BP

GO:0006260

DNA replication

The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

IEA

BP

GO:0006335

DNA replication-dependent nucleosome assembly

The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.

IDA

BP

GO:0006336

DNA replication-independent nucleosome assembly

The formation of nucleosomes outside the context of DNA replication.

IDA

BP

GO:0006338

chromatin remodeling

Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.

IDA

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0006355

regulation of transcription, DNA-templated

Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

IEA

BP

GO:0007049

cell cycle

The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.

IEA

BP

GO:0008285

negative regulation of cell proliferation

Any process that stops, prevents or reduces the rate or extent of cell proliferation.

TAS

BP

GO:0016575

histone deacetylation

The modification of histones by removal of acetyl groups.

IEA

BP

GO:0031497

chromatin assembly

The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.

IDA

BP

GO:0034080

CENP-A containing nucleosome assembly

The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.

TAS

BP

GO:0043044

ATP-dependent chromatin remodeling

Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.

IDA

BP

GO:0045814

negative regulation of gene expression, epigenetic

Any epigenetic process that stops, prevents or reduces the rate of gene expression.

TAS

BP

GO:0051726

regulation of cell cycle

Any process that modulates the rate or extent of progression through the cell cycle.

TAS

BP

GO:0060416

response to growth hormone

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 growth hormone stimulus. Growth hormone is a peptide hormone that binds to the growth hormone receptor and stimulates growth.

IEA

BP

GO:1901796

regulation of signal transduction by p53 class mediator

Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.

TAS

CC

GO:0000790

nuclear chromatin

The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.

IDA

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:0016580

Sin3 complex

A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.

NAS

CC

GO:0016581

NuRD complex

An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.

IDA|NAS

CC

GO:0016589

NURF complex

An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.

IDA

CC

GO:0033186

CAF-1 complex

A conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). In many species the CAF-1 subunits are designated p150, p60, and p48.

IDA

CC

GO:0035098

ESC/E(Z) complex

A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4.

IDA

CC

GO:0043234

protein complex

A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

IDA

MF

GO:0000978

RNA polymerase II core promoter proximal region sequence-specific DNA binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.

IDA

MF

GO:0000980

RNA polymerase II distal enhancer sequence-specific DNA binding

Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.

IDA

MF

GO:0004407

histone deacetylase activity

Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.

TAS

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:0008094

DNA-dependent ATPase activity

Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.

IDA

MF

GO:0031492

nucleosomal DNA binding

Interacting selectively and non-covalently with the DNA portion of a nucleosome.

IDA

MF

GO:0042393

histone binding

Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.

NAS

MF

GO:0042826

histone deacetylase binding

Interacting selectively and non-covalently with the enzyme histone deacetylase.

IPI