Proposal: term name changes for GO:0000987, and related

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Issue

An issue has come up with the term "regulatory transcription factor site sequence-specific DNA binding" (GO:0000987) and its children. What I really wanted to describe was binding to the region adjacent to the core promoter. However, the wording I have used (regulatory transcription factor site sequence specific DNA binding) is ambiguous because factors that bind to the enhancer could be described in the same way. I am not even sure that this name excludes basal transcription factors that bind specific DNA sites since it is becoming clear that some regulation occurs at the level of changing the basal factors that are present in a cell, e.g. during development or differentiation.

So, I would like to change the name of the term to mean what I really meant, i.e. "core promoter proximal region sequence-specific DNA binding" for all of these terms.

  • old phrase: regulatory transcription factor site sequence-specific DNA binding
  • new phrase: core promoter proximal region sequence-specific DNA binding

We think this is OK because we don't feel that we're substantially changing the terms, just clarifying the term names and definitions. In the short time that these terms have been in existence, they have been used a little bit, mostly by Val Wood for S. pombe. We have checked with her and these changes don't impact on the meaning she intended for them at the time of annotation.

Affected terms:

Binding terms

  • GO:0000987 - regulatory transcription factor site sequence-specific DNA binding
  • GO:0000978 - RNA polymerase II regulatory transcription factor site sequence-specific DNA binding
  • GO:0000986 - bacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding
  • GO:0001045 - mitochondrial RNA polymerase regulatory transcription factor sequence-specific DNA binding

Transcription factor terms

  • GO:0000982 - sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity
  • GO:0001074 - sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly
  • GO:0001077 - sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in positive regulation of transcription from RNA polymerase II promoter
  • GO:0001078 - sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in negative regulation of transcription from RNA polymerase II promoter

Annotations counts

In the brief time that the terms have existed, some annotations have been made. The breakdown by source (who made it, not which file it is contained in) and evidence code is here. Note that only the RNAP II specific terms (GO:0000978 and GO:0001077) has been used so far.


All annotations to GO:0000978 (from AmiGO)
-------------------------------------------------------
Count of GOID   Evidence
Annotation source   IC  IDA  IMP  ISO  ISS  NAS  RCA  TAS  Grand Total
         BHF-UCL          1              1                    2
   GeneDB_Spombe     6   10    2        44   13    1   14    90
             MGI          3                                   3
             RGD                    1                         1
     Grand Total     6   14    2    1   45   13    1   14    96


All annotations to GO:0001077
-------------------------------------------------------
Count of GOID   evidence
  source        IDA     ISO     ISS     Grand Total
 BHF-UCL        1               2        3
     MGI        5       1                6
     RGD                2                2
Grand Total     6       3       2       11

Proposed new names and definitions:

binding terms

The four binding terms are simpler, with just a direct replacement of the new phrase in place of the old phrase (note that I forgot the word "site" when I created the 986 and 1045 term sfor the bacterial-type and mitochondrial terms.) For the definitions, we are removing reference to transcription factors in accordance with the intent that these just indicate binding to the specified region, so the new defs are simpler.

  • GO:0000987 - core promoter proximal region sequence-specific DNA binding
    existing definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter, but which is bound by a regulatory transcription factor rather than by a basal transcription factor. The transcribed region might be described as a gene, cistron, or operon.
    proposed definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for an RNA polymerase.
  • GO:0000978 - RNA polymerase II core promoter proximal region sequence-specific DNA binding
    existing definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter, but which is bound by a regulatory transcription factor rather than by a basal transcription factor. The transcribed region might be described as a gene, cistron, or operon.
    proposed definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
  • GO:0000986 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding
    existing definition: Interacting selectively and non-covalently with the DNA sequence of regulatory transcription factor binding site that is part of a regulatory region, in addition to the basal promoter, that controls the transcription of a gene or operon by a bacterial-type RNA polymerase.
    proposed definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
  • GO:0001045 - mitochondrial RNA polymerase core promoter proximal region sequence-specific DNA binding
    existing definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a mitochondrial core promoter, but which is bound by a regulatory transcription factor and not by the basal transcription machinery.
    proposed definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a mitochondrial RNA polymerase.

transcription factor terms

The transcription factor terms that use this phrase are trickier to rename the term. The only term with existing annotations is 1077. I have thought of two or three options, depending on the exact term, but maybe others are better still. Basically the issue is that there are several possible places to mention "RNA polymerase II". I don't want to put it in all possible places, so we need to come up with a way to phrase this that seems clear enough but not too redundant. I despise the possible new names I've put in gray and indicated my preference amongst the options I've come with. The definitions are changing to parallel the changes in the DNA binding terms themselves.

GO:0000982

  1. name change
    • existing name: sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity
    • possible new names:
      1. core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity
      2. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (Karen and David's pref)
  2. refinement of definition
    • existing definition: Interacting selectively and non-covalently with the DNA sequence of a regulatory transcription factor binding site that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II (Pol II) in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    • proposed new definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
  3. relationships
    • This term does not have a part_of relationship to "regulation of transcription from RNA polymerase II promoter" (GO:0006357), though the child terms 1077 and 1078 DO have part_of relationships to the corresponding positive and negative regulation terms. this should have the part_of relationship to the regulation term

GO:0001074

  1. name change
    • existing name: sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly
    • possible new names:
      1. core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly
      2. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (Karen and David's pref)
  2. refinement of definition
    • existing definition: Interacting selectively and non-covalently with the DNA sequence of a regulatory transcription factor binding site that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II (Pol II) in order to promote formation of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from the RNA polymerase II promoter.
    • proposed new definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to promote formation of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from the RNA polymerase II promoter.

GO:0001077

  1. name change
    • existing name: sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in positive regulation of transcription from RNA polymerase II promoter
    • possible new names:
      1. core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription from RNA polymerase II promoter
      2. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription from RNA polymerase II promoter
      3. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (Karen and David's pref)
  2. refinement of definition
    • existing definition: Interacting selectively and non-covalently with the DNA sequence of a regulatory transcription factor binding site that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II (Pol II) in order to activate transcription by Pol II.
    • proposed new definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
  3. relationships
    • The 982 term does not have a part_of relationship to "regulation of transcription from RNA polymerase II promoter" (GO:0006357), though the child terms 1077 and 1078 DO have part_of relationships to the corresponding positive and negative regulation terms. see above

GO:0001078

  1. name change
    • existing name: sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in negative regulation of transcription from RNA polymerase II promoter
    • possible new names:
      1. core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in negative regulation of transcription from RNA polymerase II promoter
      2. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription from RNA polymerase II promoter
      3. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (Karen and David's pref)
  2. refinement of definition
    • existing definition: Interacting selectively and non-covalently with the DNA sequence of a regulatory transcription factor binding site that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II (Pol II) in order to repress transcription by Pol II.
    • proposed new definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
  3. relationships
    • The 982 term does not have a part_of relationship to "regulation of transcription from RNA polymerase II promoter" (GO:0006357), though the child terms 1077 and 1078 DO have part_of relationships to the corresponding positive and negative regulation terms. see above


Resolution

  • Names changed as indicated in Proposed new names and definitions: section above. For binding terms, only one option was listed. For transcription factor terms, the option flagged as (Karen and David's pref) was used.
  • Definitions changes as indicated above.
  • Part_of relationship from GO:0000982 to GO:0006357 created, as indicated above.