Fate of terms referring to general/nonspecific/basal versus specific transcription
Proposal
We propose to obsolete or merge these 12 Biological Process (BP) and 7 Molecular Function (MF) terms that represent general/nonspecific/basal transcription versus specific transcription.
In MF, there are three RNAP II specific terms for general/nonspecific/basal vs specific "transcription factor activity". The mediator term is included because it is a child of one of these terms. There are three terms for general/nonspecific/basal vs specific transcription repressor activities.
In BP, there are two terms for RNAP II processes. The rest are all regulation terms; most of these are specific to RNAP II, but three are general to any "gene-specific transcription" and one is specific to transcription involved in the unfolded protein response.
- MF terms:
- GO:0003704 specific RNA polymerase II transcription factor activity
- GO:0016252 nonspecific RNA polymerase II transcription factor activity
- GO:0016251 general RNA polymerase II transcription factor activity
- GO:0016455 RNA polymerase II transcription mediator activity
- GO:0016566 specific transcriptional repressor activity
- GO:0017163 basal transcription repressor activity
- GO:0016565 general transcriptional repressor activity
- BP terms:
- GO:0032569 gene-specific transcription from RNA polymerase II promoter
- GO:0032568 general transcription from RNA polymerase II promoter
- GO:0032583 regulation of gene-specific transcription
- GO:0043193 positive regulation of gene-specific transcription
- GO:0032582 negative regulation of gene-specific transcription
- GO:0010551 regulation of gene-specific transcription from RNA polymerase II promoter
- GO:0010552 positive regulation of gene-specific transcription from RNA polymerase II promoter
- GO:0010553 negative regulation of gene-specific transcription from RNA polymerase II promoter
- GO:0006990 positive regulation of gene-specific transcription involved in unfolded protein response
- GO:0090039 regulation of gene-specific transcription elongation from RNA polymerase II promoter
- GO:0090040 positive regulation of gene-specific transcription elongation from RNA polymerase II promoter
- GO:0090041 negative regulation of gene-specific transcription elongation from RNA polymerase II promoter
Comment Period
Date mailed:
Deadline for Comments: TBD - Unless objections are received by April ??????, we will assume that you agree to this change.
Problems with "general/non-specific/basal" vs "specific" transcription
Issues
In the [original proposal for the "general/non-specific/basal" vs "specific" terms], we proposed to try to rework these terms to be types of preinitiation complex (PIC) formation. However, we have been unable to come up with any clear distinction or separation between these terms, either in terms of function or process. Basically, these terms reflect outdating thinking, probably based in part on the use of a very limited set of promoters for in vitro experiments.
- Early on it was thought that the RNAP II "general transcription factors", or GTFs were involved in preinitation complex (PIC) formation at ALL RNAP II promoters. However, it is now clear that there is no single type of RNAP II promoter. Thus there are probably many types of PICs and the "general" factors may not be general. Thus Sikorsky & Buratowski (2009) use the term basal rather than general.
- The current definition for general says "non-specifically regulated". This is probably not really the case. Transcription of the set of genes that requires only basal transcription factors is regulated, they just don't require additional non-basal factors to recognize the promoter. It is also a quite large set of genes, larger than the typical number of genes that is responsive to a particular activator, and they are active in "standard" growth conditions. It is now known that there are some large scale changes in the transcriptome of a cell, for example during differentiation, that are regulated by changing the set of basal transcription factors that are expressed.
- It is not the case that there is one set of genes involved in basal transcription and another set involved in specific transcription. Basal refers to transcription that can occur only with basal transcription (initiation) factors. "Gene-specific" refers to cases where the promoter sequence is not recognized directly by the basal factors, but instead by a "gene-specific" regulatory transcription factor, which then initiates the process to recruit basal transcription factors and RNAP II. Everything involved in basal transcription is also involved in gene-specific transcription. Thus "gene-specific transcription" does not represent a completely separate process from "general/non-specific/basal transcription", but rather an additional level of regulation where additional factors are required for promoter recognition, but which still requires basal factors. In a comprehensive review of eukaryotic general transcription machinery, Thomas and Chiang (2006) use the phrase activator-dependent for this situation, consistent with the phrase that is used in E. coli for these cases where an "activator" is required in addition to basal machinery.
Useful reviews
- Sikorski TW, Buratowski S. The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol. 2009 Jun;21(3):344-51. PMID: 19411170
- Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78. PMID: 16858867
- Zhou Z, Lin IJ, Darst RP, Bungert J. Maneuver at the transcription start site: Mot1p and NC2 navigate TFIID/TBP to specific core promoter elements. Epigenetics. 2009 Jan;4(1):1-4. Epub 2009 Jan 27. PMID: 19077548
Reannotation suggestions
(in progress)
- MF terms:
- GO:0003704 specific RNA polymerase II transcription factor activity
- MF terms:
- GO:0016252 nonspecific RNA polymerase II transcription factor activity
- GO:0016251 general RNA polymerase II transcription factor activity
- GO:0016455 RNA polymerase II transcription mediator activity
- GO:0016566 specific transcriptional repressor activity
- For GO:0017163 basal transcription repressor activity
- For GO:0016455 RNA polymerase II transcription mediator activity
- obsolete and consider coannotation to two terms: MF RNA polymerase II transcription cofactor activity (GO:0001104) and CC mediator complex (GO:0016592)
- GO:0016565 general transcriptional repressor activity
- BP terms:
- GO:0032569 gene-specific transcription from RNA polymerase II promoter
- GO:0032568 general transcription from RNA polymerase II promoter
- BP terms:
Supporting information
Annotation counts
Annotation counts via GOOSE (Berkeley BOP) on 3/28/2011
=== grouped by term name and evidence code (non-IEA vs IEA)
Term name.................................................... aspect non-IEA IEA Grand Total .......general RNA polymerase II transcription factor activity MF 230 466 696 ...nonspecific RNA polymerase II transcription factor activity MF 1 - 1 ......specific RNA polymerase II transcription factor activity MF 596 72 668 .............RNA polymerase II transcription mediator activity MF 166 1915 2081 ........................basal transcription repressor activity MF 33 16 49 ....................general transcriptional repressor activity MF 41 17 58 ...................specific transcriptional repressor activity MF 645 39431 40076 ...gene-specific transcription from RNA polymerase II promoter BP 142 16 158 .........general transcription from RNA polymerase II promoter BP 59 60 119 .....................regulation of gene-specific transcription BP 40 39 79 ............positive regulation of gene-specific transcription BP 400 253 653 ............negative regulation of gene-specific transcription BP 269 127 396 ............regulation of gene-specific transcription from RNA BP 118 45 163 polymerase II promoter ...positive regulation of gene-specific transcription from RNA BP 759 617 1376 polymerase II promoter ...negative regulation of gene-specific transcription from RNA BP 691 306 997 polymerase II promoter ...positive regulation of gene-specific transcription involved BP 8 - 8 in unfolded protein response ..........regulation of gene-specific transcription elongation BP 7 5 12 from RNA polymerase II promoter .positive regulation of gene-specific transcription elongation BP 14 6 20 from RNA polymerase II promoter .negative regulation of gene-specific transcription elongation BP 15 10 25 from RNA polymerase II promoter Grand Total................................................... 4234 43401 47635
=== grouped by source and evidence code (non-IEA vs IEA)
Source............. non-IEA IEA Grand Total ..............AspGD 20 119 139 ................CGD 46 91 137 ..........dictyBase 48 1 49 .............EcoCyc 158 2 160 ..........EcoliWiki 126 1 127 ............Ensembl - 10 10 .................FB 318 9 327 .GeneDB_Pfalciparum 3 - 3 ......GeneDB_Spombe 308 3 311 .....GeneDB_Tbrucei 1 - 1 ...........JCVI_CMR 10 - 10 ................MGI 760 16 776 ................PDB 39 391 430 .............RefSeq - 16 16 ................RGD 506 176 682 ................SGD 346 20 366 ...............TAIR 30 19 49 ...........TIGR_CMR 21 - 21 ..........UniProtKB 1448 42485 43933 .................WB 40 17 57 ...............ZFIN 6 25 31 Grand Total........ 4234 43401 47635
Subsets
Prokaryotic GO subset:
- GO:0016566 specific transcriptional repressor activity
- GO:0017163 basal transcription repressor activity
- GO:0043193 positive regulation of gene-specific transcription
Fission yeast GO slim:
- GO:0032569 gene-specific transcription from RNA polymerase II promoter
Not present in a subset:
- GO:0003704 specific RNA polymerase II transcription factor activity
- GO:0006990 positive regulation of gene-specific transcription involved in unfolded protein response
- GO:0010551 regulation of gene-specific transcription from RNA polymerase II promoter
- GO:0010552 positive regulation of gene-specific transcription from RNA polymerase II promoter
- GO:0010553 negative regulation of gene-specific transcription from RNA polymerase II promoter
- GO:0016251 general RNA polymerase II transcription factor activity
- GO:0016252 nonspecific RNA polymerase II transcription factor activity
- GO:0016455 RNA polymerase II transcription mediator activity
- GO:0016565 general transcriptional repressor activity
- GO:0032568 general transcription from RNA polymerase II promoter
- GO:0032582 negative regulation of gene-specific transcription
- GO:0032583 regulation of gene-specific transcription
- GO:0090039 regulation of gene-specific transcription elongation from RNA polymerase II promoter
- GO:0090040 positive regulation of gene-specific transcription elongation from RNA polymerase II promoter
- GO:0090041 negative regulation of gene-specific transcription elongation from RNA polymerase II promoter
Non-definition dbxrefs
GO:0016566 - specific transcriptional repressor activity (MF)
- InterPro:IPR003012
- InterPro:IPR004111
- InterPro:IPR005650
- InterPro:IPR012771
- InterPro:IPR015893
- JCVI_TIGRFAMS:TIGR00331
- JCVI_TIGRFAMS:TIGR02404
- JCVI_TIGRFAMS:TIGR03384
- Pfam:PF02909
- Pfam:PF03965
- PRINTS:PR00400
GO:0016251 - general RNA polymerase II transcription factor activity (MF)
- COG:K
- InterPro:IPR004600
- InterPro:IPR006751
- InterPro:IPR016640
- InterPro:IPR018381
- Pfam:PF03850
- Pfam:PF04658
- PIRSF:PIRSF015849
GO:0016455 - RNA polymerase II transcription mediator activity (MF)
- InterPro:IPR007018
- InterPro:IPR008626
- InterPro:IPR008831
- InterPro:IPR009244
- InterPro:IPR009332
- InterPro:IPR009401
- InterPro:IPR011425
- InterPro:IPR013921
- InterPro:IPR013942
- InterPro:IPR013947
- InterPro:IPR014801
- InterPro:IPR016530
- InterPro:IPR016532
- InterPro:IPR016612
- InterPro:IPR016820
- InterPro:IPR018174
- InterPro:IPR019035
- InterPro:IPR019087
- InterPro:IPR019095
- InterPro:IPR019145
- InterPro:IPR019258
- InterPro:IPR019313
- InterPro:IPR019364
- InterPro:IPR019403
- InterPro:IPR019404
- InterPro:IPR019680
- InterPro:IPR020998
- Pfam:PF04934
- Pfam:PF05397
- Pfam:PF05669
- Pfam:PF05983
- Pfam:PF06333
- Pfam:PF07544
- Pfam:PF08612
- Pfam:PF08633
- Pfam:PF08638
- Pfam:PF08689
- Pfam:PF09497
- Pfam:PF09606
- Pfam:PF09637
- Pfam:PF09748
- Pfam:PF10018
- Pfam:PF10156
- Pfam:PF10232
- Pfam:PF10278
- Pfam:PF10280
- Pfam:PF10744
- Pfam:PF11593
- PIRSF:PIRSF007936
- PIRSF:PIRSF007945
- PIRSF:PIRSF013286
- PIRSF:PIRSF023869
GO:0032583 - regulation of gene-specific transcription (BP)
- InterPro:IPR016325
- PIRSF:PIRSF001863
Term Stanzas
Molecular Function terms (7)
id: GO:0016251 name: general RNA polymerase II transcription factor activity namespace: molecular_function alt_id: GO:0003703 def: "Any function that supports basal (unregulated) transcription of genes by core RNA polymerase II. Five general transcription factors are necessary and sufficient for such basal transcription in yeast: TFIIB, TFIID, TFIIE, TFIIF, TFIIH and TATA-binding protein (TBF)." [PMID:10384286, PMID:9774831] is_a: GO:0003702 ! RNA polymerase II transcription factor activity id: GO:0016252 name: nonspecific RNA polymerase II transcription factor activity namespace: molecular_function def: "Any function that supports transcription of genes by RNA polymerase II, and is not specific to a particular gene or gene set." [GOC:jl] is_a: GO:0003702 ! RNA polymerase II transcription factor activity id: GO:0003704 name: specific RNA polymerase II transcription factor activity namespace: molecular_function def: "Functions to enable the transcription of specific, or specific sets, of genes by RNA polymerase II." [GOC:ma] is_a: GO:0003702 ! RNA polymerase II transcription factor activity [Term] id: GO:0016455 name: RNA polymerase II transcription mediator activity namespace: molecular_function def: "Functions to mediate the interaction of transcriptional activators with the RNA polymerase II-general RNA polymerase II transcription factor complex." [GOC:ma] synonym: "thyroid receptor-associated protein" RELATED [] synonym: "TRAP protein" RELATED [] is_a: GO:0016251 ! general RNA polymerase II transcription factor activity id: GO:0016566 name: specific transcriptional repressor activity namespace: molecular_function def: "Any activity that stops or downregulates transcription of specific genes or sets of genes." [GOC:mah] subset: gosubset_prok is_a: GO:0016564 ! transcription repressor activity id: GO:0017163 name: basal transcription repressor activity namespace: molecular_function def: "Any transcription regulator activity that prevents or downregulates basal transcription. Basal transcription results from transcription that is controlled by the minimal complement of proteins necessary to reconstitute transcription from a minimal promoter." [GOC:dph, GOC:tb, http://tfib.med.harvard.edu/transcription/basaltx.html] subset: gosubset_prok is_a: GO:0016564 ! transcription repressor activity id: GO:0016565 name: general transcriptional repressor activity namespace: molecular_function def: "Any activity that stops or downregulates transcription of genes globally, and is not specific to a particular gene or gene set." [GOC:mah] is_a: GO:0016564 ! transcription repressor activity
Biological Process terms (12)
id: GO:0032569 name: gene-specific transcription from RNA polymerase II promoter namespace: biological_process def: "The specifically regulated synthesis of RNA from DNA encoding a specific gene or set of genes by RNA polymerase II (Pol II), originating at a Pol II-specific promoter. In addition to RNA polymerase II and the general transcription factors, specific transcription requires one or more specific factors that bind to specific DNA sequences or interact with the general transcription machinery." [GOC:mah] subset: goslim_pombe synonym: "specific transcription from RNA polymerase II promoter" EXACT [GOC:mah] is_a: GO:0006366 ! transcription from RNA polymerase II promoter id: GO:0032568 name: general transcription from RNA polymerase II promoter namespace: biological_process def: "The basal, non-specifically regulated synthesis of RNA from a DNA template by RNA polymerase II (Pol II), originating at a Pol II-specific promoter. Mediated by core RNA polymerase II and a set of general transcription factors; in Saccharomyces five transcription factors are necessary and sufficient for such basal transcription." [GOC:mah] is_a: GO:0006366 ! transcription from RNA polymerase II promoter id: GO:0032583 name: regulation of gene-specific transcription namespace: biological_process def: "Any process that modulates the DNA-dependent transcription of a specific gene or genes." [GOC:mah] is_a: GO:0006355 ! regulation of transcription, DNA-dependent id: GO:0043193 name: positive regulation of gene-specific transcription namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the DNA-dependent transcription of a specific gene or genes." [GOC:jl] subset: gosubset_prok synonym: "activation of gene-specific transcription" NARROW [] synonym: "stimulation of gene-specific transcription" NARROW [] synonym: "up regulation of gene-specific transcription" EXACT [] synonym: "up-regulation of gene-specific transcription" EXACT [] synonym: "upregulation of gene-specific transcription" EXACT [] is_a: GO:0032583 ! regulation of gene-specific transcription is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent id: GO:0032582 name: negative regulation of gene-specific transcription namespace: biological_process def: "Any process that stops, prevents or reduces the DNA-dependent transcription of a specific gene or genes." [GOC:mah] synonym: "down regulation of gene-specific transcription" EXACT [] synonym: "down-regulation of gene-specific transcription" EXACT [] synonym: "downregulation of gene-specific transcription" EXACT [] synonym: "inhibition of gene-specific transcription" NARROW [] is_a: GO:0032583 ! regulation of gene-specific transcription is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent id: GO:0010551 name: regulation of gene-specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the specifically regulated synthesis of RNA from DNA encoding a specific gene or set of genes by RNA polymerase II (Pol II), originating at a Pol II-specific promoter." [GOC:dph, GOC:tb] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0032583 ! regulation of gene-specific transcription intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter relationship: regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter id: GO:0010552 name: positive regulation of gene-specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that increases the frequency, rate or extent of the specifically regulated synthesis of RNA from DNA encoding a specific gene or set of genes by RNA polymerase II (Pol II), originating at a Pol II-specific promoter." [GOC:dph, GOC:tb] is_a: GO:0010551 ! regulation of gene-specific transcription from RNA polymerase II promoter is_a: GO:0043193 ! positive regulation of gene-specific transcription is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter relationship: positively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter id: GO:0010553 name: negative regulation of gene-specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the specifically regulated synthesis of RNA from DNA encoding a specific gene or set of genes by RNA polymerase II (Pol II), originating at a Pol II-specific promoter." [GOC:dph, GOC:tb] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0010551 ! regulation of gene-specific transcription from RNA polymerase II promoter is_a: GO:0032582 ! negative regulation of gene-specific transcription intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter relationship: negatively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter id: GO:0006990 name: positive regulation of gene-specific transcription involved in unfolded protein response namespace: biological_process def: "The activation of genes whose promoters contain a specific sequence elements such as the unfolded protein response element (UPRE; consensus CAGCGTG) or the ER stress-response element (ERSE; CCAAN(N)9CCACG), as a result of signaling via the unfolded protein response." [GOC:dph, GOC:mah, GOC:tb, PMID:12042763] synonym: "positive regulation of transcription of target genes involved in unfolded protein response" EXACT [GOC:dph, GOC:tb] synonym: "unfolded protein response, activation of target gene transcription" NARROW [] synonym: "unfolded protein response, positive regulation of target gene transcription" EXACT [GOC:tb] synonym: "unfolded protein response, stimulation of target gene transcription" NARROW [] synonym: "unfolded protein response, target gene transcriptional activation" BROAD [] synonym: "unfolded protein response, up regulation of target gene transcription" EXACT [] synonym: "unfolded protein response, up-regulation of target gene transcription" EXACT [] synonym: "unfolded protein response, upregulation of target gene transcription" EXACT [] is_a: GO:0043193 ! positive regulation of gene-specific transcription is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0043193 ! positive regulation of gene-specific transcription intersection_of: part_of GO:0030968 ! endoplasmic reticulum unfolded protein response relationship: part_of GO:0030968 ! endoplasmic reticulum unfolded protein response id: GO:0090039 name: regulation of gene-specific transcription elongation from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene-specific RNA elongation, the extension of an RNA molecule from a specific gene or genes after transcription initiation by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:dph, GOC:tb] is_a: GO:0032583 ! regulation of gene-specific transcription is_a: GO:0034243 ! regulation of transcription elongation from RNA polymerase II promoter created_by: tanyaberardini creation_date: 2009-08-03T11:39:30Z id: GO:0090040 name: positive regulation of gene-specific transcription elongation from RNA polymerase II promoter namespace: biological_process def: "Any process that increases the frequency, rate or extent of gene-specific RNA elongation, the extension of an RNA molecule from a specific gene or genes after transcription initiation by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:dph, GOC:tb] is_a: GO:0043193 ! positive regulation of gene-specific transcription is_a: GO:0090039 ! regulation of gene-specific transcription elongation from RNA polymerase II promoter created_by: tanyaberardini creation_date: 2009-08-03T11:45:24Z id: GO:0090041 name: negative regulation of gene-specific transcription elongation from RNA polymerase II promoter namespace: biological_process def: "Any process that decreases the frequency, rate or extent of gene-specific RNA elongation, the extension of an RNA molecule from a specific gene or genes after transcription initiation by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:dph, GOC:tb] is_a: GO:0032582 ! negative regulation of gene-specific transcription is_a: GO:0090039 ! regulation of gene-specific transcription elongation from RNA polymerase II promoter created_by: tanyaberardini creation_date: 2009-08-03T11:46:32Z