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting the base added at each step. Solutions of A, C, G, and T nucleotides are sequentially added and removed from the reaction. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions that produce chemiluminescent signals allows the determination of the sequence of the template.
See real-time PCR (rt-PCR).
Temperature-sensitive replication mutants that are defective in replication elongation during synthesis of DNA.
The sequences that are repeated at the ends of a retroviral RNA. They are called R-U5 and U3-R.
Protein required for DNA cleavage in V(D)J recombination. It recognizes the nonamer consensus sequences for recombination. It works together with RAG2 to undertake the catalytic reactions of cleaving and rejoining DNA, and also provides a structural framework within which the whole recombination reaction occurs.
Protein required for DNA cleavage in V(D)J recombination. It is recruited by RAG1 and cleaves DNA at the heptamer. It works together with RAG1 to undertake the catalytic reactions of cleaving and rejoining DNA, and also provides a structural framework within which the whole recombination reaction occurs.
Use of a random hexamer to prepare labeled DNA probes from templates for hybridization and to prime mRNAs with or without poly(A) for first strand cDNA synthesis.
A germline subset of miRNA transcribed from transposable elements and other repeated elements that is used to silence them.
Genes encoding ribosomal RNA (rRNA).
One of three possible ways of reading a nucleotide sequence. Each divides the sequence into a series of successive triplets.
Occurs at transcription or translation when RNA polymerase or the ribosome, respectively, ignores a termination signal because of a mutation of the template or the behavior of an accessory factor.
Technique with continuous monitoring of product formation as the process proceeds, usually through fluorometric methods. Also known as quantitative PCR (qPCR). Not to be confused with reverse transcription PCR (RT-PCR), which is a method that allows detection of RNAs by PCR.
Events that occur when the meaning of a codon or series of codons is changed from that predicted by the genetic code. It may involve altered interactions between aminoacyl-tRNA and mRNA that are influenced by the ribosome.
One of the two helices of the helix-turn-helix motif that makes contacts with DNA that are specific for particular bases. This determines the specificity of the DNA sequence that is bound.
A DNA molecule composed of sequences from two different sources.
The point at which two recombining molecules of duplex DNA are connected (the edge of the heteroduplex region).
Enzyme that catalyzes site-specific recombination.
Genes that encode enzymes that play an important role in the rearrangement and recombination of the genes of immunoglobulin and T cell receptor molecules during the process of V(D)J recombination. The cellular expression of two recombination activating gene products, RAG1 and RAG2, is restricted to developing lymphocytes.
Dense objects present on the synaptonemal complex; they may represent protein complexes involved in crossing over.
A mode of filling a gap in one strand of duplex DNA by retrieving a homologous single strand from another duplex.
Consist of conserved nonamers:12 or 23 spacer:heptamer sequences flanking one end of the coding sequence of Ig and TCR V(D)J genes.
The concept that two or more genes may fulfill the same function, so that no single one of them is essential.
A gene that codes for a product (typically protein) that controls the expression of other genes (usually at the level of transcription).
An enzyme that cuts one strand of DNA and binds to the free 5′ end.
In Escherichia coli, these do not display the stringent response to starvation for amino acids (or other nutritional deprivation).
A bacterial complex assembled for the purpose of conjugation, transferring genetic material between bacteria.
A protein required to terminate polypeptide translation to cause release of the completed polypeptide chain and the ribosome from mRNA.
The reassociation of denatured complementary single strands of a DNA double helix.
DNA that is present in many (related or identical) copies in a genome.
A region in which DNA has been replicated within a longer, unreplicated region.
The pathway for assembling chromatin from an equal mix of old and new histones during the S phase of the cell cycle.
A virus that cannot sustain the infective cycle by itself but that is perpetuated in the company of a helper virus that provides the missing viral functions.
A virus that cannot perpetuate an infective cycle because some of the necessary genes are absent (replaced by host DNA in a transducing virus) or mutated.
The point at which strands of parental duplex DNA are separated so that replication can proceed. A complex of proteins including DNA polymerase is found there.
Pathway for assembling nucleosomes during phases of the cell cycle that do not involve DNA synthesis; may be necessary due to damage to the DNA or because of displacement of the nucleosome during transcription.
The movement of a transposon by a mechanism in which first it is replicated, and then one copy is transferred to a new site.
A unit of the genome in which DNA is replicated. Each contains an origin for initiation of replication.
The multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA. It contains DNA polymerase and other enzymes.
A gene attached to another promoter and/or gene that encodes a product that is easily identified or measured.
A gene that is turned off by its product.
The ability to prevent synthesis of certain enzymes when their products are present; more generally, it refers to inhibition of transcription (or translation) by binding of repressor protein to a specific site on DNA (or mRNA).
A protein that inhibits expression of a gene. It may act to prevent transcription by binding to an enhancer or silencer.
Process that occurs by a homologous recombination reaction between the two copies of the transposon in a cointegrate. The reaction generates the donor and target replicons, each with a copy of the transposon.
The enzyme activity involved in site-specific recombination between two copies of a transposon that has been duplicated.
An enzyme that recognizes specific short sequences of DNA and cleaves the duplex (sometimes at the target site, sometimes elsewhere, depending on type).
Enzymes that cut the DNA molecule at a particular location. The enzyme locates a particular sequence (usually four to six nucleotides) on the DNA strand and then stops and cuts at or near the recognition nucleotide sequence. In bacteria, these enzymes provide a defense against invading viruses. They are also used as a tool in genetic engineering to extract genes from organisms that can then be inserted into other organisms.
Determination of a linear array of sites on DNA cleaved by various restriction endonucleases.
The point in G1 of the cell cycle when the cell becomes committed to S phase.
A transposon that mobilizes via an RNA form; the DNA element is transcribed into RNA, and then reverse-transcribed into DNA, which is inserted at a new site in the genome. It does not have an infective (viral) form.
An RNA virus with the ability to convert its sequence into DNA by reverse transcription.
An enzyme that uses single-stranded RNA as a template to synthesize a complementary DNA strand.
Synthesis of DNA on a template of RNA. It is accomplished by the enzyme reverse transcriptase.
A technique for the detection and quantification of expression of a gene by reverse transcription and amplification of RNAs from a cell sample.
Reversions of a mutant cell or organism to the wild-type phenotype.
The bacterial release factor that recognizes UAA and UAG as signals to terminate polypeptide translation.
The bacterial release factor that recognizes UAA and UGA as signals to terminate polypeptide translation.
A polypeptide translation termination factor related to the elongation factor EF-G. It functions to release the factors RF1 or RF2 from the ribosome when they act to terminate polypeptide translation.
Transcriptional termination by bacterial RNA polymerase in the presence of the rho factor.
A protein involved in assisting Escherichia coli RNA polymerase to terminate transcription at certain terminators (called rho-dependent terminators).
Plasmids found in Agrobacterium tumefaciens. Like Ti plasmids, they carry genes that cause disease in infected plants. The disease may take the form of either hairy root disease or crown gall disease.
An enzyme that cleaves phosphodiester linkages between RNA ribonucleotides.
A complex of RNA and proteins. Larger complexes are sometimes called ribonucleoprotein particles.
A major component of the ribosome.
A large assembly of RNA and proteins that synthesizes proteins under direction from an mRNA template.
A sequence on bacterial mRNA that includes an initiation codon that is bound by a 30S subunit in the initiation phase of polypeptide translation.
The inhibition of movement that occurs when a ribosome reaches a codon for which there is no corresponding charged aminoacyl-tRNA.
A catalytic RNA whose activity responds to a small ligand.
An RNA that has catalytic activity.
RNA-induced silencing complex, a ribonucleoprotein particle composed of a short, single-stranded siRNA and a nuclease that cleaves mRNAs complementary to the siRNA. It receives siRNA from Dicer and delivers it to the mRNA.
RNA-induced transcriptional silencing. Small RNAs that can downregulate transcription of specific genes at the level of chromatin modification.
A protein containing one or more domains that confer an affinity for RNA, usually in an RNA sequence- or structure-specific manner.
An RNA polymerase that uses RNA as the template to synthesize a new strand.
A change of sequence at the level of RNA following transcription.
A mechanism of gene expression silencing carried out by microRNAs.
A process by which short 21- to 23-nucleotide antisense RNAs, derived from longer double-stranded RNAs, can modulate expression of mRNA by translation inhibition or degradation.
An enzyme that functions in tRNA splicing to make a phosphodiester bond between the two exon sequences that are generated by cleavage of the intron.
An enzyme that synthesizes RNA using a DNA template.
Modifications to RNA transcripts of genes. This may include alterations to the 3′ and 5′ ends and the removal of introns.
A set of RNAs that are coregulated by the same set of RNA-binding proteins that control their splicing, stability, localization, etc.
The ability of an RNA, especially ncRNA, to alter chromatin structure in order to prevent gene transcription.
The process of excising introns from RNA and connecting the exons into a continuous mRNA.
Systems that check RNAs (or RNPs) for errors. The system recognizes an invalid sequence or structure and triggers a response.
An enzyme that degrades RNA.
A mode of replication in which a replication fork proceeds around a circular template for an indefinite number of revolutions; the DNA strand newly synthesized in each revolution displaces the strand synthesized in the previous revolution, giving a tail containing a linear series of sequences complementary to the circular template strand.
The location of the histone octamer relative to turns of the double helix that determines which face of DNA is exposed on the nucleosome surface.
See recombination signal sequences (RSSs).
The sequence of RNA that is recognized by the rho termination factor.
The restricted part of the eukaryotic cell cycle during which synthesis of DNA occurs.
See switch (S) region.
DNA that consists of many tandem repeats (identical or related) of a short, basic repeating unit. See also virusoid.
DNA sites attached to proteinaceous structures in both metaphase and interphase nuclei. Chromatin appears to be attached to an underlying structure in vivo; evidence suggests that this attachment is necessary for transcription or replication
mRNA that consists of a large number of individual mRNA species, each present in very few copies per cell. This accounts for most of the sequence complexity in RNA.
A disease caused by an infective agent made of protein (a prion).
Highly abundant cytoplasmic RNAs of approximately 300 nucleotides.
Complexes of small cytoplasmic RNAs and proteins that make up the spliceosome.
Rule discovered by Edwin Chargaff that, to a close approximation, there are equal amounts of adenine (A) and thymine (T) and equal amounts of cytosine (C) and guanine (G) in each single strand of the DNA duplex.
A second mutation suppressing the effect of a first mutation.
DNA sequences that do not contribute to the phenotype of the organism but that have self-perpetuation within the genome as their sole function.
See autosplicing.
DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand.
The mode of replication in which one new strand is synthesized continuously while the other is synthesized discontinuously.
A complex of several proteins coded by fts genes of Escherichia coli that forms at the midpoint of the cell. It gives rise to the septum at cell division. The first of the proteins to be incorporated is FtsZ, which gave rise to the original name of the Z-ring.
The structure that forms in the center of a dividing bacterium, providing the site at which the daughter bacteria will separate. The same term is used to describe the cell wall that forms between plant cells at the end of mitosis.
The sequence surrounding a consensus sequence. It may modulate the activity of the consensus sequence.
Syndrome that stems from mutations in different genes that result in B and/or T cell deficiency.
A complex of six telomeric proteins in mammals that function to protect telomeres from DNA damage repair pathways and to regulate telomere length control by telomerase.
The polypurine sequence AGGAGG centered about 10 bp before the AUG initiation codon on bacterial mRNA. It is complementary to the sequence at the 3′ end of 16S rRNA.
A major class of short (less than 500 bp) nonautonomous retrotransposons that occupy approximately 13% of the human genome (see also retrotransposon).
See somatic hypermutation (SHM).
A cloning vector that can be used in more than one species of host cell.
The subunit of bacterial RNA polymerase needed for initiation; it is the major influence on selection of promoters.
End produced at the termini of the cleaved fragment containing the recombination signal sequences during recombination of immunoglobulin and T cell receptor genes. Their subsequent joining yields a signal joint.
The process by which a stimulus or cellular state is sensed by and transmitted to pathways within the cell.
A short sequence of DNA that can inactivate expression of a gene in its vicinity.
A mutation that does not change the sequence of a polypeptide because it produces synonymous codons.
Short, repeating units of DNA sequence.
A type of replication control in bacteria resulting from the fact that a genome in a bacterial cell has a single replication origin and thus constitutes a single replicon. Because units of replication and segregation coincide, initiation at a single origin sponsors replication of the entire genome, once for every cell division.
A control system in which there is only one copy of a replicon per unit bacterium. The bacterial chromosome and some plasmids have this type of regulation.
A polymorphism (variation in sequence between individuals) caused by a change in a single nucleotide. This is responsible for most of the genetic variation between individuals.
The protein that attaches to single-stranded DNA, thereby preventing the DNA from forming a duplex.
A reaction in which one of the strands of a duplex of DNA leaves its former partner and instead pairs with the complementary strand in another molecule, displacing its homologue in the second duplex.
The process in which a single strand of DNA displaces its homologous strand in a duplex.
The theory that describes the inactivation of one X chromosome in female mammals.
Short interfering RNA, an miRNA that prevents gene expression.
Each of two identical copies of a replicated chromosome; this term is used as long as the two copies remain linked at the centromere. They separate during anaphase in mitosis or anaphase II in meiosis.
Method used to create targeted changes in the DNA sequence of a gene or a gene product. Basic technique relies on the introduction of a synthetic primer that contains the mutation and that is complementary to the template DNA around the mutation site.
Recombination that occurs between two specific sequences, as in phage integration/excision or resolution of cointegrate structures during transposition.
A set of protein factors that target nonstop decay (NSD) substrates for degradation.
Temperature-sensitive replication mutants that are defective in initiation of replication.
See spliced leader RNA (SL RNA).
RNAs that are present in the cytoplasm (and sometimes also in the nucleus).
One of many small RNA species confined to the nucleus; several of them are involved in splicing or other RNA-processing reactions.
A small nuclear RNA that is localized in the nucleolus.
Complexes of snRNAs and proteins that make up the spliceosome.
The process of joining V(D)J gene segments in a B or T lymphocyte to generate a B or T cell receptor. Also underlies Ig class switching.
An active process of mutation in B cells but not T cells. It introduces mutations in rearranged immunoglobulin V(D)J genes at a rate that is at least 106 higher than that of spontaneous mutations in the genome at large. These mutations can change the sequence of the antibody, especially in its antigen-binding site.
A mutation occurring in a somatic cell, therefore affecting only its daughter cells; it is not inherited by descendants of the organism.
Recombination that occurs in nongerm cells (i.e., it does not occur during meiosis). Most commonly used to refer to recombination in the immune system, in which case it refers to the process of joining V(D)J gene segments in a B or T lymphocyte to generate a B or T cell receptor; in this case it is also called V(D)J recombination. Process also underlies Ig class switching.
A process for the transfer of DNA bands separated by gel electrophoresis from the gel matrix to a solid support matrix such as a nylon membrane for subsequent probing and detection.
A structure made up of microtubules that guides the movements of the chromosomes during mitosis.
DNA that results from a Holliday junction being resolved by cutting the nonexchanged strands. Both strands of DNA before the exchange point come from one chromosome; the DNA after the exchange point come from the homologous chromosome.
A small RNA that donates an exon in the trans-splicing reaction of trypanosomes and nematodes.
A complex that is required for RNA splicing, formed by snRNPs and additional protein factors.
The process of excising introns from RNA and connecting the exons into a continuous mRNA.
A protein component of the spliceosome that is not part of one of the snRNPs.
Mutations occurring in the absence of any added reagent to increase the mutation rate, as the result of errors in replication (or other events involved in the reproduction of DNA) or by random changes to the chemical structure of bases.
The generation of a spore by a bacterium (by morphological conversion) or by a yeast (as the product of meiosis).
A protein that has a variable length of a Ser-Arg–rich region and is involved in splicing.
A small bacterial RNA that functions as a regulator of gene expression.
One of a variety of cis sequences present in some mRNAs that confers a long half-life on that mRNA.
The position on DNA corresponding to the first base incorporated into RNA.
The concentration of population of molecules when the rates of synthesis and degradation are constant.
A secondary structure that appears in RNAs consisting of a base-paired region (stem) and a terminal loop of single-stranded RNA. Both are variable in size.
Transcription factors that are activated by binding of a steroid ligand.
One of three triplets (UAG, UAA, or UGA) that cause polypeptide translation to terminate. They are also known historically as nonsense codons. The UAA codon is called ochre and the UAG codon is called amber, after the names of the nonsense mutations by which they were originally identified.
A mode of replication of some viruses in which a new DNA strand grows by displacing the previous (homologous) strand of the duplex.
Cytoplasmic particles containing translationally inactive mRNAs that form in response to a general inhibition of translation initiation.
A measure of the exactness of complementarity required between two DNA strands to allow them to hybridize. It is related to buffer ionic strength and reaction temperature above or below TM, with lower ionic strengths and higher temperatures having higher values (i.e., greater exactness required).
The protein RelA, which is associated with ribosomes; synthesizes ppGpp and pppGpp when an uncharged tRNA enters the ribosome.
The ability of a bacterium to shut down synthesis of ribosomes and tRNA in a poor growth medium.
Short temporal RNA, a form of miRNA in eukaryotes that modulates mRNA expression during development.
A gene that codes for any RNA or polypeptide product other than a regulator.
The process of breaking a cloned fragment into smaller fragments for further cloning.
The coiling of a closed duplex DNA in space so that it crosses over its own axis.
A set of genes all related by presumed descent from a common ancestor but now showing considerable variation.
A second event eliminates the effects of a mutation without reversing the original change in DNA.
A sequence involved in immunoglobulin class switch DNA recombination. Consists of repetitive 3- to 5-kb sequences upstream of the each cluster of gene segments encoding the heavy chain constant regions.
The association of the two pairs of sister chromatids (representing homologous chromosomes) that occurs at the start of meiosis; the resulting structure is called a bivalent.
The morphological structure of synapsed chromosomes.
Codons that have the same meaning (specifying the same amino acid, or specifying termination of translation) in the genetic code.
A mutation in a coding region that does not alter the amino acid sequence of the polypeptide product.
A relationship between chromosomal regions of different species where homologous genes occur in the same order.
An automated technique in budding yeast whereby a mutant is crossed to an array of approximately 5,000 deletion mutants to determine whether the mutations interact to cause a synthetic lethal phenotype.
Two mutations that are viable by themselves but lethal when combined.
The antigen receptor on T lymphocytes; it is clonally expressed and binds to a complex of MHC class I or class II protein and antigen-derived peptide.
Lymphocytes of the T (thymic) lineage. They differentiate in the thymus from stem cells of bone marrow origin. They are grouped into several functional types (subsets) according to their phenotype, mainly expression of surface CD4, CD8, or CD25. Different subsets are involved in different cell-mediated immune responses.
The part of the Ti plasmid that is transferred from Agrobacterium into a plant cell. It is required for infection.
Structure characterized by a series of TTAGGG repeats that are displaced to form a single-stranded region, and the tail of the telomere is paired with the homologous strand.
The subunits of TFIID that assist TBP in binding to DNA. They also provide points of contact for other components of the transcription apparatus.
Generation of a chromosome segment that is identical to the segment immediately adjacent to it.
The subunit of transcription factor TFIID that binds to the TATA box in the promoter and is positioned at the promoters that do not contain a TATA box by other factors.
A conserved AT-rich octamer found about 25 bp before the start point of each eukaryotic RNA polymerase II transcription unit; it is involved in positioning the enzyme for correct initiation.
A gene promoter that does not have a TATA box in the sequence upstream of its start point.
See T cell receptor (TCR).
See terminal deoxynucleotidyl transferase (TdT).
The ribonucleoprotein enzyme that creates repeating units of one strand at the telomere by adding individual bases to the DNA 3′ end, as directed by an RNA sequence in the RNA component of the enzyme.
The natural end of a chromosome; the DNA sequence consists of a simple repeating unit with a protruding single-stranded end.
The repression of gene activity that occurs in the vicinity of a telomere.
A bacteriophage that can follow the lytic or lysogenic pathway.
The DNA strand that is copied by the polymerase.
The DNA sequence that signals for the termination of replication.
A growth in which many differentiated cell types—including skin, teeth, bone, and others—grow in a disorganized manner after an early embryo is transplanted into one of the tissues of an adult animal.
An enzyme that catalyzes the insertion of unencoded (N) nucleotides into V-D-J coding sequences during V(D)J recombination.
A protein that allows replication of a linear phage genome to start at the very end. It attaches to the 5′ end of the genome through a covalent bond, is associated with a DNA polymerase, and contains a cytosine residue that serves as a primer.
An enzyme that cleaves multimers of a viral genome and then uses hydrolysis of ATP to provide the energy to translocate the DNA into an empty viral capsid starting with the cleaved end.
A separate reaction that ends a macromolecular synthesis reaction (replication, transcription, or translation) by stopping the addition of subunits and (typically) causing disassembly of the synthetic apparatus.
One of the three codons (UAA, UAG, UGA) that signal the termination of translation of a polypeptide.
A sequence of DNA that causes RNA polymerase to terminate transcription.
A segment of DNA at which replication ends.
The complex in initiation of transcription that consists of RNA polymerase and DNA as well as a dinucleotide that represents the first two bases in the RNA product.
A four-part structure that forms during the prophase of meiosis. Consists of two homologous chromosomes, each composed of two sister chromatids.
The transcription factor that binds to the TATA sequence upstream of the start point of promoters for RNA polymerase II. It consists of TBP (TATA-binding protein) and the TAF subunits that bind to TBP.
A disease of red blood cells resulting from lack of either α or β globin.
The lesser effect on codon meaning of the nucleotide present in the third (3′) codon position.
The thermocycle number in a real-time PCR or RT-PCR reaction at which the product signal rises above a specified cutoff value to indicate that amplicon production is occurring.
An episome of the bacterium Agrobacterium tumefaciens that carries the genes responsible for the induction of crown gall disease in infected plants.
An array of immobilized nucleic acid sequences that together represent the entire genome of an organism. The shorter each array spot is, the larger the total number of spots required, but the greater the genetic resolution of the array.
See Toll-like receptors (TLRs).
Enzyme that plays a role in a DNA damage tolerance process that enables replication past lesions such as thymine dimers or areas of stalled DNA replication.
The theoretical melting temperature of a duplex nucleic acid segment into separate strands. It is dependent on parameters such as sequence composition, duplex length, and buffer ionic strength.
A tRNA–mRNA hybrid that allows recycling of stalled ribosomes.
A key signaling domain that is unique to the Toll-like receptor (TLR) system. Located in the cytosolic face of each TLR, and also in the TLR signaling adaptors. Similar to the TLRs, the adaptors are conserved across many species. The five known adaptors are MyD88, MyD88-adaptor-like (MAL, also known as TIRAP), TIR-domain-containing adaptor protein inducing IFN-β (TRIF; also known as TICAM1), TRIF-related adaptor molecule (TRAM; also known as TICAM2), and sterile armadillo-motif-containing protein (SARM).
A family of proteins that play a fundamental role in recognition of microbes and activation of innate immunity. These transmembrane proteins are expressed on the cell surface and the endocytic compartment and recognize microbe-associated molecular patterns (MAMPs) on microorganisms.
An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other. It does this by cutting the DNA, passing DNA through the break, and resealing the DNA.
Molecules with the same chemical formula but different bond connectivities, thus resulting in different topologic structures. Examples include DNA, which can have different numbers of supercoils.
An untranslated sequence at the 3′ end of an mRNA following the termination codon.
A protein complex that identifies and polyadenylates aberrant nuclear RNAs in yeast, recruiting the nuclear exosome for degradation.
A product that can function on any copy of its target DNA. This implies that it is a diffusible protein or RNA.
Synthesis of RNA from a DNA template.
The sequence between sites of initiation and termination by RNA polymerase; it may include more than one gene.
The phenomenon in which transcription from one promoter interferes directly with transcription from a second, linked promoter.
The complete set of RNAs present in a cell, tissue, or organism. Its complexity is due mostly to mRNAs, but it also includes noncoding RNAs.
A virus that carries part of the host genome in place of part of its own sequence. The best known examples are retroviruses in eukaryotes and DNA phages in Escherichia coli.
In eukaryotic cells, it is the acquisition of new genetic markers by incorporation of added DNA.
A large (approximately 33 kb) region of an F plasmid that is required for bacterial conjugation. It contains genes that are required for the transmission of DNA.
The intermediate in protein synthesis that interprets the genetic code. Each molecule can be linked to an amino acid. It has an anticodon sequence that is complementary to a triplet codon representing the amino acid.
In bacteria, it is the acquisition of new genetic material by incorporation of added DNA.
DNA that is taken up by a bacterium and whose expression then changes the properties of the recipient cell.
Transmission of nongenetic information (epigenetic states) from an organism to its offspring.
Organism created by introducing DNA prepared in test tubes into the germline. The DNA may be inserted into the genome or exist in an extrachromosomal structure.
A mutation in which one pyrimidine is replaced by the other, or in which one purine is replaced by the other.
Synthesis of protein on an mRNA template.
The location of a histone octamer at successive turns of the double helix that determines which sequences are located in linker regions.
Involved in bypass of base damage in DNA. In general, displays low fidelity and low processivity and is error prone when copying undamaged DNA templates.
A DNA damage tolerance process that can bypass replication blocks caused by damaged DNA by switching out regular DNA polymerases for specialized translesion polymerases that are able to replicate DNA over the damaged area.
(1) The movement of the ribosome one codon along mRNA after the addition of each amino acid to the polypeptide chain. (2) The reciprocal or nonreciprocal exchange of chromosomal material between nonhomologous chromosomes.
The part of a protein that spans the membrane bilayer. It is hydrophobic and in many cases contains approximately 20 amino acids that form an α-helix.
The enzyme activity involved in insertion of transposon at a new site.
The movement of a transposon to a new site in the genome.
A DNA sequence able to insert itself (or a copy of itself) at a new location in the genome without having any sequence relationship with the target locus.
A mutation in which a purine is replaced by a pyrimidine or vice versa.
The special RNA used to initiate polypeptide translation in bacteria. It mostly uses AUG but can also respond to GUG and CUG.
The bacterial tRNA that inserts methionine at internal AUG codons.
A positive transcription faction that functions by making contact, direct or indirect, with the basal apparatus to activate transcription.
A mutation that restores the original sequence of the DNA.
A type of methyl-lysine binding domain characterized by a specific sequence of approximately 60 amino acids.
A class of proteins that guard the cell cycle, ensuring that the cell size and absence of DNA damage criteria are met. These proteins act as brakes on the cell cycle, preventing the cell from progressing from G1 to S.
In the DNA double helix, the rotation of one strand about the other.
The repeated sequence at the 3′ end of a retroviral RNA.
The repeated sequence at the 5′ end of a retroviral RNA.
See upstream activating sequence (UAS).
B-form DNA that has fewer than 10.5 base pairs per turn of the helix.
The result of an error in pairing and crossing over in which nonequivalent sites are involved in a recombination event. It produces one recombinant with a deletion of material and one with a duplication.
Enzyme required for both class switch recombination (CSR) and somatic hypermutation (SHM). It deglycosylates the deoxyuridines generated by the deamination of deoxycytidines to give rise to abasic sites. B cells that are deficient in this enzyme have a 10-fold reduction in CSR, suggesting that the enzyme is critical for the generation of double-strand breaks (DSBs). Different events follow in the CSR and SHM processes.
An open reading frame with an as yet undetermined function.
The movement of a single replication fork from a given origin.
A mutant in which the affected gene(s) cannot be expressed.
The time in millions of years that it takes for 1% divergence in evolutionary divergent sequences.
A sequence in bacteria adjacent to the promoter, upstream of the −35 element, that enhances transcription.
A set of protein factors that target nonsense-mediated decay (NMD) substrates for degradation.
Sequences in the opposite direction from expression.
The equivalent in yeast of the enhancer in higher eukaryotes that is bound by transcriptional activator proteins; a UAS cannot function downstream of the promoter.
A mutation in a promoter that increases the rate of transcription.
A member of a highly conserved and specific class of DNA repair enzymes. Biological function is the specific removal of the normal RNA base uracil from DNA. It eliminates uracil from DNA molecules and generates abasic sites, thereby initiating the base excision repair (BER) pathway. This enzyme has been identified in a variety of prokaryotic and eukaryotic organisms and in different families of viruses. In class switch recombination and somatic hypermutation, it deglycosylates deoxyuridines emerging from AID-mediated deamination of deoxycytosines.
Very short repeated sequences, including microsatellites and mini-satellites.
An antigen-binding site of an immunoglobulin or T cell receptor molecule. They are composed of the variable domains of the component chains. They are coded by V gene segments and vary extensively among antigen receptors as the result of multiple, different genomic copies and of changes introduced during synthesis.
An engineered DNA molecule used to transfer and propagate various insert DNAs.
The period of normal growth and division of a bacterium. For a bacterium that can sporulate, this contrasts with the sporulation phase, when spores are being formed.
A small infectious nucleic acid that does not have a protein coat.
Phage mutants that are unable to establish lysogeny.
A bacteriophage that can only follow the lytic cycle.
A small infectious nucleic acid that is encapsidated by a plant virus together with its own genome.
Analytical technique used to detect specific proteins in a sample of tissue homogenate or extract. Artificial antibodies are introduced to the sample that will react with a specific target protein. The sample is then placed on a membrane. If a stained band appears after gel electrophoresis is performed on the sample, then the specific protein is present in the sample.
The ability of a tRNA to recognize more than one codon by unusual (non–G-C, non–A-T) pairing with the third base of a codon.
In DNA, the turning of the axis of the duplex in space.
A disease caused by mutation in one of the XP genes, which results in hypersensitivity to sunlight (particularly ultraviolet light), skin disorders, and cancer predisposition.
A cloning vector used in yeast that can hold up to 3,000 kb of DNA and that contains a centromere, telomeres, and origin of replication.
See septal ring.
A DNA-binding motif that typifies a class of transcription factor.
Any of the number of mRNA cis elements involved in directing cellular localization.