BP

GO:0000122

negative regulation of transcription from RNA polymerase II promoter

Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.

IEA

BP

GO:0006284

base-excision repair

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.

IDA

BP

GO:0006285

base-excision repair, AP site formation

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.

IBA

BP

GO:0006298

mismatch repair

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.

IDA

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0009790

embryo development

The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.

ISS

BP

GO:0016569

chromatin modification

The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups.

IEA

BP

GO:0016925

protein sumoylation

The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.

TAS

BP

GO:0032091

negative regulation of protein binding

Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.

IEA

BP

GO:0035511

oxidative DNA demethylation

Removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.

TAS

BP

GO:0035562

negative regulation of chromatin binding

Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.

IEA

BP

GO:0040029

regulation of gene expression, epigenetic

Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.

ISS

BP

GO:0045008

depyrimidination

The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.

TAS

BP

GO:0080111

DNA demethylation

The removal of a methyl group from one or more nucleotides within an DNA molecule.

ISS

CC

GO:0005634

nucleus

A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

IDA

CC

GO:0005654

nucleoplasm

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

IDA|TAS

CC

GO:0005886

plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

IDA

CC

GO:0016605

PML body

A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.

IEA

MF

GO:0001104

RNA polymerase II transcription cofactor activity

Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.

IEA

MF

GO:0003684

damaged DNA binding

Interacting selectively and non-covalently with damaged DNA.

TAS

MF

GO:0003690

double-stranded DNA binding

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

IDA

MF

GO:0004844

uracil DNA N-glycosylase activity

Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.

IBA

MF

GO:0005080

protein kinase C binding

Interacting selectively and non-covalently with protein kinase C.

IEA

MF

GO:0008134

transcription factor binding

Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.

IEA

MF

GO:0008263

pyrimidine-specific mismatch base pair DNA N-glycosylase activity

Catalysis of the removal of mismatched pyrimidine bases in DNA. Enzymes with this activity recognize and remove pyrimidines present in mismatches by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apyrimidinic (AP) site.

IDA

MF

GO:0019104

DNA N-glycosylase activity

Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.

IDA|TAS

MF

GO:0019904

protein domain specific binding

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

IEA

MF

GO:0030983

mismatched DNA binding

Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.

IDA

MF

GO:0032183

SUMO binding

Interacting selectively and non-covalently with the small ubiquitin-like protein SUMO.

IEA

MF

GO:0042803

protein homodimerization activity

Interacting selectively and non-covalently with an identical protein to form a homodimer.

IDA

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.

ISS