Fate of terms referring to general/nonspecific/basal versus specific transcription: Difference between revisions
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= Proposal = | = Proposal = | ||
We propose to obsolete or merge these | We propose to obsolete or merge these 13 Biological Process (BP) and 7 Molecular | ||
Function (MF) terms that represent general/nonspecific/basal | Function (MF) terms that represent general/nonspecific/basal | ||
transcription versus specific transcription | 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. | |||
#*BP terms: | 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. | ||
#** GO:0032569 gene-specific transcription from RNA polymerase II promoter | |||
#** GO: | #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: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:0032569 gene-specific transcription from RNA polymerase II promoter | |||
#* GO:0032582 negative regulation of gene-specific transcription | |||
#* GO:0032583 regulation of gene-specific transcription | |||
#* GO:0043193 positive 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 | |||
= Comment Period = | = Comment Period = |
Revision as of 14:45, 28 March 2011
Proposal
We propose to obsolete or merge these 13 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: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:0032569 gene-specific transcription from RNA polymerase II promoter
- GO:0032582 negative regulation of gene-specific transcription
- GO:0032583 regulation of gene-specific transcription
- GO:0043193 positive 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
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 3/23/2011 or 3/24/2011 (mediator term only)
grouped by term name and evidence code (non-IEA vs IEA)
=== grouped by term name and evidence code (non-IEA vs IEA) Term name.................................................. aspect non-IEA IEA Grand Total ......general transcription from RNA polymerase II promoter BP 59 60 119 gene-specific transcription from RNA polymerase II promoter BP 142 16 158 ....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 27 16 43 .................general transcriptional repressor activity MF 41 17 58 ................specific transcriptional repressor activity MF 645 39431 40076 Grand Total................................................ 1907 41993 43900
grouped by annotation source and evidence code (non-IEA vs IEA)
Source............ non-IEA IEA Grand Total .............AspGD 4 84 88 ...............CGD 28 71 99 .........dictyBase 45 1 46 ............EcoCyc 56 2 58 .........EcoliWiki 43 1 44 ...........Ensembl 10 10 ................FB 268 9 277 GeneDB_Pfalciparum 3 - 3 .....GeneDB_Spombe 262 3 265 ....GeneDB_Tbrucei 1 - 1 ..........JCVI_CMR 10 - 10 ...............MGI 209 16 225 ...............PDB 389 389 ............RefSeq 16 16 ...............RGD 119 53 172 ...............SGD 276 18 294 ..............TAIR 13 19 32 ..........TIGR_CMR 21 - 21 .........UniProtKB 541 41259 41800 ................WB 12 17 29 ..............ZFIN 2 25 27 Grand Total....... 1913 41993 43906
Subsets
Prokaryotic GO subset
- GO:0016566 specific transcriptional repressor activity
- GO:0017163 basal transcription repressor activity Prokaryotic GO subset
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:0016251 general RNA polymerase II transcription factor activity
- GO:0016252 nonspecific RNA polymerase II transcription factor activity
- GO:0016565 general transcriptional repressor activity
- GO:0032568 general transcription from RNA polymerase II promoter
Non-definition dbxrefs
GO:0016251 - general RNA polymerase II transcription factor activity
- COG:K
- InterPro:IPR004600
- InterPro:IPR006751
- InterPro:IPR016640
- InterPro:IPR018381
- Pfam:PF03850
- Pfam:PF04658
- PIRSF:PIRSF015849
GO:0016566 - specific transcriptional repressor activity
- 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
Term Stanzas
Biological Process terms (2)
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
Molecular Function terms (6)
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 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