LiteFold/GO huggingface dataset:
DNA replication, synthesis of primer (GO:0006269)
Namespace: biological_process
Definition: The synthesis of a short nucleotide polymer using one strand of unwound DNA as a template. The product is usually a RNA molecule between 4-15 nucleotides long that provides a free 3'-OH that can be extended by DNA-directed DNA polymerases. In certain conditions, for example in response to DNA damage, some primases synthesize a DNA primer.
Synonyms: DNA priming; DNA replication, synthesis of DNA primer; DNA replication, synthesis of RNA primer; replication priming
DNA replication initiation (GO:0006270)
Namespace: biological_process
Definition: The process in which DNA-dependent DNA replication is started; it begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, followed by DNA unwinding.
Synonyms: DNA endoreduplication initiation; DNA re-replication initiation; DNA-dependent DNA replication initiation
DNA strand elongation involved in DNA replication (GO:0006271)
Namespace: biological_process
Definition: The process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication.
Synonyms: DNA replication elongation; DNA strand elongation during DNA replication
lagging strand elongation (GO:0006273)
Namespace: biological_process
Definition: The process in which an existing DNA strand is extended in a net 3' to 5' direction by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork.
DNA replication termination (GO:0006274)
Namespace: biological_process
Definition: The process in which DNA replication at a replication fork ceases; occurs when the replication fork reaches a specific termination site or when two replication forks meet.
regulation of DNA replication (GO:0006275)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of DNA replication.
plasmid maintenance (GO:0006276)
Namespace: biological_process
Definition: The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
DNA amplification (GO:0006277)
Namespace: biological_process
Definition: The process in which the number of copies of a gene is increased in certain cells as extra copies of DNA are made in response to certain signals of cell development or of stress from the environment.
RNA-templated DNA biosynthetic process (GO:0006278)
Namespace: biological_process
Definition: A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
Synonyms: RNA-dependent DNA biosynthetic process
premeiotic DNA replication (GO:0006279)
Namespace: biological_process
Definition: The replication of DNA that precedes meiotic cell division.
Synonyms: DNA replication during S phase involved in meiotic cell cycle; DNA replication involved in S phase involved in meiotic cell cycle; DNA replication involved in S-phase involved in meiotic cell cycle; meiotic cell cycle DNA replication; meiotic DNA replication; meiotic DNA synthesis; meiotic nuclear cell cycle DNA replication; nuclear cell cycle DNA replication involved in meiotic cell cycle; premeiotic DNA synthesis
obsolete mutagenesis (GO:0006280)
Namespace: biological_process
Definition: OBSOLETE. The process by which genetic material undergoes a detectable and heritable structural change. There are three categories of mutation: genome mutations, involving addition or subtraction of one or more whole chromosomes; chromosome mutations, which alter the structure of chromosomes; and gene mutations, where the structure of a gene is altered at the molecular level.
Synonyms: mutagenesis
Comment: This term was made obsolete because mutagenesis is not a valid biological process in which gene products would normally participate. Rather, mutations arise from DNA replication errors or damage by an extrinsic agent.
DNA repair (GO:0006281)
Namespace: biological_process
Definition: The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
regulation of DNA repair (GO:0006282)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of DNA repair.
transcription-coupled nucleotide-excision repair (GO:0006283)
Namespace: biological_process
Definition: The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
Synonyms: TC-NER; TCR; transcription-coupled NER; transcription-coupled repair
base-excision repair (GO:0006284)
Namespace: biological_process
Definition: In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
Synonyms: BER
base-excision repair, AP site formation (GO:0006285)
Namespace: biological_process
Definition: The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
obsolete base-excision repair, DNA ligation (GO:0006288)
Namespace: biological_process
Definition: OBSOLETE. The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
Comment: The reason for obsoletion is that the term represents a molecular function.
nucleotide-excision repair (GO:0006289)
Namespace: biological_process
Definition: A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
Synonyms: intrastrand cross-link repair; NER; pyrimidine-dimer repair, DNA damage excision
Comment: Note that although intrastrand cross-link repair is not exactly synonymous with nucleotide excision repair, nucleotide excision repair includes the repair of intrastrand cross-links. The synonym field is being used to reflect the broad substrate specificity of nucleotide excision repair.
pyrimidine dimer repair (GO:0006290)
Namespace: biological_process
Definition: The repair of UV-induced T-T, C-T and C-C dimers.
obsolete pyrimidine-dimer repair, DNA damage excision (GO:0006291)
Namespace: biological_process
Definition: OBSOLETE. The excision of damaged DNA during pyrimidine-dimer repair. A large multienzyme complex scans the DNA for a distortion in the double helix rather than for a specific base change. Once a bulky lesion is found, the phosphodiester backbone of the abnormal strand is cleaved on both sides of the distortion, and the portion of the strand containing the lesion (an oligonucleotide) is peeled away from the DNA double helix by a DNA helicase enzyme.
Synonyms: pyrimidine-dimer repair, DNA damage excision
Comment: This term was made obsolete because this process can be subdivided into multiple processes.
obsolete pyrimidine-dimer repair, DNA damage recognition (GO:0006292)
Namespace: biological_process
Definition: OBSOLETE. The location of pyrimidine dimers by a large multienzyme complex that scans the DNA for distortions in the double helix caused by pyrimidine dimers.
Synonyms: pyrimidine-dimer repair, DNA damage recognition
Comment: This term was made obsolete because it is a substrate specific DNA repair process.
nucleotide-excision repair, preincision complex stabilization (GO:0006293)
Namespace: biological_process
Definition: The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
obsolete nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)
Namespace: biological_process
Definition: OBSOLETE. The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
Synonyms: nucleotide-excision repair, DNA incision, 3' to lesion
Comment: This term was obsoleted because it represents a molecular function.
obsolete nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)
Namespace: biological_process
Definition: OBSOLETE. The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
Synonyms: nucleotide-excision repair, DNA incision, 5' to lesion
Comment: This term was obsoleted because it represents a molecular function.
nucleotide-excision repair, DNA gap filling (GO:0006297)
Namespace: biological_process
Definition: Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
mismatch repair (GO:0006298)
Namespace: biological_process
Definition: A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
Synonyms: long patch mismatch repair system; mismatch repair, MutL-like pathway; MMR; MutS/MutL/MutH pathway
obsolete short patch mismatch repair system (GO:0006299)
Namespace: biological_process
Definition: OBSOLETE. The repair of mismatched DNA where the gap to be repaired is only one nucleotide. DNA polymerase is the preferred polymerase in short patch repair, performing gap filling DNA synthesis and removal of the 5'-deoxyribose phosphate of the abasic site.
Synonyms: short patch mismatch repair system
Comment: This term was made obsolete because 'short patch' is a relative statement, often used ambiguously, and does not necessarily represent a process; the processes it can stand for are base excision repair, nucleotide excision repair, transcription-coupled nucleotide excision repair, and mismatch repair.
DNA damage tolerance (GO:0006301)
Namespace: biological_process
Definition: A process that promotes the bypass of single-stranded DNA lesions encountered by DNA polymerases during DNA replication, thereby preventing replication fork stalling and allowing completion of DNA replication without removing the damage.
Synonyms: postreplication DNA repair; postreplication repair
double-strand break repair (GO:0006302)
Namespace: biological_process
Definition: The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
Comment: Note that the processes of nuclear double-strand break repair and mitochondrial double-strand break repair are genetically separable (PMID:22214610). To annotate gene products involved in mitochondrial double-strand break repair, please use GO:0097551 'mitochondrial double-strand break repair'.
obsolete DNA alkylation (GO:0006305)
Namespace: biological_process
Definition: OBSOLETE. The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis.
Comment: This term was obsoleted because it represents a molecular function.
obsolete DNA methylation (GO:0006306)
Namespace: biological_process
Definition: OBSOLETE. The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
Comment: This term was obsoleted because it represents a molecular function.
DNA alkylation repair (GO:0006307)
Namespace: biological_process
Definition: The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases.
Synonyms: DNA dealkylation involved in DNA repair
DNA catabolic process (GO:0006308)
Namespace: biological_process
Definition: The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
Synonyms: DNA breakdown; DNA catabolism; DNA degradation
apoptotic DNA fragmentation (GO:0006309)
Namespace: biological_process
Definition: The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
Synonyms: chromatinolysis; DNA catabolic process during apoptosis; DNA catabolism during apoptosis; DNA fragmentation; DNA fragmentation involved in apoptotic nuclear change; endonucleolytic DNA catabolic process involved in apoptosis
Comment: DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341).
DNA recombination (GO:0006310)
Namespace: biological_process
Definition: Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
meiotic gene conversion (GO:0006311)
Namespace: biological_process
Definition: The cell cycle process in which genetic information is transferred from one helix to another. It often occurs in association with general genetic recombination events, and is believed to be a straightforward consequence of the mechanisms of general recombination and DNA repair. For example, meiosis might yield three copies of the maternal version of an allele and only one copy of the paternal allele, indicating that one of the two copies of the paternal allele has been changed to a copy of the maternal allele.
Synonyms: gene conversion without reciprocal crossover
mitotic recombination (GO:0006312)
Namespace: biological_process
Definition: The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous DNA region that occurs during mitotic cell cycles.
DNA transposition (GO:0006313)
Namespace: biological_process
Definition: A type of transposition in which a transposable element (transposon) is moved to another part of a genome, either by a cut-and-paste mechanism or a replicative mechanism.
Synonyms: Class II transposition; transposition, DNA-mediated
intron homing (GO:0006314)
Namespace: biological_process
Definition: Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
homing of group II introns (GO:0006315)
Namespace: biological_process
Definition: Lateral transfer of a group II intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron; group II introns are self-splicing introns with a conserved secondary structure.
movement of group I intron (GO:0006316)
Namespace: biological_process
Definition: Lateral transfer of a group I intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron; group I introns are self-splicing introns that use guanosine as a cofactor in the splicing reaction.
obsolete S phase-specific histone modification (GO:0006324)
Namespace: biological_process
Definition: OBSOLETE. The covalent alteration of one or more amino acid residues within a histone protein that takes place during, and results in a modification pattern characteristic of, S phase of the cell cycle.
Synonyms: S phase-specific histone modification; S-phase-specific histone modification
Comment: This term was made obsolete because it represents a molecular function.
obsolete bent DNA binding (GO:0006326)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: bent DNA binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
obsolete random coil binding (GO:0006327)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: random coil binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
obsolete AT binding (GO:0006328)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: AT binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
obsolete satellite DNA binding (GO:0006329)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: satellite DNA binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
obsolete single-stranded DNA binding (GO:0006330)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: single-stranded DNA binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
DNA replication-dependent chromatin assembly (GO:0006335)
Namespace: biological_process
Definition: The formation of nucleosomes on newly synthesized DNA, coupled to strand elongation.
Synonyms: DNA replication-dependent chromatin organization; DNA replication-dependent nucleosome assembly; DNA replication-dependent nucleosome organisation; DNA replication-dependent nucleosome organization
nucleosome disassembly (GO:0006337)
Namespace: biological_process
Definition: The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
chromatin remodeling (GO:0006338)
Namespace: biological_process
Definition: A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication.
Synonyms: ATP-dependent chromatin remodeling; ATP-dependent chromatin remodelling; chromatin modeling; chromatin modelling; chromatin remodelling
obsolete negative regulation of transcription of homeotic gene (Polycomb group) (GO:0006340)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription of homeotic genes of the Polycomb group.
Synonyms: negative regulation of transcription of homeotic gene (Polycomb group)
Comment: This term was made obsolete because it relates to a specific gene family rather than a process.
obsolete chromatin insulator sequence binding (GO:0006341)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: chromatin insulator sequence binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
DNA methylation-dependent constitutive heterochromatin formation (GO:0006346)
Namespace: biological_process
Definition: Formation of constitutive heterochromatin by a pathway that includes methylation of genomic DNA such as CpG islands.
Synonyms: DNA methylation-dependent heterochromatin assembly; DNA methylation-dependent heterochromatin formation; methylation-dependent chromatin silencing; methylation-dependent heterochromatic silencing
obsolete regulation of gene expression by genomic imprinting (GO:0006349)
Namespace: biological_process
Definition: OBSOLETE. An epigenetic mechanism of regulation of gene expression in which epigenetic modifications (imprints) are established during gametogenesis. For a given gene to show parentally biased expression, the imprint are established exclusively in one of the two parental genomes, thus generating an asymmetry between the maternal and paternal alleles.
Synonyms: regulation of gene expression by DNA imprinting; regulation of gene expression by genetic imprinting
Comment: This term was obsoleted because it represents the same concept as its parent, GO:0071514 genomic imprinting, also a regulatory process.
DNA-templated transcription (GO:0006351)
Namespace: biological_process
Definition: The synthesis of an RNA transcript from a DNA template.
Synonyms: bacterial transcription; cellular transcription; DNA-dependent transcription; transcription; transcription from bacterial-type RNA polymerase promoter; transcription, DNA-dependent; transcription, DNA-templated