GO:0006233

BP

dTDP biosynthetic process

The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).

DTYMK, CMPK2

GO:0006235

BP

dTTP biosynthetic process

The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.

TYMS, DTYMK, CMPK2

GO:0006238

BP

CMP salvage

Any process that generates CMP, cytidine monophosphate, from derivatives of it without de novo synthesis.

UCK2

GO:0006241

BP

CTP biosynthetic process

The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.

NME4, NME6, NME1, CTPS1, NME2, NME7

GO:0006258

BP

UDP-glucose catabolic process

The chemical reactions and pathways resulting in the breakdown of UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.

GALT

GO:0006259

BP

DNA metabolic process

Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.

TK1, NME1, LIG1, NT5E, IGFBP4, ADRA1D, MKI67, KPNA2, POLG, TOPBP1, TREX2

GO:0006260

BP

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.

CDC7, NFIB, CHEK1, ORC5, RAD1, NBN, RNASEH2A, RECQL4, IGF1, CDK1, NFIC, POLA1, TOP1, PTMS, RRM1, CDK2, MCM3, POLD1, RBMS1, CDC25A, CDC25C, RRM2, DUT, MCM4, MCM5, MCM7, RPA3, RFC4, RFC2, BRCA1, FEN1, RFC5, RFC3, NASP, MCM2, MRE11A, DNA2, BLM, NAP1L1, POLE2, SET, SSBP1, POLE, SSRP1, RBBP4, CHAF1A, CHAF1B, ORC1, POLA2, MCM6, KIAA0101, CCDC88A, TBRG1, RAD9B, NOL8, MCM10, RBBP6, INO80E, CHTF18, ATRIP, KCTD13, TOPBP1, RAD50, RAD9A, BARD1, CDC6, RHNO1, DSCC1, TIPIN, REPIN1, CDT1, POLD4, POLE3, DTL, ORC3, POLK, DBF4, MCM8, POLI, TIMELESS, EXO1, POLH, SUPT16H, ORC6

GO:0006261

BP

DNA-dependent DNA replication

A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.

CDK2AP1, REV3L, POLQ, POLG, POLE2, TFAM, POLD4, BAZ1A

GO:0006264

BP

mitochondrial DNA replication

The process in which new strands of DNA are synthesized in the mitochondrion.

DNA2, POLG, PRIMPOL, PEO1, MGME1

GO:0006265

BP

DNA topological change

The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.

HMGB1, TOP1, TOP2A, HMGB2

GO:0006266

BP

DNA ligation

The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.

TOP2A

GO:0006267

BP

pre-replicative complex assembly involved in nuclear cell cycle DNA replication

The aggregation, arrangement and bonding together of a set of components to form the nuclear pre-replicative complex, a protein-DNA complex that forms at the eukaryotic DNA replication origin and is required for replication initiation.

ORC3

GO:0006268

BP

DNA unwinding involved in DNA replication

The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.

TOP2A, HMGA1, MCM4, MCM7, MCM2, PURA, RAD51, MCM6, PEO1

GO:0006269

BP

DNA replication, synthesis of RNA primer

The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.

POLA1, PRIM1, PRIM2, PRIMPOL

GO:0006270

BP

DNA replication initiation

The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.

CDC7, ORC5, CCNE2, POLA1, MCM3, MCM4, MCM5, MCM7, CDC34, PRIM1, PRIM2, MCM2, POLE2, PURA, POLE, ORC1, POLA2, MCM6, MCM10, TOPBP1, CDC6, SLF1, GINS4, ORC3, LRWD1, ORC6

GO:0006271

BP

DNA strand elongation involved in DNA replication

The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.

POLA1, PCNA, POLD1, RFC4, RFC3, PRIM1, PRIM2, POLA2, GINS1, POLD3, GINS4, GINS3, POLD4, GINS2

GO:0006272

BP

leading strand elongation

The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.

POLA1, PCNA

GO:0006273

BP

lagging strand elongation

The synthesis of DNA from a template strand in a net 3' to 5' direction. 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.

PARP1, POLA1, PARP2

GO:0006275

BP

regulation of DNA replication

Any process that modulates the frequency, rate or extent of DNA replication.

PPP2R1A, ID3, CCDC88A, ESCO2, RBBP6, ZBTB38, EHMT2, DSCC1, NUCKS1, SMC3

GO:0006278

BP

RNA-dependent DNA biosynthetic process

A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.

PPIA, PTGES3, TEP1

GO:0006281

BP

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.

EYA2, CHEK1, BACH1, FANCG, RAD51C, RAD1, CDC14B, POLQ, RAD51D, RECQL4, UBR5, MBD4, EYA4, PTTG1, ACTL6A, CDK1, NPM1, ERCC1, PARP1, UNG, LIG1, MSH3, GADD45A, CDK2, POLD1, GTF2H1, NUDT1, FEN1, RFC5, MSH2, RECQL, ATRX, CSNK1D, UBE2A, CSNK1E, MRE11A, MSH6, BLM, VCP, POLE2, UBE2D3, UBE2B, BTG2, XPC, RAD51, FOXM1, SSRP1, CHAF1A, CHAF1B, TRIM28, ALKBH1, SMC1A, KIF22, PSME4, SHPRH, MORF4L2, NONO, PDS5A, EPC2, INO80D, ERCC6L2, INTS3, NFRKB, RFWD3, INO80C, RAD9B, USP45, RPS27L, EMSY, CHD1L, SLF2, EID3, APITD1, JMY, INO80E, BOD1L1, TOPBP1, RAD54L, GTF2H4, RAD50, ERCC4, NABP1, RAD51AP1, UBE2W, OTUB1, SMG1, USP28, UHRF1, CDC5L, RAD9A, NABP2, TREX2, SLF1, PAGR1, TEX15, FANCD2, INO80B, TAOK3, PIF1, UBE2T, INIP, RAD18, PDS5B, TDP1, PARPBP, NSMCE4A, BCCIP, POLK, PARP2, MUTYH, FZR1, POLI, STUB1, EXO1, SMC3, RUVBL2, POLH, RUVBL1, ASF1A, FAN1, TRRAP, SUPT16H, UCHL5

GO:0006282

BP

regulation of DNA repair

Any process that modulates the frequency, rate or extent of DNA repair.

USP1, UBE2V1, UBE2V2, POLH

GO:0006283

BP

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.

POLR2D, ERCC1, UBC, PCNA, ERCC2, LIG1, POLR2E, XPA, POLR2A, POLD1, POLR2B, GTF2H1, RPA3, RFC4, RFC2, POLR2I, RFC5, RFC3, CDK7, POLR2J, POLR2K, POLR2G, POLR2L, RBX1, RPS27A, UBA52, EP300, CUL4A, CUL4B, GTF2H2, POLD3, COPS6, GTF2H4, ERCC4, COPS8, COPS7B, POLD4, POLK, PRPF19, PPIE

GO:0006284

BP

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.

POLQ, RECQL4, TP53, UNG, LIG1, XPA, MPG, RPA3, FEN1, DNA2, HMGA2, TDG, SMUG1, HUWE1, NEIL3, PRMT6, PARP2

GO:0006285

BP

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.

NTHL1, TDG

GO:0006287

BP

base-excision repair, gap-filling

Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template.

POLD1, POLG, POLE

GO:0006289

BP

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).

RAD51D, TP53, ERCC1, ERCC2, RPA3, BRCA2, ATXN3, RAD23A, RAD23B, XPC, GTF2H2C_2, SLC30A9, NEIL3, GTF2H4, ERCC4, FAN1

GO:0006290

BP

pyrimidine dimer repair

The repair of UV-induced T-T, C-T and C-C dimers.

POLH

GO:0006293

BP

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.

ERCC1, PARP1, ERCC2, XPA, GTF2H1, RPA3, RBX1, CUL4A, CUL4B, GTF2H2, CHD1L, GTF2H4, ERCC4

GO:0006294

BP

nucleotide-excision repair, preincision complex assembly

The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.

PARP1, UBC, ERCC2, XPA, GTF2H1, RPA3, CDK7, RAD23B, RBX1, RPS27A, UBA52, XPC, CUL4A, CUL4B, GTF2H2, CHD1L, GTF2H4

GO:0006295

BP

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.

ERCC1, PARP1, ERCC2, XPA, GTF2H1, RPA3, RBX1, CUL4A, CUL4B, GTF2H2, CHD1L, GTF2H4, ERCC4

GO:0006296

BP

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.

ERCC1, PARP1, UBC, PCNA, ERCC2, XPA, POLD1, GTF2H1, RPA3, RFC4, RFC2, RFC5, RFC3, RBX1, RPS27A, UBA52, NTHL1, CUL4A, CUL4B, GTF2H2, POLD3, CHD1L, GTF2H4, ERCC4, POLD4, POLK

GO:0006297

BP

nucleotide-excision repair, DNA gap filling

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.

UBC, PCNA, LIG1, POLD1, RPA3, RFC4, RFC2, RFC5, RFC3, RPS27A, UBA52, POLE, POLD3, POLD4, POLK

GO:0006298

BP

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.

RNASEH2A, PCNA, LIG1, MSH3, POLD1, RPA3, MLH1, MSH2, MSH6, PMS1, XPC, TDG, POLD3, POLD4, MLH3, MUTYH, EXO1

GO:0006301

BP

postreplication repair

The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.

BRCA1, MSH2, UBE2A, UBE2B, UBE2V1, UBE2V2, RAD18

GO:0006302

BP

double-strand break repair

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

MEIOC, EME2, APBB1, BACH1, RAD21, SMARCA5, NBN, POLQ, RNF8, RECQL4, TDP2, ERCC1, PARP1, XRCC5, H2AFX, BRCA1, FEN1, MSH2, BRCC3, MRE11A, BRCA2, VCP, PRKDC, MTA1, XRCC4, TRIP13, ESCO2, SETX, RAD50, EME1, CDCA5, CIB1, MND1, TDP1, BAZ1B, KIAA0430

GO:0006303

BP

double-strand break repair via nonhomologous end joining

The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.

NBN, RNF8, WHSC1, POLA1, XRCC5, H2AFX, BRCA1, MLH1, BRCC3, MRE11A, HIST1H4A, PRKDC, XRCC4, MDC1, UBE2V2, RIF1, RAD50, DCLRE1C, BARD1, PRPF19, KDM2A, XRCC6BP1

GO:0006306

BP

DNA methylation

The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.

FOS, DNMT1, ATRX, GNAS, EZH2, GNAS, ATF7IP, GATAD2A, KMT2E, EHMT2, DNMT3B

GO:0006307

BP

DNA dealkylation involved in DNA repair

The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).

MPG, ALKBH1, ASCC3, FTO, ASCC2

GO:0006308

BP

DNA catabolic process

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.

AIFM1, TATDN1

GO:0006309

BP

apoptotic DNA fragmentation

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.

DFFA, HMGB1, HMGB2, KPNA1, FOXL2, KPNB1, DICER1

GO:0006310

BP

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.

BACH1, HMGB3, RAD51C, RAD21, RECQL4, ACTL6A, ERCC1, HMGB1, XRCC5, RAG1, ATRX, MRE11A, BLM, RAD51, XRCC4, NONO, TSN, INO80D, NFRKB, INO80C, SETX, SUPV3L1, EID3, INO80E, RAD54L, RAD50, PAGR1, INO80B, PIF1, NSMCE4A, PSMC3IP, EXO1, RUVBL2, RUVBL1, UCHL5

GO:0006311

BP

meiotic gene conversion

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.

MSH2

GO:0006312

BP

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.

RAD51C, RAD51D, FSBP, ERCC1, TOP2A, RAD51, APITD1, RAD54B

GO:0006323

BP

DNA packaging

Any process in which DNA and associated proteins are formed into a compact, orderly structure.

KAT6A, ASH1L

GO:0006325

BP

chromatin organization

Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.

HDAC3, SOX15, HMGB2, HMGA2, SATB1, HDAC1, TAF5, EZH2, SETD7, ZNF462, HDAC8, NUCKS1, SMARCAD1, TCF7L1, HMG20A, LRWD1, PADI4, HDAC5, L3MBTL1, LAS1L

GO:0006333

BP

chromatin assembly or disassembly

The formation or destruction of chromatin structures.

HIRIP3, HDAC8, SUV39H2, BAZ1B

GO:0006334

BP

nucleosome assembly

The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

SMARCA5, HIST1H2BK, H2AFY, NPM1, HIST1H1E, H2AFX, HIST1H1C, BRD2, HMGB2, HIST1H2BB, ATRX, SOX9, CENPA, MCM2, NAP1L1, HIST1H2BD, HIST1H4A, HIST1H2BC, HIST1H3D, H3F3A, SET, HIST1H1A, SHPRH, SART3, HIST2H2BE, SPTY2D1, TSPYL5, KAT6B, H1FX, ANP32B, KAT6A, HIST1H2BH, NAP1L5, RSF1, NAP1L3, NAP1L4, ANP32E, TSPYL2, SMYD3, NAA60, H2AFY2, TSPYL4, NAP1L2, PADI4, ASF1A

GO:0006335

BP

DNA replication-dependent nucleosome assembly

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

NASP, HIST1H4A, HIST1H3D, RBBP4, CHAF1A, CHAF1B, IPO4, ASF1B, ASF1A

GO:0006336

BP

DNA replication-independent nucleosome assembly

The formation of nucleosomes outside the context of DNA replication.

ATRX, NASP, HIRA, HIST1H4A, H3F3A, RBBP4, IPO4, ASF1B, ASF1A, CABIN1

GO:0006337

BP

nucleosome disassembly

The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

ARID1A, HMGA1, SMARCA4, SET, SMARCD3, HIST3H2A, SMARCC2, SMARCC1, SMARCD1, SUPT16H

GO:0006338

BP

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.

SUPT5H, ARID1A, CHD1, SMARCA5, TADA2A, ACTL6A, MYC, ESR1, RB1, TOP1, SMARCA1, DEK, ATRX, SOX9, SMARCA2, SMARCA4, HDAC4, SATB1, RBBP4, CBX3, HDAC1, MORF4L2, INO80C, SMARCD3, SUPT6H, TADA2B, PBRM1, CHD1L, SMARCC2, HDAC2, KAT2B, SMARCC1, SMARCD1, RSF1, FOXP3, INO80B, ACTR6, SMARCAD1, SUV39H2, CHRAC1, BAZ1A, CHD7, RERE, MORF4L1, NUDT5, PADI4, HDAC5, RUVBL2, RUVBL1

GO:0006342

BP

chromatin silencing

Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.

H2AFY, H2AFZ, HIST1H2AG, H2AFX, HIST1H2AD, MORF4L2, HIST2H2AA3, H2AFV, HIST3H2A, SIRT2, HIST1H2AC, H2AFJ, H2AFY2, MORF4L1, HDAC5

GO:0006344

BP

maintenance of chromatin silencing

The maintenance of chromatin in a transcriptionally silent state such as heterochromatin.

ARID1A, UBE2B, HDAC2

GO:0006346

BP

methylation-dependent chromatin silencing

Repression of transcription by methylation of DNA, leading to the formation of heterochromatin.

MBD3, HDAC1, HELLS

GO:0006348

BP

chromatin silencing at telomere

Repression of transcription of telomeric DNA by altering the structure of chromatin.

SIRT2

GO:0006349

BP

regulation of gene expression by genetic imprinting

Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.

DIRAS3, IGF2, BRCA1, GSK3B, ARID4B, CTCFL

GO:0006351

BP

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

E2F8, MED19, ZNF320, CNOT1, ZNF233, ZNF785, VGLL3, AHRR, ZNF879, NACA, EYA2, APBB1, HIP1, ARNTL, WASL, FOXN3, SAP18, ZNF593, DDX3X, ARID1A, BHLHE40, CHD1, CHD2, ITGB1BP1, ZNF213, IRF6, RGS12, TFEC, HNRNPDL, ZNF646, ZBTB5, SMAD7, SMAD9, MAPK13, HMGB3, HDAC3, BIRC5, TOX3, FOXP2, PER1, ZSCAN9, ZBTB24, DAPK3, ZNF264, PAX4, MAP3K7, HOXA2, HOXA3, TBX1, CBFA2T2, SMAD6, SNAI2, PARK2, ZNF862, ZEB2, KDM1A, NUPR1, HBP1, CREBL2, LPXN, CTNND1, PQBP1, EDF1, BRD4, TBL1X, ZNF623, CNOT3, SIN3B, ZNF253, ZNF217, ERN1, PSIP1, KHDRBS3, TADA3, MYCBP2, TCEA3, ZNF189, KLF7, SEC14L2, URI1, SUPT7L, ABLIM3, KDM4B, TRIM37, HEXIM1, FSBP, ZNF205, ZBTB7A, YEATS4, EYA4, IL33, CBX7, MBD3, ACTL6A, WHSC1, ESR1, NR3C1, MYCN, ERBB2, PRKCB, RB1, PTMA, ENO1, ZFY, COL4A2, HOXC4, ZNF688, TRAPPC2, AR, TXN, FGFR1, SKI, XRCC5, ETS2, FOSL2, ZNF44, ZNF250, TCF3, GCFC2, ZNF823, ZFX, ZNF12, ZNF14, ZNF17, ZNF19, ZNF20, ZNF182, ZNF22, ZNF23, ZNF24, ZKSCAN1, ZNF25, ZNF43, TAL1, ATF7, ATF6, TFEB, BCL3, MAK, NME2, SFPQ, SP100, NR2F2, NFYB, BRD2, YY1, DNMT1, HMGB2, ARNT, HOXD10, SMARCA1, MAPK1, RBL1, EEF1D, HOXA6, FOXN2, CTNNB1, SOX6, ZNF93, NUP62, ZEB1, BRCA1, ANP32A, PBX2, ID1, BCL6, MNDA, STAT5A, LRPPRC, NR4A2, NKX2-1, ATRX, ID4, RFX2, RFX5, NRIP1, HOXA1, HINT1, FHIT, LHX2, MXI1, ERF, ASCL1, ZNF83, ZNF84, SMARCA2, SMARCA4, AFF3, HDGF, MAP2K6, STAT2, ZNF133, ZNF140, ZNF138, HIRA, ATXN3, ATXN1, ATN1, PRKAA2, MLLT10, FOXG1, HDAC4, CTBP2, PRDM15, SOX8, KLF3, ZNF445, DYNLL1, EEF1A1, IRX3, BTG2, SIM1, SMAD3, FOXK1, ZBED6, ZXDB, ZNF200, PURA, E2F1, INSM1, RELB, DR1, SATB1, EWSR1, BNC1, MEF2A, ID2, SP3, ID3, HHEX, POU3F1, CREM, ZNF85, ZNF117, ZNF92, TLE1, TLE3, MXD1, EGR4, ZNF91, ZBTB16, RING1, PAX8, ZNF33A, EGR3, C1QBP, KHDRBS1, FOXM1, AES, ZNF844, ZNF616, RBBP4, ZNF763, ELP6, ZNF816, MN1, SREBF2, FOXO1, PNRC1, TFCP2, TCF15, ILF2, ILF3, PRDM2, ZBTB17, CHAF1B, KLF10, CBX3, MTA1, ITGB3BP, ZNF211, IKZF1, MAMLD1, MED21, HDAC1, TDG, PWP1, NACA, NCOA4, KLF9, C1D, CUX1, HNRNPD, TFDP1, SIM2, NPAT, HES1, RBM39, MXD4, ZNF268, ZNF273, KANK1, LPIN1, ZNF846, CHD4, POU6F1, ARID5B, DRAP1, ZNF638, MORF4L2, SUZ12, BRD3, TCEAL1, NONO, RNPS1, RBBP5, ERBB4, ZMYND11, NCOA2, JMJD1C, TRIP6, TWIST1, NCOA1, CCDC85B, ADIRF, EZH2, ZNF77, ZNF124, PKN1, PKN2, CRY1, MAPK14, IFI16, ZSCAN26, ZNF423, ZNF630, LRRFIP1, PCGF3, ZNF791, CHD9, ZSCAN23, GON4L, ZNF568, ZNF404, ZFP69, KMT5B, ARID4B, LIN52, EPC2, TAF1B, INO80D, ZNF326, ZNF789, BCORL1, ZNF766, ZNF667, ZNF506, HABP4, SAMD4B, BRMS1L, DNTTIP2, ZBTB41, LRIF1, ZNF684, ZNF648, PHF19, ZNF618, DEPDC1, ZNF658, ATF7IP2, IRAK1BP1, KANK2, SPTY2D1, ZNF776, ZNF57, ZNF518A, ZNF787, JADE1, ADNP2, ZNF280D, JMJD6, GTF2H2C_2, ZNF529, ZNF585A, ZNF449, INO80C, ATAD2, SLC30A9, SMARCD3, CRTC3, ZNF562, ATF7IP, KDM7A, SPOCD1, BNC2, ZNF600, ZNF621, TSHZ1, KCTD1, CENPU, ZNF534, ASXL2, SUPT6H, BZW1, ZNF765, ZNF771, BEND5, ZNF627, CXXC5, ZNF367, ZNF550, MIER3, DENND4A, COMMD6, EMSY, ARHGAP22, IRF2BP2, ZNF467, ZSCAN2, PCGF5, ZBTB33, TADA2B, PBRM1, CASZ1, JAZF1, ZSCAN30, SPATA24, GPBP1, CARM1, COMMD2, ZNF677, KMT5C, ZNF573, ZNF280B, GATAD2A, MINA, CREBRF, AEBP1, FOXP4, MGA, WWC1, CCAR1, TP53INP2, SIRT2, YAF2, ZNF440, TRIM22, HACE1, ZNF101, KMT2E, ZNF654, EID3, ZFP82, CCAR2, ZNF567, ASCC3, PHTF2, ZNF808, ZNF276, ZCCHC9, NKAP, COMMD1, EID2, ZNF655, ZNF283, ZNF513, ZNF615, ZNF709, ZNF557, ZNF565, BANP, ZNF610, ZNF579, ZBTB38, ZNF511, INO80E, ZNF485, ZBTB34, RCBTB1, ZNF248, ZNF548, ZNF555, KMT2C, ZMIZ2, ZNF397, ARID1B, BHLHE22, ZFP28, NCOA7, GABPB2, SMARCC2, ZNF420, OSR1, ZSCAN18, ZNF502, ZNF564, ZNF596, ZNF507, ZNF675, DDX54, RB1CC1, ZNF721, ZNF526, ZNF384, SETD7, GTF3C2, PHF10, PPP1R13L, CHURC1, HDAC7, ZFPM2, ZNF606, PSPC1, BBX, ARNTL2, KAT6B, JDP2, HDAC2, DPF3, PROX1, KAT6A, EZH1, DDX17, SMARCC1, KHSRP, RBPMS, TCEAL3, L3MBTL2, ZNF566, UTP4, TP53INP1, TADA1, ZNF669, ZNF689, ZBTB10, TCEAL4, FAM120B, SGF29, ZNF503, ZNF274, CDCA7L, ZNF486, ZNF764, ZNF419, HES6, ZNF625, AJUBA, ZNF845, PAWR, HIC2, EAF1, ZNF333, ZNF462, L3MBTL3, LCOR, ZBTB45, ZNF521, SCYL1, ZNF512B, PRMT6, ZSCAN31, ZNF75A, ZNF578, ZNF641, ZNF285, ZFP3, TOX2, ZNF317, PPP1R10, PURB, PHF12, ZNF300, CIC, CITED4, TRIB3, CCNL2, ZNF347, ZNF607, ZNF587, ATOH8, ZNF382, SPEN, UHRF1, MYCBP, CDC5L, MPHOSPH8, KLF6, PHB2, SMAD5, LITAF, NPAS2, CITED1, CITED2, HOPX, TCF25, MYBBP1A, ZNF559, ZNF2, WAC, DIDO1, PAGR1, ZNF692, HNRNPUL1, ZNF426, PHF20, CDCA7, SSBP3, NAA15, HDAC8, NFKBIZ, HELZ2, WHSC1L1, TBL1XR1, FOXP3, INO80B, ZNF518B, ZNF436, ZNF407, POLR2J2, SLIRP, PEG3, ZNF350, COMMD4, ZNF700, DNTTIP1, BCL11A, ASCC2, EPC1, TSPYL2, IKZF4, DHX36, HIPK2, PNN, FOXP1, TXNIP, ZNF335, SUV39H2, IKZF5, ZNF552, SUDS3, ZNF430, NOL11, ZNF395, MED20, MEAF6, SAP30L, SP110, RRAGC, ZNF287, GPBP1L1, ZBTB20, HES4, ZNF532, ZNF160, CHD8, TCF7L1, ZNF334, SRA1, HMG20A, MYNN, BRD7, PNRC2, TCF7L2, KMT5A, PRDM10, PRDM6, ZNF331, ZNF71, ZNF302, SLC2A4RG, TSHZ2, BAZ1A, ZNF277, HELLS, BRWD1, ZFP64, TXLNG, ASF1B, MTPAP, THAP1, RLIM, ZNF358, MED9, ARGLU1, SLTM, ING3, ZNF586, BCLAF1, ZNF226, RBAK, PRR13, ZNF224, LMCD1, CCDC59, ZKSCAN7, HMG20B, ZBTB4, ZNF492, CHD7, RCOR3, MYEF2, RERE, NLK, UXT, ASH2L, HDAC6, RNF14, MORF4L1, ZMYM2, KDM5B, LIMD1, TCF20, MLX, SAP30BP, PUF60, ZNF230, BAZ1B, CNOT7, ZMYM5, ZFP69B, ZNF112, ZNF222, ZNF580, CCNL1, GTF3C4, HDAC9, AGO2, ZHX1, ZNF236, MYT1L, MKL2, ZBTB21, ZMIZ1, CNOT6, PADI4, KMT2B, PHTF1, SCML1, TIMELESS, TRIM33, USP22, FOXJ3, PA2G4, HDAC5, SCML2, RUVBL2, CDYL, TCF19, LZTS1, RUVBL1, ASF1A, DRG1, MYRF, KDM2A, ZNF337, TSC22D4, NOC2L, L3MBTL1, ZNF175, TRRAP, ZNF451, LOXL2, HES2, PAXBP1, HEY1, UCHL5, KLF2, NCOR2, EID1, COMMD10, CHCHD2, NCOA3

GO:0006352

BP

DNA-templated transcription, initiation

Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.

SMARCA5, TCF4, HIST1H4A, TAF10, TAF5, TAF12, NAT14, RSF1

GO:0006353

BP

DNA-templated transcription, termination

The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.

POLR2A, SETX, MTERF1, TTF2

GO:0006354

BP

DNA-templated transcription, elongation

The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.

SUPT5H

GO:0006355

BP

regulation of transcription, DNA-templated

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

ZNF320, SBNO1, ZNF233, USP27X, ZNF785, VGLL3, PHF20L1, ZNF879, NACA, PDLIM1, EYA2, APBB1, HIP1, ARNTL, WASL, ELL2, NR5A2, BHLHE40, ZNF213, BACH1, TFEC, HNRNPDL, ZNF646, ZBTB5, MAPK13, HMGB3, ZSCAN9, ZBTB24, DAPK3, ZNF264, HOXA3, ZNF207, SOX15, ZNF862, HBP1, FADS1, PDE8A, PRMT3, LPXN, CTNND1, PQBP1, GAS7, EDF1, MITF, FZD7, ZNF623, TSC22D2, CNOT3, ZNF253, ZNF217, TULP3, ERN1, PSIP1, SUPT3H, SRSF10, KHDRBS3, RPS6KA5, MYCBP2, CAPN15, SUPT7L, KDM4B, FSBP, ZFPL1, ZNF205, ZRANB2, EYA4, APBB3, PTTG1, INS, IGF2, ESR1, NR3C1, TP53, INSR, ZFY, HOXC4, ZNF688, TRAPPC2, ESRRA, BMP2, HCLS1, VAV1, ZNF44, ZNF250, TCF3, GCFC2, ZNF823, ZFX, ZNF14, ZNF17, ZNF19, ZNF20, ZNF182, ZNF22, ZNF23, ZKSCAN1, ZNF25, ZNF43, HMGA1, ATF7, CEBPB, ATF4, TFEB, WT1, BTF3, MAK, CDK11B, NME2, POLR2A, NFYB, CALR, MZF1, EEF1D, PPP2R1A, HOXA6, HIVEP2, PHB, RORA, DDIT3, SOX6, AHR, ACVR1B, TGFBR1, ANP32A, STAT3, MNDA, TMPO, TMPO, LRPPRC, GATA4, ATRX, NOTCH1, ZFP36L2, HOXA1, HINT1, FHIT, MXI1, ZNF83, ZNF84, SMARCA2, AFF3, MAP2K6, GTF2A1, ZNF133, ZNF140, ZNF138, HMGA2, RCAN1, ATXN3, PRKAA2, MAZ, PRDM15, KLF3, NUP107, ZNF445, BTG1, DYNLL1, YBX1, EEF1A1, IRX3, SSBP2, TMF1, SARNP, ZXDB, FOXO4, ZNF200, GTF2B, IRF9, E2F1, EWSR1, POU5F1, BNC1, SP3, CREM, ZNF85, ZNF117, ZNF92, NOTCH2, TLE3, EMX2, PRKCQ, EGR4, MEF2C, ZNF33A, EGR3, SOX4, ZFP36L1, SSRP1, ZNF844, ZNF616, RBBP4, EP300, ZNF816, MN1, PNRC1, EFEMP1, FOXC1, TAF10, PRDM2, CHAF1B, MTA1, ITGB3BP, ZNF211, UBE2V1, NFATC2, ACVR2B, RUNX3, NACA, GTF2H2, NFYC, HNRNPD, E2F2, RBM39, ZNF268, ZNF273, KANK1, ZNF846, POU6F1, ZNF638, NR1D2, NONO, RBBP5, TAF5, TAF11, TEAD2, TAF1C, TAF1A, NCOA2, ZNHIT3, JMJD1C, TRIP6, TSC22D1, EZH2, ZFHX3, ZNF141, ZNF77, ZNF124, PKN2, SNAPC1, HIF1A, ZSCAN26, ZNF630, PCGF3, ZNF791, CHD9, ZSCAN23, ZNF568, ZNF404, ZFP69, KMT5B, TAF1B, INO80D, ZNF789, BCORL1, ZNF766, KRBOX4, ZNF506, HABP4, SAMD4B, DNTTIP2, ZBTB41, LRIF1, ZNF684, ZNF648, PHF19, ZNF618, ATF7IP2, IRAK1BP1, SPTY2D1, ZNF776, ZNF57, ZNF787, RALGAPA1, ADNP2, JMJD6, PTRF, GTF2H2C_2, ZNF529, ZNF585A, NFRKB, ZNF449, ZNF880, INO80C, ZNF562, BNC2, ZNF600, ZNF621, USP34, USP51, CENPU, ZNF534, SUPT6H, BZW1, ZNF765, ZNF771, ZNF627, ZNF720, ZNF550, MIER3, DENND4A, EMSY, ARHGAP22, IRF2BP2, ZNF467, ZSCAN2, PBRM1, CASZ1, ZSCAN30, SPATA24, GPBP1, CARM1, COMMD2, ZNF677, KMT5C, ZNF573, PPARGC1B, ERC1, CREBRF, MGA, CCAR1, ZNF440, TRIM22, HACE1, ZNF101, ZNF654, EID3, ZFP82, ASCC3, PHTF2, ZNF808, ZNF276, ZNF655, ZNF283, ZNF513, ZNF615, ZNF709, ZNF557, ZNF565, ZNF610, ZNF579, ZNF511, INO80E, ZNF485, ZBTB34, RCBTB1, ZNF248, ZNF548, ZNF555, KMT2C, ZNF397, NUP35, ZFP28, ZNF420, ZNF502, ZNF596, ZNF507, DDX54, RB1CC1, ZNF721, ZNF526, ZNF384, PHF10, GATAD1, RNF141, ZNF606, PSPC1, BBX, ARNTL2, KAT6B, AHCTF1, GTF3A, ESR2, DPF3, CREBBP, APBB2, KHSRP, SNAPC3, USP13, RBPMS, L3MBTL2, ZNF566, UTP4, FUBP1, TADA1, ZNF669, ZNF689, ZBTB10, FAM120B, SGF29, NRBF2, ZNF503, ZNF274, CDCA7L, ZNF486, ZNF764, ZNF419, CDKN2AIPNL, HES6, ZNF625, AJUBA, GMCL1, ZNF845, EAF1, ZNF333, L3MBTL3, LCOR, ZBTB45, ZNF521, SCYL1, ZNF512B, ZSCAN31, ZNF75A, ZNF578, ZNF285, ZFP3, TOX2, ZNF317, TEFM, ZNF300, ZNF347, ZNF607, ZNF587, MYCBP, PFDN5, MTERF1, TSC22D3, PITX2, PRMT1, MYBBP1A, ZNF559, ZNF2, ZNF692, HNRNPUL1, ZNF426, PHF20, CDCA7, SALL3, WHSC1L1, FOXP3, INO80B, ZNF436, ZNF407, SLIRP, ZNF350, COMMD4, RNF38, ZNF700, DNTTIP1, ASCC2, TSPYL2, PNN, ZNF335, TAF1D, IKZF5, SOX17, TLE6, ZNF430, ZNF395, LIN28A, MEAF6, SAP30L, SP110, PATZ1, GPBP1L1, HES4, ZNF532, ZNF160, TCF7L1, ZNF334, SRA1, HMG20A, MYNN, PNRC2, PRDM10, ZNF331, ZNF71, ZNF302, SLC2A4RG, TULP4, BAZ1A, ZNF277, GLRX2, ZFP64, TXLNG, ASF1B, THAP1, RLIM, ZNF358, ARGLU1, ING3, ZNF586, CDKN2AIP, ZNF226, RBAK, PRR13, CCDC59, ZKSCAN7, HMG20B, ZNF492, CHD7, ZNFX1, NLK, PPARGC1A, ASH2L, RNF14, LIMD1, TCF20, MLX, AFF4, SAP30BP, PUF60, ZNF230, BAZ1B, ZFP69B, ZNF112, ZNF222, ZNF580, NOCT, ZNF236, TCFL5, MYT1L, ZBTB21, CNOT6, PADI4, PHTF1, SUFU, SCML1, GTF2A1L, PPIE, TTF2, SAMD4A, CDK11A, MAPK8IP1, SCML2, CDYL, LZTS1, RNF6, KDM2A, CARHSP1, ZNF337, ZNF175, TRRAP, CSDC2, UCHL5, LRRFIP2, COMMD10

GO:0006356

BP

regulation of transcription from RNA polymerase I promoter

Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter.

UBTF, POLR2K, POLR2L, TFAM

GO:0006357

BP

regulation of transcription from RNA polymerase II promoter

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

SAP18, ARID1A, CHD1, CHD2, SOX12, MAFG, TBX1, MED7, FOXO3, RAD21, MED14, SOX15, SMARCA5, TRAK2, KDM1A, NUPR1, MAF, TADA2A, SUPT3H, TADA3, MED6, CREG1, TCEA3, KLF7, CIAO1, URI1, IKBKAP, ZMYM6, ZBED1, ACTL6A, FOS, SOD2, MYCN, PRKCB, INHBA, HMGB1, ANXA4, PRKAR1A, THRA, FOSL1, FOSL2, JUNB, JUND, TAL1, ATF6, PAM, WT1, HNF1A, ATP2B4, NR2F2, PTAFR, BRD2, YY1, UCP1, HMGB2, DEK, AHR, SREBF1, ZEB1, BRCA1, STAT3, BUD31, STAT5A, ID4, RFX2, RFX5, IFNAR2, SMARCA2, SMARCA4, STAT5B, STAT2, CEBPG, SUB1, HIRA, FOXG1, GTF2I, ELF3, SIM1, SMAD3, FOXK1, ZBED6, PURA, PPARD, GLO1, ZNF763, ELP6, TFCP2, TCF15, MAMLD1, MED21, CAMK2D, RUNX3, KLF9, CUX1, RUNX2, CBFB, NFYC, VEZF1, TFDP1, SIM2, ZMYM3, NFE2L1, CHD4, MTF1, BRD3, TCEB1, TEAD4, NEDD8, PKN1, MAPK14, QRICH1, LRRFIP1, ZBED5, ARID4B, EPC2, ZNF667, ZNF518A, BRWD3, SMARCD3, TSHZ1, EPM2AIP1, ZNF367, TADA2B, FOXP4, BBS7, ZBED8, LCORL, KIAA1958, JMY, BHLHE22, SMARCC2, ZSCAN18, ARNTL2, SMARCC1, TCEAL3, ELP4, TCEAL4, ZBED6CL, ZNF274, SMARCD1, MED30, ZNF641, CITED4, MED15, TCF12, CDC5L, TEAD3, PITX2, LITAF, CITED1, HOPX, HTATIP2, NFKBIZ, ZNF518B, CTDSP1, NUCKS1, BLZF1, FOXP1, ZNF395, MED20, ELP3, TCF7L1, ENY2, BRD7, MED4, TCF7L2, TSHZ2, BRWD1, MED17, MED9, SLTM, RNF14, ZMYM2, ZMYM5, ELF5, MAFF, TRAK1, FOXJ3, TCF19, RUVBL1, MED16, NFE2L3, MAFB, HCFC2

GO:0006359

BP

regulation of transcription from RNA polymerase III promoter

Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter.

POLR3G, BRCA1, ZNF345, POLR3GL, POLR3C, POLR3F

GO:0006360

BP

transcription from RNA polymerase I promoter

The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.

POLR1C, UBTF, GTF2H1, TAF1C, TAF1A

GO:0006361

BP

transcription initiation from RNA polymerase I promoter

Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.

POLR1C, CD3EAP, POLR1A, UBTF, ERCC2, POLR2E, MAPK3, GTF2H1, CDK7, POLR2K, POLR2L, GTF2H2, TAF1C, TAF1A, TAF1B, PTRF, GTF2H4, POLR1E, TAF1D, RRN3, ZNRD1, POLR1D

GO:0006362

BP

transcription elongation from RNA polymerase I promoter

The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.

POLR1C, CD3EAP, POLR1A, UBTF, ERCC2, POLR2E, GTF2H1, CDK7, POLR2K, POLR2L, GTF2H2, TAF1C, TAF1A, TAF1B, GTF2H4, POLR1E, TAF1D, ZNRD1, POLR1D

GO:0006363

BP

termination of RNA polymerase I transcription

The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.

POLR1C, CD3EAP, POLR1A, UBTF, ERCC2, POLR2E, GTF2H1, CDK7, POLR2K, POLR2L, GTF2H2, TAF1C, TAF1A, TAF1B, PTRF, GTF2H4, POLR1E, TAF1D, ZNRD1, POLR1D

GO:0006364

BP

rRNA processing

Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

NOP56, RIOK3, DKC1, NPM3, UTP20, RPP40, POP4, RPLP1, RPLP2, RPLP0, RPS17, RPSA, RPS2, RPL35A, RPL7, RPL17, RPS4Y1, RPL13, RPL10, RPL12, RPL22, RPL4, RPL13A, SKIV2L2, RPS27, RPL35, RPL27A, RPL5, RPL21, RPL28, RPS9, RPS5, RPS10, RPL29, CSNK1D, RPL34, CSNK1E, RPL14, SNU13, GEMIN4, YBEY, RPS20, RPS3A, RPL26, RPL15, RPL27, RPL37A, RPL37, RPS7, RPS8, RPS15A, RPS16, RPS14, RPS18, RPS13, RPS11, RPL7A, RPL23A, RPS6, RPS25, RPS26, RPL30, RPL31, RPL10A, RPL32, RPL11, RPL41, RPS27A, UBA52, RPL38, RPS21, RPP30, RPL24, RPL36A, RPL19, RPL18A, RNASEL, EXOSC9, RPL18, TBL3, EXOSC2, C1D, BOP1, RRP1B, EXOSC7, TSR1, EXOSC6, RPS27L, NOL8, DHX37, PAPD5, WDR36, UTP15, EMG1, UTP4, ISG20, EXOSC8, DDX27, NAF1, EBNA1BP2, RPP25, WDR12, DDX47, SENP3, NOL11, EXOSC4, EXOSC3, MDN1, DCAF13, CHD7, MRTO4, NOB1, WDR3, PA2G4, DIS3, RCL1, DDX52, FCF1, RRP7A, SBDS, RPL36, LAS1L, UTP18, DDX49

GO:0006366

BP

transcription from RNA polymerase II promoter

The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).

SUPT5H, WWP2, MEIS1, NFIB, BACH1, PLSCR1, SOX12, POLR2D, MAFG, TGFB1I1, KLF4, FOXO3, TCF21, RAD21, CCNT1, CCNT2, MITF, NCOR1, MAF, TADA2A, SUPT3H, NFAT5, NFATC1, PTTG1, FOS, MYC, ESR1, NR3C1, TP53, JUN, NFIC, HOXB5, PARP1, GLI2, GLI3, MYBL1, MYBL2, THRA, IRF1, EGR2, GTF2F2, FOSL1, HIVEP1, CREB1, HMGA1, JUNB, JUND, CEBPB, XBP1, ERCC2, EGR1, ATF1, ATF3, ATF4, POLR2E, ELK1, WT1, NFKB1, BTF3, HNF1A, POLR2A, MZF1, KDM5A, POLR2B, HOXA10, HIVEP2, OTX2, GTF2H1, GTF2F1, DEK, AHR, POLR2I, RBMX, PBX1, STAT3, ETV5, ELK3, GATA4, SOX9, CEBPD, MEOX1, ETV1, CDK7, STAT5B, POLR2J, GTF2A1, GTF2A2, ZNF136, HMGA2, FOSB, CEBPG, POLR2K, SUB1, DLX5, FOXL2, LMO4, POLR2G, POLR2L, YBX1, GTF2I, ELF3, TMF1, FOXO4, TFAM, GTF2B, IRF9, RUNX1, POU5F1, MEF2A, CREB5, CEBPZ, RELA, REL, MEF2C, GABPA, PAX8, SOX4, DLX2, SSRP1, NCBP1, EP300, FOXC1, TAF10, TARDBP, NMI, NFATC2, SMAD4, RUNX3, BMPR2, GTF2H2, RUNX2, CBFB, NFYC, VEZF1, NFE2L1, ZNF345, MEF2D, MTF1, NFATC4, TCEB1, TCEB2, TAF5, TAF11, TAF1C, TAF1A, TRIP11, TRIP13, TSC22D1, SMAD2, SMAD1, USF2, ZFHX3, ZIC1, ZNF141, TAF12, HLF, NFIL3, HIF1A, HIVEP3, PLAG1, NFRKB, NFXL1, AKNA, LCORL, GLIS3, CTCFL, CSRNP3, GTF2H4, GATA6, SNAPC3, FUBP1, CREB3L1, CSRNP1, TCF12, MNT, MEIS3, PITX2, EPAS1, ARID3A, SALL3, BACH2, POLR2J2, CSRNP2, NUCKS1, MED20, EBF2, PATZ1, TAF9B, MED4, HEYL, ASH1L, EHF, GRHL1, PHRF1, ASH2L, AFF4, TRPS1, ZNF639, KLF15, NOCT, ELF5, TCFL5, MAFF, PLAGL1, GTF2A1L, ZNF148, HIF3A, MED16, KLF13, NFE2L3, SUPT16H, MAFB, CAMTA1

GO:0006367

BP

transcription initiation from RNA polymerase II promoter

Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.

NR5A2, POLR2D, MED7, MED14, MED6, ESR1, NR3C1, PGR, AR, NR2F1, THRA, VDR, ESRRA, GTF2F2, TCF4, ERCC2, POLR2E, NR1D1, NR4A1, POLR2A, RXRB, CTGF, POLR2B, GTF2H1, GTF2F1, RORA, POLR2I, PPARG, NR4A2, NOTCH1, YAP1, CDK8, CDK7, NR0B1, POLR2J, GTF2A1, GTF2A2, POLR2K, NR1H2, MAZ, POLR2G, POLR2L, GTF2I, GTF2B, PPARD, NOTCH2, PPARA, TAF10, NR1H3, TRIM28, GTF2H2, E2F2, NR1D2, NR0B2, TAF5, TAF11, TEAD4, TEAD2, TAF12, MAML2, NR4A3, ESR2, GTF2H4, CREBBP, KAT2B, MED12, NRBF2, MED30, MAML3, NR1H4, MED15, TEAD3, MED20, TAF9B, MED4, MED17, PPARGC1A, GTF2A1L, THRAP3, MED16

GO:0006368

BP

transcription elongation from RNA polymerase II promoter

The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.

SUPT5H, ELL2, POLR2D, CCNT1, CCNT2, IKBKAP, GTF2F2, ERCC2, POLR2E, POLR2A, POLR2B, GTF2H1, GTF2F1, POLR2I, CDK7, POLR2J, GTF2A1, GTF2A2, POLR2K, ELOF1, POLR2G, POLR2L, GTF2B, SSRP1, NCBP1, TAF10, GTF2H2, TCEB1, TCEB2, TAF5, TAF11, ADRM1, TAF12, THOC7, RTF1, GTF2H4, ELP4, ELP3, TAF9B, ENY2, SUPT16H

GO:0006369

BP

termination of RNA polymerase II transcription

The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.

DDX39A, NUDT21, ZC3H11A, SNRPB, PAPOLA, MAZ, SNRPF, SNRPD3, SARNP, SRSF2, SRSF11, SRSF1, NCBP1, CPSF1, CSTF3, SRSF9, SRSF5, SRSF6, SLBP, RNPS1, THOC7, FIP1L1, SETX, PABPN1, ALYREF, SRRM1, THOC2, THOC3, POLDIP3, SSU72, CPSF2, TTF2, RBM8A

GO:0006370

BP

7-methylguanosine mRNA capping

Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.

SUPT5H, POLR2D, GTF2F2, ERCC2, POLR2E, POLR2A, POLR2B, GTF2H1, GTF2F1, POLR2I, CDK7, POLR2J, POLR2K, POLR2G, POLR2L, NCBP1, GTF2H2, NCBP3, CMTR2, GTF2H4

GO:0006376

BP

mRNA splice site selection

Selection of a splice site by components of the assembling spliceosome.

NOL3, SRSF10, LUC7L3, SRSF1, SRSF9, SRSF5, SRSF6, SETX, YTHDC1, LUC7L, PTBP2, LUC7L2

GO:0006378

BP

mRNA polyadenylation

The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.

NUDT21, AHCYL1, APP, PAPOLA, CPSF1, GRSF1, CSTF3, PABPC1L, ZC3H3, SYMPK, PAPOLG, SSU72, MTPAP, CPSF2

GO:0006379

BP

mRNA cleavage

Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.

ERN1, POP4, RNASE4, CPSF1, CSTF3, CPSF2

GO:0006382

BP

adenosine to inosine editing

The conversion of an adenosine residue to inosine in an RNA molecule by deamination.

ADARB1, NUDT16

GO:0006383

BP

transcription from RNA polymerase III promoter

The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.

POLR1C, CRCP, TROVE2, POLR2E, POLR2K, POLR2L, ZNF345, GTF3C2, GTF3A, SNAPC3, POLR3C, POLR3F, POLR3B, GTF3C4, POLR1D, POLR3K, IVNS1ABP

GO:0006384

BP

transcription initiation from RNA polymerase III promoter

Any process involved in the assembly of the RNA polymerase III preinitiation complex (PIC) at an RNA polymerase III promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.

POLR3G, CRCP, POLR3GL, GTF3C4

GO:0006386

BP

termination of RNA polymerase III transcription

The process in which transcription by RNA polymerase III is terminated; Pol III has an intrinsic ability to terminate transcription upon incorporation of 4 to 6 contiguous U residues.

POLR3K

GO:0006388

BP

tRNA splicing, via endonucleolytic cleavage and ligation

Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.

CPSF1, FAM98B, TRPT1, ZBTB8OS, TSEN15, RTCB

GO:0006390

BP

transcription from mitochondrial promoter

The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase.

MRPL12, TFAM, PPARGC1B, TEFM, PEO1

GO:0006391

BP

transcription initiation from mitochondrial promoter

A transcription initiation process that takes place at a promoter on the mitochondrial chromosome, and results in RNA synthesis by a mitochondrial RNA polymerase.

TFAM

GO:0006393

BP

termination of mitochondrial transcription

The process in which the synthesis of an RNA molecule using a mitochondrial DNA template is completed.

MTERF1

GO:0006396

BP

RNA processing

Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.

RTCA, U2SURP, ZFC3H1, SYNCRIP, DKC1, DUSP11, CELF2, HNRNPL, RBMS1, HNRNPH3, HNRNPH1, NOVA1, RBM5, ATXN1, RBM6, RBM3, HNRNPU, HNRNPD, RBM39, RBMS2, LARP7, DHX30, SETX, DHX29, PABPN1, TMTC1, CHERP, DHX40, DHX37, AGGF1, TDRD9, DDX54, DDX17, RBPMS, SNRNP40, BICD1, LARP6, HNRNPUL1, RBM4, DHX36, DHX35, YTHDC2, DDX20, NUFIP1, LSM7, CCNL1

GO:0006397

BP

mRNA processing

Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

SAP18, DHX15, RBFOX2, HNRNPR, PRPF3, NUDT21, ZPR1, KHDRBS3, ZRANB2, CELF2, PTBP3, HNRNPA1, PRKACA, LGALS3, SON, HNRNPA2B1, SFPQ, PTBP1, RBM25, AFF2, LSM3, ADARB1, SRSF2, SRSF11, RNASEL, FMR1, C1QBP, KHDRBS1, SRSF1, SF3A3, TARDBP, SRSF9, SRSF5, RBM39, WTAP, NONO, PAN3, ZNF326, RBM26, MBNL2, ARL6IP4, JMJD6, ALKBH5, PAPD4, SUPT6H, RBBP6, SUGP2, CCAR2, AGGF1, SREK1IP1, PAPD5, TSEN15, SREK1, KHSRP, QKI, SRPK1, SCAF11, PRPF18, RBM4B, RBM4, DDX47, RBM38, MBNL1, MBNL3, RBFOX1, AURKAIP1, CDK12, PHRF1, PPARGC1A, PUF60, NOCT, TTF2, SCAF8, THRAP3, LSM5, CSDC2

GO:0006398

BP

mRNA 3'-end processing by stem-loop binding and cleavage

Any mRNA 3'-end processing that involves the binding to and cleavage of a stem-loop structure. For example, histone mRNAs contain a highly conserved stem-loop sequence at the 3' end of the mRNA with a 6 base pairs (bp) stem and a 4-nt loop. The mRNA is cleaved between these two elements, after the fourth or fifth nucleotide, which is typically an adenosine.

SLBP, CPSF2

GO:0006399

BP

tRNA metabolic process

The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.

DTD2

GO:0006400

BP

tRNA modification

The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.

SSB, NSUN2, CDKAL1, TRUB1, TRMT6

GO:0006401

BP

RNA catabolic process

The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.

RNASET2, RNASEH2A, RNASE2, SKIV2L2, HNRNPD, EXOSC7, RNASEH2B, SUPV3L1, PNPT1, ISG20

GO:0006402

BP

mRNA catabolic process

The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.

ERN1, DXO, RNH1, ZFP36, ZFP36L2, DCP2, PNPT1, KHSRP, NUDT16, AGO4, DIS3

GO:0006403

BP

RNA localization

A process in which RNA is transported to, or maintained in, a specific location.

YY1

GO:0006404

BP

RNA import into nucleus

The import of RNA from the cytoplasm to the nucleus.

TPR

GO:0006405

BP

RNA export from nucleus

The directed movement of RNA from the nucleus to the cytoplasm.

DDX39A, ZC3H11A, NUP155, EIF4E, HNRNPA1, TPR, NUP62, RANBP1, SARNP, SRSF2, SRSF11, SRSF1, NCBP1, SRSF9, SRSF5, SRSF6, RNPS1, THOC7, ALYREF, SRRM1, THOC2, THOC3, POLDIP3, NUP62CL, NXF1, NXT1, RBM8A

GO:0006406

BP

mRNA export from nucleus

The directed movement of mRNA from the nucleus to the cytoplasm.

DDX39A, NUPL2, ZC3H11A, SRSF10, NUP155, EIF4E, TPR, HNRNPA2B1, NUP62, NUP153, RANBP2, AGFG1, NUP107, SHFM1, EIF5A, RAE1, SARNP, SRSF2, HHEX, SRSF11, SRSF1, NCBP1, CPSF1, NUP160, SRSF9, SRSF5, SRSF6, SLBP, RNPS1, THOC7, ALKBH5, FIP1L1, ALYREF, SRRM1, NUP93, NUP43, NUP37, NUP35, THOC2, NUP210, NUP205, SEH1L, THOC3, SMG1, NUP88, BUD13, NDC1, NUP58, NUP85, POLDIP3, UPF2, CPSF2, NXF1, NXT1, NUP50, SMG5, RBMX2, RBM8A

GO:0006407

BP

rRNA export from nucleus

The directed movement of rRNA from the nucleus to the cytoplasm; the rRNA is usually in the form of ribonucleoproteins.

RPSA

GO:0006408

BP

snRNA export from nucleus

The directed movement of snRNA from the nucleus to the cytoplasm.

PHAX

GO:0006409

BP

tRNA export from nucleus

The directed movement of tRNA from the nucleus to the cytoplasm.

NUPL2, NUP155, TPR, NUP62, NUP153, RANBP2, NUP107, RAE1, NUP160, NUP93, NUP43, NUP37, NUP35, NUP210, NUP205, SEH1L, NUP88, NDC1, NUP58, NUP85, NUP50