BP

GO:0000710

meiotic mismatch repair

A system for the identification and correction of base-base mismatches, small insertion-deletion loops, and regions of heterology that are present in duplex DNA formed with strands from two recombining molecules. Correction of the mismatch can result in non-Mendelian segregation of alleles following meiosis.

IBA

BP

GO:0000720

pyrimidine dimer repair by nucleotide-excision repair

The repair of UV-induced T-T, C-T, and C-C dimers by the recognition and removal of the damaged DNA strand 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.

IEA

BP

GO:0001302

replicative cell aging

The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.

IEA

BP

GO:0006281

DNA repair

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.

IMP

BP

GO:0006283

transcription-coupled nucleotide-excision repair

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.

TAS

BP

GO:0006289

nucleotide-excision repair

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).

IDA|IGI

BP

GO:0006293

nucleotide-excision repair, preincision complex stabilization

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.

TAS

BP

GO:0006295

nucleotide-excision repair, DNA incision, 3'-to lesion

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.

IMP|TAS

BP

GO:0006296

nucleotide-excision repair, DNA incision, 5'-to lesion

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.

IMP|TAS

BP

GO:0006302

double-strand break repair

The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

IEA

BP

GO:0006310

DNA recombination

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. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

IGI

BP

GO:0006312

mitotic recombination

The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles.

IMP

BP

GO:0006949

syncytium formation

The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.

IEA

BP

GO:0006979

response to oxidative stress

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

IMP

BP

GO:0007283

spermatogenesis

The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.

IEA

BP

GO:0007584

response to nutrient

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.

IEA

BP

GO:0008283

cell proliferation

The multiplication or reproduction of cells, resulting in the expansion of a cell population.

IEA

BP

GO:0008584

male gonad development

The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.

IEA

BP

GO:0009650

UV protection

Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV.

IEA

BP

GO:0009744

response to sucrose

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sucrose stimulus.

IEA

BP

GO:0010165

response to X-ray

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).

IEA

BP

GO:0010259

multicellular organism aging

An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700).

IEA

BP

GO:0032205

negative regulation of telomere maintenance

Any process that stops, prevents, or reduces the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.

IMP

BP

GO:0033683

nucleotide-excision repair, DNA incision

A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.

TAS

BP

GO:0035166

post-embryonic hemopoiesis

The stages of blood cell formation that take place after completion of embryonic development.

IEA

BP

GO:0035264

multicellular organism growth

The increase in size or mass of an entire multicellular organism, as opposed to cell growth.

IEA

BP

GO:0036297

interstrand cross-link repair

Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.

TAS

BP

GO:0045190

isotype switching

The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus.

IEA

BP

GO:0048477

oogenesis

The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.

IEA

BP

GO:0048568

embryonic organ development

Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.

IEA

BP

GO:0070911

global genome nucleotide-excision repair

The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.

TAS

BP

GO:0070914

UV-damage excision repair

A DNA repair process that is initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced damage site. UV-damage excision repair acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs).

IBA

BP

GO:0090656

t-circle formation

A telomere maintenance process that results in the formation of a telomeric circle, or t-circle. A t-circle is an extrachromosomal duplex or single-stranded circular DNA molecule composed of t-arrays. T-circles are involved in the control of telomere length via alternative-lengthening of telomeres (ALT) pathway and telomere rapid deletion (TRD).

ISS

BP

GO:1904431

positive regulation of t-circle formation

Any process that activates or increases the frequency, rate or extent of t-circle formation.

ISS

CC

GO:0000109

nucleotide-excision repair complex

Any complex formed of proteins that act in nucleotide-excision repair.

IDA

CC

GO:0000110

nucleotide-excision repair factor 1 complex

One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p; in human the subunits are ERCC4/XPF, ERCC1 and XPA, respectively.

IDA

CC

GO:0000784

nuclear chromosome, telomeric region

The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.

IDA

CC

GO:0005654

nucleoplasm

That part of the nuclear content other than the chromosomes or the nucleolus.

IDA|TAS

CC

GO:0005669

transcription factor TFIID complex

A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

IEA

CC

GO:0005737

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

IDA

CC

GO:0070522

ERCC4-ERCC1 complex

A heterodimeric nucleotide-excision repair complex that has endonuclease activity specific for bubble structures characteristic of certain DNA lesions. The subunits are known as XPF/ERCC4 and ERCC1 in mammals, and Rad1p and Rad10p in S. cerevisiae.

IDA

MF

GO:0000014

single-stranded DNA endodeoxyribonuclease activity

Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.

IDA

MF

GO:0001094

TFIID-class transcription factor binding

Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.

IEA

MF

GO:0003684

damaged DNA binding

Interacting selectively and non-covalently with damaged DNA.

IDA

MF

GO:0003697

single-stranded DNA binding

Interacting selectively and non-covalently with single-stranded DNA.

IDA

MF

GO:0005515

protein binding

Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

IPI

MF

GO:0008022

protein C-terminus binding

Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.

IPI

MF

GO:0019904

protein domain specific binding

Interacting selectively and non-covalently with a specific domain of a protein.

IPI

MF

GO:0043566

structure-specific DNA binding

Interacting selectively and non-covalently with DNA of a specific structure or configuration e.g. triplex DNA binding or bent DNA binding.

IDA