Fate of terms referring to general/nonspecific/basal versus specific transcription: Difference between revisions

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== Annotation counts ==
== Annotation counts ==


Annotation counts via GOOSE (Berkeley BOP) on 3/23/2011 or 3/24/2011 (mediator term only)
Annotation counts via GOOSE (Berkeley BOP) on 3/28/2011


=== grouped by term name and evidence code (non-IEA vs IEA)===
=== grouped by term name and evidence code (non-IEA vs IEA)
<pre>
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
 
...positive regulation of gene-specific transcription involved  BP      8      -      8
        in unfolded protein response
 
............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


<pre>
..........regulation of gene-specific transcription elongation  BP      7      5      12
=== grouped by term name and evidence code (non-IEA vs IEA)
        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


Term name..................................................    aspect  non-IEA IEA    Grand Total
Grand Total...................................................         4234   43401   47635
......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
</pre>
</pre>


=== grouped by annotation source and evidence code (non-IEA vs IEA)===
 
=== grouped by source and evidence code (non-IEA vs IEA)
<pre>
<pre>
Source............     non-IEA IEA    Grand Total
Source.............    non-IEA IEA    Grand Total
.............AspGD      4      84      88
..............AspGD     20     119    139
...............CGD      28     71      99
................CGD     46     91     137
.........dictyBase     45     1      46
..........dictyBase     48     1      49
............EcoCyc     56      2      58
.............EcoCyc     158    2      160
.........EcoliWiki     43      1      44
..........EcoliWiki     126    1      127
...........Ensembl     10      10
............Ensembl     -      10      10
................FB     268     9      277
.................FB     318     9      327
GeneDB_Pfalciparum     3      -      3
.GeneDB_Pfalciparum     3      -      3
.....GeneDB_Spombe     262     3      265
......GeneDB_Spombe     308     3      311
....GeneDB_Tbrucei     1      -      1
.....GeneDB_Tbrucei     1      -      1
..........JCVI_CMR     10      -      10
...........JCVI_CMR     10      -      10
...............MGI     209     16      225
................MGI     760     16      776
...............PDB      389     389
................PDB     39     391     430
............RefSeq     16      16
.............RefSeq     -      16      16
...............RGD     119     53      172
................RGD    506    176    682
...............SGD     276     18     294
................SGD    346    20     366
..............TAIR     13     19      32
...............TAIR     30     19      49
..........TIGR_CMR     21      -      21
...........TIGR_CMR     21      -      21
.........UniProtKB     541     41259   41800
..........UniProtKB    1448    42485   43933
................WB     12     17      29
.................WB     40     17      57
..............ZFIN     2       25      27
...............ZFIN     6       25      31
Grand Total.......     1913   41993   43906
Grand Total........    4234   43401   47635


</pre>
</pre>

Revision as of 15:24, 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.

  1. 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
  2. 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

Reannotation suggestions

(in progress)

    • 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
      • 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

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

...positive regulation of gene-specific transcription involved  BP      8       -       8
        in unfolded protein response

............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

..........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 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