Fate of terms referring to general/nonspecific/basal versus specific transcription: Difference between revisions
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* Two basic process terms trying to distinguish "gene-specific" vs "general" transcription | * Two basic process terms trying to distinguish "gene-specific" vs "general" transcription | ||
*: <font color="red">Merge</font> these two terms into '''transcription from RNA polymerase II promoter''' (GO:0006366) | *: <font color="red">Merge</font> these two terms into '''transcription from RNA polymerase II promoter''' (GO:0006366) | ||
** '''gene-specific transcription from RNA polymerase II promoter''' (GO:0032569) | ** '''gene-specific transcription from RNA polymerase II promoter''' (GO:0032569) <font color="red">done</font> | ||
** '''general transcription from RNA polymerase II promoter''' (GO:0032568) | ** '''general transcription from RNA polymerase II promoter''' (GO:0032568) <font color="red">done</font> | ||
*: These terms both relate to transcription from an RNAP II promoter. We are moving the annotations up to the parent term since "gene-specific transcription" and "general transription are not distinct processes. | *: These terms both relate to transcription from an RNAP II promoter. We are moving the annotations up to the parent term since "gene-specific transcription" and "general transription are not distinct processes. | ||
* Three regulation terms at the general level of "gene-specific transcription" | * Three regulation terms at the general level of "gene-specific transcription" | ||
** <font color="red">Merge</font> '''regulation of gene-specific transcription''' (GO:0032583) into '''regulation of transcription, DNA-dependent''' (GO:0006355) | ** <font color="red">Merge</font> '''regulation of gene-specific transcription''' (GO:0032583) into '''regulation of transcription, DNA-dependent''' (GO:0006355) <font color="red">done</font> | ||
** <font color="red">Merge</font> '''positive regulation of gene-specific transcription''' (GO:0043193) into '''positive regulation of transcription, DNA-dependent''' (GO:0045893) | ** <font color="red">Merge</font> '''positive regulation of gene-specific transcription''' (GO:0043193) into '''positive regulation of transcription, DNA-dependent''' (GO:0045893) <font color="red">done</font> | ||
** <font color="red">Merge</font> '''negative regulation of gene-specific transcription''' (GO:0032582) into '''negative regulation of transcription, DNA-dependent''' (GO:0045892) | ** <font color="red">Merge</font> '''negative regulation of gene-specific transcription''' (GO:0032582) into '''negative regulation of transcription, DNA-dependent''' (GO:0045892) <font color="red">done</font> | ||
*: These terms are all already defined in terms of DNA-dependent transcription, so if any annotations were made for "RNA-dependent transcription", they were made incorrectly. However, based on what we have seen, we feel that the vast majority of annotations will be for DNA-dependent transcription. Thus, we are moving the annotations up to the parent term since "gene-specific transcription" isn't a distinct process. | *: These terms are all already defined in terms of DNA-dependent transcription, so if any annotations were made for "RNA-dependent transcription", they were made incorrectly. However, based on what we have seen, we feel that the vast majority of annotations will be for DNA-dependent transcription. Thus, we are moving the annotations up to the parent term since "gene-specific transcription" isn't a distinct process. | ||
* Three regulation terms for "gene-specific transcription from RNA polymerase II promoter" | * Three regulation terms for "gene-specific transcription from RNA polymerase II promoter" | ||
** <font color="red">Merge</font> '''regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010551) into '''regulation of transcription from RNA polymerase II promoter''' (GO:0006357) | ** <font color="red">Merge</font> '''regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010551) into '''regulation of transcription from RNA polymerase II promoter''' (GO:0006357) <font color="red">done</font> | ||
** <font color="red">Merge</font> '''positive regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010552) into '''positive regulation of transcription from RNA polymerase II promoter''' (GO:0045944) [NOTE: fix def of 45994, use 'an' instead of 'the' to preface promoter.] | ** <font color="red">Merge</font> '''positive regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010552) into '''positive regulation of transcription from RNA polymerase II promoter''' (GO:0045944) [NOTE: fix def of 45994, use 'an' instead of 'the' to preface promoter.] <font color="red">done</font> | ||
** <font color="red">Merge</font> '''negative regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010553) into '''negative regulation of transcription from RNA polymerase II promoter''' (GO:0000122) | ** <font color="red">Merge</font> '''negative regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010553) into '''negative regulation of transcription from RNA polymerase II promoter''' (GO:0000122) <font color="red">done</font> | ||
*: We are just moving all these annotations up to the corresponding parent terms since "gene-specific transcription" isn't a distinct process. | *: We are just moving all these annotations up to the corresponding parent terms since "gene-specific transcription" isn't a distinct process. | ||
* Three regulation terms for "gene-specific transcription elongation from RNA polymerase II promoter" | * Three regulation terms for "gene-specific transcription elongation from RNA polymerase II promoter" | ||
** <font color="red">Merge</font> '''regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090039) into '''regulation of transcription elongation from RNA polymerase II promoter''' (GO:0034243) | ** <font color="red">Merge</font> '''regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090039) into '''regulation of transcription elongation from RNA polymerase II promoter''' (GO:0034243) <font color="red">done</font> | ||
** <font color="red">Merge</font> '''positive regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090040) into '''positive regulation of transcription elongation from RNA polymerase II promoter''' (GO:0032968) | ** <font color="red">Merge</font> '''positive regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090040) into '''positive regulation of transcription elongation from RNA polymerase II promoter''' (GO:0032968) <font color="red">done</font> | ||
** <font color="red">Merge</font> '''negative regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090041) into '''negative regulation of transcription elongation from RNA polymerase II promoter''' (GO:0034244) | ** <font color="red">Merge</font> '''negative regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090041) into '''negative regulation of transcription elongation from RNA polymerase II promoter''' (GO:0034244) <font color="red">done</font> | ||
* One term for a specific set of RNAP II genes | * One term for a specific set of RNAP II genes | ||
** '''positive regulation of gene-specific transcription involved in unfolded protein response''' (GO:0006990) | ** '''positive regulation of gene-specific transcription involved in unfolded protein response''' (GO:0006990) | ||
*: <font color="red">Rename</font> to '''positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response''' | *: <font color="red">Rename</font> to '''positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response''' <font color="red">done</font> | ||
*: This term is already defined in terms of RNAP II transcription and already has appropriate is_a parentage under a term that will not be affected by the transcription overhaul. | *: This term is already defined in terms of RNAP II transcription and already has appropriate is_a parentage under a term that will not be affected by the transcription overhaul. | ||
= Supporting information = | = Supporting information = |
Revision as of 18:25, 12 May 2011
Proposal
This is a group of 12 Biological Process (BP) and 7 Molecular Function (MF) terms that represent general/nonspecific/basal transcription versus specific transcription.
- MERGE 6 MF terms into equivalent BP terms: In MF, there are three terms for general/nonspecific/basal vs specific transcription repressor activities and there are three RNAP II specific terms for general/nonspecific/basal vs specific "transcription factor activity". We propose to MERGE these 6 MF terms into the BP terms with the same meanings because they are defined only in terms of affect on a process and not in terms of how they act, which is how we are now defining MF terms.
- - There was a counterproposal to the original proposal to MERGE; thus instead, these will be OBSOLETED.
- 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:0016566 specific transcriptional repressor activity
- GO:0017163 basal transcription repressor activity
- GO:0016565 general transcriptional repressor activity
- MERGE 1 MF term into a more general MF term: The mediator activity MF term is included here because it is a child of one of the above terms. We propose to merge it into a more general MF term that is defined in terms of how this class of factors act.
- GO:0016455 RNA polymerase II transcription mediator activity
- MERGE 11 BP terms into parent 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". We propose to MERGE these 11 BP terms into parent 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: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
- RENAME 1 BP term One of these BP terms merely needs to be renamed to be consistent with its existing definition and placement in the structure.
- GO:0006990 positive regulation of gene-specific transcription involved in unfolded protein response
Comment Period
Date mailed: 3/30/2011
Deadline for Comments: 4/19/2011 - Unless objections are received by April 19th, we will assume that you agree to this change.
Summary of Actions Taken
- As proposed, merged RNA polymerase II transcription mediator activity (GO:0016455) into MF term RNA polymerase II transcription cofactor activity (GO:0001104) [done 5/11/2011]
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 typical "gene-specific" 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 or some subsequent step, 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
MF terms
- For RNA polymerase II transcription mediator activity (GO:0016455)
- Merge into MF term RNA polymerase II transcription cofactor activity (GO:0001104)
- Also consider annotating to the CC term mediator complex (GO:0016592)
- For these three 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
- Merge all 3 into BP term transcription from RNA polymerase II promoter (GO:0006366)
- These three terms are all defined in terms of the process affected, but not in terms of how the function is carried out. Thus, although these terms have been present in the MF ontology, they actually represent BP information. Since the general/non-specific vs specific distinction is not valid with respect to process and these terms are all specific to RNAP II without conveying any additional detail, this is the term to which all annotations can be transferred without review.
- For reannotation in the MF tree, consider these terms and their children:
- GO:0001076 - RNA polymerase II transcription factor binding transcription factor activity
- GO:0000991 - core RNA polymerase II binding transcription factor activity
- GO:0000981 - sequence-specific DNA binding RNA polymerase II transcription factor activity
- For these three terms:
- GO:0016566 specific transcriptional repressor activity
- GO:0017163 basal transcription repressor activity
- GO:0016565 general transcriptional repressor activity
- Merge all 3 into BP term negative regulation of transcription, DNA-dependent (GO:0045892)
- These three terms are all defined in terms of the process affected, but not in terms of how the function is carried out. Thus, although these terms have been present in the MF ontology, they actually represent BP information. Since the general/non-specific vs specific distinction is not valid with respect to process and these terms are all related to repression of transcription, this is the term to which all annotations can be transferred without review. Similarly to the merge of "transcription" and its regulation terms into "transcription, DNA-dependent" and its regulation terms, we are suggesting merging into the "DNA-dependent" form of the the term because we feel that the majority of the annotations are already intended to be for DNA-dependent transcription.
- For reannotation in the MF tree, consider these terms and their children or requesting similar terms under protein binding transcription factor activity (GO:0000988):
- GO:0001141 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
- GO:0001078 - RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
BP terms
- Two basic process terms trying to distinguish "gene-specific" vs "general" transcription
- Merge these two terms into transcription from RNA polymerase II promoter (GO:0006366)
- gene-specific transcription from RNA polymerase II promoter (GO:0032569) done
- general transcription from RNA polymerase II promoter (GO:0032568) done
- These terms both relate to transcription from an RNAP II promoter. We are moving the annotations up to the parent term since "gene-specific transcription" and "general transription are not distinct processes.
- Three regulation terms at the general level of "gene-specific transcription"
- Merge regulation of gene-specific transcription (GO:0032583) into regulation of transcription, DNA-dependent (GO:0006355) done
- Merge positive regulation of gene-specific transcription (GO:0043193) into positive regulation of transcription, DNA-dependent (GO:0045893) done
- Merge negative regulation of gene-specific transcription (GO:0032582) into negative regulation of transcription, DNA-dependent (GO:0045892) done
- These terms are all already defined in terms of DNA-dependent transcription, so if any annotations were made for "RNA-dependent transcription", they were made incorrectly. However, based on what we have seen, we feel that the vast majority of annotations will be for DNA-dependent transcription. Thus, we are moving the annotations up to the parent term since "gene-specific transcription" isn't a distinct process.
- Three regulation terms for "gene-specific transcription from RNA polymerase II promoter"
- Merge regulation of gene-specific transcription from RNA polymerase II promoter (GO:0010551) into regulation of transcription from RNA polymerase II promoter (GO:0006357) done
- Merge positive regulation of gene-specific transcription from RNA polymerase II promoter (GO:0010552) into positive regulation of transcription from RNA polymerase II promoter (GO:0045944) [NOTE: fix def of 45994, use 'an' instead of 'the' to preface promoter.] done
- Merge negative regulation of gene-specific transcription from RNA polymerase II promoter (GO:0010553) into negative regulation of transcription from RNA polymerase II promoter (GO:0000122) done
- We are just moving all these annotations up to the corresponding parent terms since "gene-specific transcription" isn't a distinct process.
- Three regulation terms for "gene-specific transcription elongation from RNA polymerase II promoter"
- Merge regulation of gene-specific transcription elongation from RNA polymerase II promoter (GO:0090039) into regulation of transcription elongation from RNA polymerase II promoter (GO:0034243) done
- Merge positive regulation of gene-specific transcription elongation from RNA polymerase II promoter (GO:0090040) into positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968) done
- Merge negative regulation of gene-specific transcription elongation from RNA polymerase II promoter (GO:0090041) into negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244) done
- One term for a specific set of RNAP II genes
- positive regulation of gene-specific transcription involved in unfolded protein response (GO:0006990)
- Rename to positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response done
- This term is already defined in terms of RNAP II transcription and already has appropriate is_a parentage under a term that will not be affected by the transcription overhaul.
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