Fate of terms referring to general/nonspecific/basal versus specific transcription

Proposal

We propose to obsolete these 2 Biological Process (BP) and 6 Molecular Function (MF) terms that represent general/nonspecific/basal transcription versus specific transcription.

1. • MF terms:
     • GO:0016251 general RNA polymerase II transcription factor activity
     • GO:0016252 nonspecific RNA polymerase II transcription factor activity
     • GO:0003704 specific RNA polymerase II transcription factor 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

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

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