Fate of "transcription regulator activity" and its remaining child terms
Proposal
merge Function term into Process term
- GO:0030528 MF transcription regulator activity
- GO:0016563 MF transcription activator activity
- GO:0042156 MF zinc-mediated transcriptional activator activity
- GO:0016564 MF transcription repressor activity
- GO:0003701 MF RNA polymerase I transcription factor activity
- GO:0003702 MF RNA polymerase II transcription factor activity
- GO:0003709 MF RNA polymerase III transcription factor activity
- GO:0003711 MF transcription elongation regulator activity
- GO:0008148 MF negative transcription elongation factor activity
- GO:0008159 MF positive transcription elongation factor activity
- GO:0016943 MF RNA polymerase I transcription elongation factor activity
- GO:0016944 MF RNA polymerase II transcription elongation factor activity
- GO:0016945 MF RNA polymerase III transcription elongation factor activity
- GO:0003715 MF transcription termination factor activity
- GO:0003716 MF RNA polymerase I transcription termination factor activity
- GO:0003717 MF RNA polymerase II transcription termination factor activity
- GO:0003718 MF RNA polymerase III transcription termination factor activity
- GO:0016986 MF transcription initiation factor activity
- GO:0030401 MF transcription antiterminator activity
??
- GO:0003706 MF ligand-regulated transcription factor activity
def includes binding
- GO:0016988 MF transcription initiation factor antagonist activity
related regulation terms
- GO:0090046 regulation of transcription regulator activity
- GO:0090047 positive regulation of transcription regulator activity
- GO:0090048 negative regulation of transcription regulator activity
Comment Period
Date mailed:
Deadline for Comments: TBD - Unless objections are received by April ??????, we will assume that you agree to this change.
Problems
in progress
Function terms with Process definitions
The problem with most of these terms is the same as that for transcription regulator activity (GO:0030528). As we said in the [http://wiki.geneontology.org/index.php/Proposals_to_overhaul_transcription_in_GO_-_2010#transcription_regulator_activity_-_GO:0030528 original proposal], the term "transcription regulator activity" is the highest level Function term for transcription and it is essentially identical to a Process term. It conveys exactly the same information as the Process term regulation of transcription and it does NOT convey any information about the molecular nature of the regulator activity. In addition, it is grouping the child terms below it based on involvement in a common Process, not based on having a common Function and it currently includes functions based on binding DNA and functions based on interacting with other proteins.
MF: transcription regulator activity - GO:0030528 Current definition: Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.
BP: regulation of transcription - GO:0045449 Current definition: Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
This problem applies to most of the MF terms that still remain under transcription regulator activity (GO:0030528). All of these terms have definitions that specify only process information; thus we feel that they need to be merged into process terms.
- GO:0030528 transcription regulator activity
- GO:0003701 RNA polymerase I transcription factor activity
- GO:0003702 RNA polymerase II transcription factor activity
- GO:0003709 RNA polymerase III transcription factor activity
- GO:0016563 transcription activator activity
- GO:0042156 zinc-mediated transcriptional activator activity
- GO:0016564 transcription repressor activity
- GO:0003711 transcription elongation regulator activity
- GO:0008148 negative transcription elongation factor activity
- GO:0008159 positive transcription elongation factor activity
- GO:0016943 RNA polymerase I transcription elongation factor activity
- GO:0016944 RNA polymerase II transcription elongation factor activity
- GO:0016945 RNA polymerase III transcription elongation factor activity
- GO:0003715 transcription termination factor activity
- GO:0003716 RNA polymerase I transcription termination factor activity
- GO:0003717 RNA polymerase II transcription termination factor activity
- GO:0003718 RNA polymerase III transcription termination factor activity
- GO:0016986 transcription initiation factor activity
- GO:0030401 transcription antiterminator activity
what about this one?
Issues for these terms:
- GO:0003706 MF ligand-regulated transcription factor activity
rework, or merge into another MF term?
def includes binding
- GO:0016988 MF transcription initiation factor antagonist activity
Regulation terms for "transcription regulator activity"
- GO:0090046 regulation of transcription regulator activity
- GO:0090047 positive regulation of transcription regulator activity
- GO:0090048 negative regulation of transcription regulator activity
Reannotation suggestions
merge Function term into Process term
- For current top level MF term:
- GO:0030528 transcription regulator activity
- Existing definition already specifies DNA, so we can clearly select a "transcription, DNA-dependent" term without being concerned about the RNA-dependent type of transcription. We considered both transcription, DNA-dependent (GO:0006351) and regulation of transcription, DNA-dependent (GO:0006355) and we looked at some existing annotations to transcription regulator activity to consider which of these two terms would be most appropriate to transfer them to. While the majority of annotations (from both MGI and SGD) are "regulatory" transcription factors, the SGD set of annotations, which was small enough to look at in its entirety, includes annotations for basal transcription factors and RNA polymerase subunits, via both manual and computational methods. Thus, we felt that the term has been used so broadly that it would be better to select the more general term.
- merge into BP term::
- transcription, DNA-dependent (GO:0006351)
- GO:0030528 transcription regulator activity
- Three high level (not specific to a specific RNAP) terms for activators or repressors
- GO:0016563 transcription activator activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- positive regulation of transcription, DNA-dependent (GO:0045893)
- GO:0042156 zinc-mediated transcriptional activator activity
- Def: Initiates or upregulates transcription in the presence of zinc.
- Brief look at PMID:10952993 indicates that they show MTF-1 binds DNA in the presence of zinc (EMSA), not sure if this shows direct binding to zinc, or if we care
- only existing term for any kind of regulation of transcription in relation to zinc is not appropriate
- regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation (GO:0034225)
- convert to BP term?
- positive regulation of DNA-dependent transcription in response to zinc
- GO:0016564 transcription repressor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- negative regulation of transcription, DNA-dependent (GO:0045892)
- GO:0016563 transcription activator activity
- Three terms for transcription factors for specific (eukaryotic nuclear) RNAPs
- GO:0003701 RNA polymerase I transcription factor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- transcription from RNA polymerase I promoter (GO:0006360)
- GO:0003702 RNA polymerase II transcription factor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- GO:0003701 RNA polymerase I transcription factor activity
- GO:0003709 RNA polymerase III transcription factor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- GO:0003709 RNA polymerase III transcription factor activity
- GO:0003711 MF transcription elongation regulator activity
- GO:0008148 MF negative transcription elongation factor activity
- GO:0008159 MF positive transcription elongation factor activity
- GO:0016943 MF RNA polymerase I transcription elongation factor activity
- GO:0016944 MF RNA polymerase II transcription elongation factor activity
- GO:0016945 MF RNA polymerase III transcription elongation factor activity
- GO:0003715 MF transcription termination factor activity
- GO:0003716 MF RNA polymerase I transcription termination factor activity
- GO:0003717 MF RNA polymerase II transcription termination factor activity
- GO:0003718 MF RNA polymerase III transcription termination factor activity
- GO:0016986 MF transcription initiation factor activity
- GO:0030401 MF transcription antiterminator activity
??
- GO:0003706 MF ligand-regulated transcription factor activity
def includes binding
- GO:0016988 MF transcription initiation factor antagonist activity
related regulation terms
- GO:0090046 regulation of transcription regulator activity
- GO:0090047 positive regulation of transcription regulator activity
- GO:0090048 negative regulation of transcription regulator activity
Supporting information
Annotation counts
via GOOSE (Berkeley BOP) on 3/30/2011
=== Summary of GO annotation counts, by source === Source............ non-IEA IEA Grand Total ..............ASAP 9 - 9 .............AspGD 17 51 68 ...............CGD 71 35 106 .........dictyBase 36 33 69 ............EcoCyc 337 30 367 .........EcoliWiki 146 40 186 ...........Ensembl - 208 208 ................FB 374 126 500 GeneDB_Pfalciparum 4 - 4 .....GeneDB_Spombe 56 7 63 ....GeneDB_Tbrucei 4 - 4 ........GR_protein 306 - 306 ..........JCVI_CMR 314 - 314 ...............MGI 888 345 1233 ..............NCBI 2 - 2 ...............PDB 4 753 757 .........PseudoCAP 142 - 142 ............RefSeq - 129 129 ...............RGD 763 478 1241 ...............SGD 186 54 240 ...............SGN 1 - 1 ..............TAIR 315 79 394 ..........TIGR_CMR 299 - 299 .........UniProtKB 1650 93884 95534 ................WB 36 167 203 ..............ZFIN 61 576 637 Grand Total....... 6021 96995 103016
=== Summary of GO annotation counts, by term === GO Term...................................................... aspect non-IEA IEA Grand Total .............................transcription regulator activity MF 1238 62032 63270 .............................transcription activator activity MF 2354 6847 9201 .............zinc-mediated transcriptional activator activity MF 10 7 17 .............................transcription repressor activity MF 1554 9353 10907 ...............RNA polymerase I transcription factor activity MF 32 12 44 ..............RNA polymerase II transcription factor activity MF 383 3913 4296 .............RNA polymerase III transcription factor activity MF 49 13 62 ..................transcription elongation regulator activity MF 69 8348 8417 ............negative transcription elongation factor activity MF 12 7 19 ............positive transcription elongation factor activity MF 23 150 173 ....RNA polymerase I transcription elongation factor activity MF - - - ...RNA polymerase II transcription elongation factor activity MF 54 125 179 ..RNA polymerase III transcription elongation factor activity MF - - - ....................transcription termination factor activity MF 80 5011 5091 ...RNA polymerase I transcription termination factor activity MF 17 4 21 ..RNA polymerase II transcription termination factor activity MF 5 3 8 .RNA polymerase III transcription termination factor activity MF 2 - 2 .....................transcription initiation factor activity MF 39 699 738 ........................transcription antiterminator activity MF 43 420 463 ...............ligand-regulated transcription factor activity MF 39 33 72 ..........transcription initiation factor antagonist activity MF 3 4 7 .............. regulation of transcription regulator activity BP - - - ......positive regulation of transcription regulator activity BP 15 14 29 ......negative regulation of transcription regulator activity BP - - - Grand Total.................................................. 6021 96995 103016
Subsets
All subsets for "transcription regulator activity"
- Prokaryotic GO subset
- Candida GO slim
- GOA and proteome slim
- PIR GO slim
- Plant GO slim
- Yeast GO slim
Prokaryotic GO subset
- GO:0030528 - transcription regulator activity
- GO:0016563 - transcription activator activity
- GO:0016564 - transcription repressor activity
- GO:0016986 - transcription initiation factor activity
- GO:0016988 - transcription initiation factor antagonist activity
- GO:0003711 - transcription elongation regulator activity
- GO:0003715 - transcription termination factor activity
- GO:0030401 - transcription antiterminator activity
Terms not in subsets
- GO:0042156 zinc-mediated transcriptional activator activity
- GO:0003701 - RNA polymerase I transcription factor activity
- GO:0003702 - RNA polymerase II transcription factor activity
- GO:0003709 - RNA polymerase III transcription factor activity
- GO:0008159 - positive transcription elongation factor activity
- GO:0008148 - negative transcription elongation factor activity
- GO:0016943 - RNA polymerase I transcription elongation factor activity
- GO:0016944 - RNA polymerase II transcription elongation factor activity
- GO:0016945 - RNA polymerase III transcription elongation factor activity
- GO:0003716 - RNA polymerase I transcription termination factor activity
- GO:0003717 - RNA polymerase II transcription termination factor activity
- GO:0003718 - RNA polymerase III transcription termination factor activity
- GO:0090046 - regulation of transcription regulator activity
- GO:0090047 - positive regulation of transcription regulator activity
- GO:0090048 - negative regulation of transcription regulator activity
Sample of existing annotations to transcription regulator activity
Manual annotations for S. cerevisiae genes
Gene Annot Name Evidence Date Source Description BRE2 ISS 4/2/03 SGD Subunit of COMPASS (Set1C) complex, which methylates Lys4 of histone H3 and functions in silencing at telomeres ASK10 TAS 3/11/03 SGD Component of RNA polymerase II holoenzyme, phosphorylated in response to oxidative stress RLF2 IMP 2/16/05 SGD Largest subunit (p90) of the Chromatin Assembly Complex (CAF-1) with Cac2p and Msi1p that assembles newly synthesized histones onto recently replicated DNA DEP1 IMP 2/9/06 SGD Transcriptional modulator involved in regulation of structural phospholipid biosynthesis genes and metabolically unrelated genes, as well as maintenance of telomeres, mating efficiency, and sporulation BDF1 ISS|IMP 3/11/03 SGD Protein involved in transcription initiation at TATA-containing promoters UME6 IMP|IDA 2/26/02 SGD Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p UME6 IMP|IDA 2/26/02 SGD Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p IME1 TAS 3/11/03 SGD Master regulator of meiosis that is active only during meiotic events, activates transcription of early meiotic genes through interaction with Ume6p, degraded by the 26S proteasome following phosphorylation by Ime2p MSI1 IMP 2/16/05 SGD Subunit of chromatin assembly factor I (CAF-1), negative regulator of the RAS/cAMP pathway via sequestration of Npr1p kinase LAP3 IDA 9/30/02 SGD Cysteine aminopeptidase with homocysteine-thiolactonase activity SUS1 IDA 2/17/09 SGD Protein involved in mRNA export coupled transcription activation and elongation GTS1 IDA|IPI 4/14/08 SGD Arf3p GTPase Activating Protein (GAP) that localizes to endocytic patches RTG2 IDA 5/8/03 SGD Sensor of mitochondrial dysfunction LRE1 IDA 10/1/02 SGD Protein involved in control of cell wall structure and stress response CAC2 IMP 2/16/05 SGD Component of the chromatin assembly complex (with Rlf2p and Msi1p) that assembles newly synthesized histones onto recently replicated DNA, required for building functional kinetochores, conserved from yeast to humans
Computational annotations for S. cerevisiae genes
Gene Annot Name Ev Code With (or) From Date Source Description YOX1 IEA EBI:IPR017970 1/10/11 InterPro Homeodomain-containing transcriptional repressor, binds to Mcm1p and to early cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed in M/G1 phase YHP1 IEA EBI:IPR017970 1/10/11 InterPro One of two homeobox transcriptional repressors (see also Yox1p), that bind to Mcm1p and to early cell cycle box (ECB) elements of cell cycle regulated genes, thereby restricting ECB-mediated transcription to the M/G1 interval PHO2 IEA EBI:IPR017970 1/10/11 InterPro Homeobox transcription factor RPA12 IEA EBI:IPR001222 1/10/11 InterPro RNA polymerase I subunit A12.2 RPB9 IEA EBI:IPR001222 1/10/11 InterPro RNA polymerase II subunit B12.6 TYE7 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Serine-rich protein that contains a basic-helix-loop-helix (bHLH) DNA binding motif MAF1 IEA EBI:IPR017152 1/10/11 InterPro Negative regulator of RNA polymerase III INO2 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Component of the heteromeric Ino2p/Ino4p basic helix-loop-helix transcription activator that binds inositol/choline-responsive elements (ICREs), required for derepression of phospholipid biosynthetic genes in response to inositol depletion HAP4 IEA EBI:IPR018287 1/10/11 InterPro Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression HMRA1 IEA EBI:IPR017970 1/10/11 InterPro Silenced copy of a1 at HMR DST1 IEA EBI:IPR001222|EBI:IPR010990 1/10/11 InterPro General transcription elongation factor TFIIS, enables RNA polymerase II to read through blocks to elongation by stimulating cleavage of nascent transcripts stalled at transcription arrest sites HIR1 IEA EBI:IPR011494|EBI:IPR019015 1/10/11 InterPro Subunit of the HIR complex, a nucleosome assembly complex involved in regulation of histone gene transcription YAP7 IEA EBI:IPR018287 1/10/11 InterPro Putative basic leucine zipper (bZIP) transcription factor PHO4 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Basic helix-loop-helix (bHLH) transcription factor of the myc-family CDC36 IEA EBI:IPR007282 1/10/11 InterPro Component of the CCR4-NOT complex, which has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs by deadenylation RTG1 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Transcription factor (bHLH) involved in interorganelle communication between mitochondria, peroxisomes, and nucleus YKR023W IEA EBI:IPR009349 1/10/11 InterPro Putative protein of unknown function RPL7A IEA EBI:IPR005998 1/10/11 InterPro Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins HIR2 IEA EBI:IPR011494 1/10/11 InterPro Subunit of the HIR complex, a nucleosome assembly complex involved in regulation of histone gene transcription NOT5 IEA EBI:IPR007282|EBI:IPR007207|EBI:IPR012270 1/10/11 InterPro Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation RTG3 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor that forms a complex with another bHLH/Zip protein, Rtg1p, to activate the retrograde (RTG) and TOR pathways RPL7B IEA EBI:IPR005998 1/10/11 InterPro Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Ap and has similarity to E. coli L30 and rat L7 ribosomal proteins HMS1 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Basic helix-loop-helix (bHLH) protein with similarity to myc-family transcription factors CBF1 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Helix-loop-helix protein that binds the motif CACRTG, which is present at several sites including MET gene promoters and centromere DNA element I (CDEI) TAF5 IEA EBI:IPR007582 1/10/11 InterPro Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification INO4 IEA EBI:IPR001092|EBI:IPR011598 1/10/11 InterPro Transcription factor required for derepression of inositol-choline-regulated genes involved in phospholipid synthesis RPC11 IEA EBI:IPR001222 1/10/11 InterPro RNA polymerase III subunit C11 NOT3 IEA EBI:IPR007282|EBI:IPR007207|EBI:IPR012270 1/10/11 InterPro Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation SUA7 IEA EBI:IPR000812 1/10/11 InterPro Transcription factor TFIIB, a general transcription factor required for transcription initiation and start site selection by RNA polymerase II BRF1 IEA EBI:IPR000812 1/10/11 InterPro TFIIIB B-related factor, one of three subunits of RNA polymerase III transcription initiation factor TFIIIB, binds TFIIIC and TBP and recruits RNA pol III to promoters, amino-terminal half is homologous to TFIIB