Fate of "transcription regulator activity" and its remaining child terms

From GO Wiki
Revision as of 16:49, 6 April 2011 by Kchris (talk | contribs) (Reannotation suggestions)

Jump to: navigation, search

Proposal

merge Function term into Process term


  • GO:0030528 MF transcription regulator activity
  • GO:0016563 MF transcription activator activity
  • GO:0042156 MF zinc-mediated transcriptional activator activity
  • GO:0016564 MF transcription repressor activity
  • GO:0003701 MF RNA polymerase I transcription factor activity
  • GO:0003702 MF RNA polymerase II transcription factor activity
  • GO:0003709 MF RNA polymerase III transcription factor activity
  • GO:0003711 MF transcription elongation regulator activity
  • GO:0008148 MF negative transcription elongation factor activity
  • GO:0008159 MF positive transcription elongation factor activity
  • GO:0016943 MF RNA polymerase I transcription elongation factor activity
  • GO:0016944 MF RNA polymerase II transcription elongation factor activity
  • GO:0016945 MF RNA polymerase III transcription elongation factor activity
  • GO:0003715 MF transcription termination factor activity
  • GO:0003716 MF RNA polymerase I transcription termination factor activity
  • GO:0003717 MF RNA polymerase II transcription termination factor activity
  • GO:0003718 MF RNA polymerase III transcription termination factor activity
  • GO:0016986 MF transcription initiation factor activity
  • GO:0030401 MF transcription antiterminator activity


def includes binding


  • GO:0016988 MF transcription initiation factor antagonist activity


related regulation terms


  • GO:0090046 regulation of transcription regulator activity
  • GO:0090047 positive regulation of transcription regulator activity
  • GO:0090048 negative regulation of transcription regulator activity

Comment Period

Date mailed:

Deadline for Comments: TBD - Unless objections are received by April ??????, we will assume that you agree to this change.

Problems

in progress

Function terms with Process definitions

The problem with most of these terms is the same as that for transcription regulator activity (GO:0030528). As we said in the [http://wiki.geneontology.org/index.php/Proposals_to_overhaul_transcription_in_GO_-_2010#transcription_regulator_activity_-_GO:0030528 original proposal], the term "transcription regulator activity" is the highest level Function term for transcription and it is essentially identical to a Process term. It conveys exactly the same information as the Process term regulation of transcription and it does NOT convey any information about the molecular nature of the regulator activity. In addition, it is grouping the child terms below it based on involvement in a common Process, not based on having a common Function and it currently includes functions based on binding DNA and functions based on interacting with other proteins.

MF: transcription regulator activity - GO:0030528 Current definition: Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.

BP: regulation of transcription - GO:0045449 Current definition: Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA.

This problem applies to most of the MF terms that still remain under transcription regulator activity (GO:0030528). All of these terms have definitions that specify only process information; thus we feel that they need to be merged into process terms.

  • GO:0030528 transcription regulator activity
  • GO:0003701 RNA polymerase I transcription factor activity
  • GO:0003702 RNA polymerase II transcription factor activity
  • GO:0003709 RNA polymerase III transcription factor activity
  • GO:0016563 transcription activator activity
  • GO:0042156 zinc-mediated transcriptional activator activity
  • GO:0016564 transcription repressor activity
  • GO:0003711 transcription elongation regulator activity
  • GO:0008148 negative transcription elongation factor activity
  • GO:0008159 positive transcription elongation factor activity
  • GO:0016943 RNA polymerase I transcription elongation factor activity
  • GO:0016944 RNA polymerase II transcription elongation factor activity
  • GO:0016945 RNA polymerase III transcription elongation factor activity
  • GO:0003715 transcription termination factor activity
  • GO:0003716 RNA polymerase I transcription termination factor activity
  • GO:0003717 RNA polymerase II transcription termination factor activity
  • GO:0003718 RNA polymerase III transcription termination factor activity
  • GO:0016986 transcription initiation factor activity
  • GO:0030401 transcription antiterminator activity

what about this one?

Issues for these terms:

  • GO:0003706 MF ligand-regulated transcription factor activity


rework, or merge into another MF term?

def includes binding


  • GO:0016988 MF transcription initiation factor antagonist activity


Regulation terms for "transcription regulator activity"


  • GO:0090046 regulation of transcription regulator activity
  • GO:0090047 positive regulation of transcription regulator activity
  • GO:0090048 negative regulation of transcription regulator activity



Reannotation suggestions

merge Function term into Process term


  • For top level MF term: GO:0030528 transcription regulator activity
    - Existing definition already specifies DNA, so we can clearly select a "transcription, DNA-dependent" term without being concerned about the RNA-dependent type of transcription.
    - We considered both transcription, DNA-dependent (GO:0006351) and regulation of transcription, DNA-dependent (GO:0006355) and we looked at some existing annotations to transcription regulator activity to consider which of these two terms would be most appropriate to transfer them to. While the majority of annotations (from both MGI and SGD) are "regulatory" transcription factors, the SGD set of annotations, which was small enough to look at in its entirety, includes annotations for basal transcription factors and RNA polymerase subunits, via both manual and computational methods. Thus, we felt that the term has been used so broadly that it would be better to select the more general term.
    merge into BP term: transcription, DNA-dependent (GO:0006351)
  • For other high level terms, not specific to a particular RNAP
    - These definitions do not mention DNA specifically, but the terms are direct children of "transcription regulator activity".
    - Based on a quick glance at some of the annotations and the logic we used for the merge of the transcription BP terms into the transcription, DNA-dependent BP terms, we think this is reasonable, i.e. that there will be very little which should actually be annotated to a transcription, RNA-dependent term instead.
    • GO:0016563 transcription activator activity
      merge into BP term positive regulation of transcription, DNA-dependent (GO:0045893)
    • GO:0016564 transcription repressor activity
      merge into BP term negative regulation of transcription, DNA-dependent (GO:0045892)
    • GO:0003711 transcription elongation regulator activity
      merge into BP term regulation of transcription elongation, DNA-dependent (GO:0032784)
    • GO:0008148 negative transcription elongation factor activity
      merge into BP term negative regulation of transcription elongation, DNA-dependent (GO:0032785)
    • GO:0008159 positive transcription elongation factor activity
      merge into BP term positive regulation of transcription elongation, DNA-dependent (GO:0032786)


  • Three terms for transcription factors for specific (eukaryotic nuclear) RNAPs
    - These terms mention specific RNA polymerases, so there is no confusion with respect to DNA-dependent vs RNA-dependent.
    - The definitions of these terms say "Functions to initiate or regulate RNA polymerase ____ transcription." Thus these definitions encompass both the basal or essential factors required for PIC assembly as well as any factors which might regulate transcription by one of these RNAPs. Thus we think that the general terms are a better option than the regulation terms.
    • GO:0003701 RNA polymerase I transcription factor activity
      merge into BP term:
      • transcription from RNA polymerase I promoter (GO:0006360)
    • GO:0003702 RNA polymerase II transcription factor activity
      merge into BP term:
      • GO:0006366 transcription from RNA polymerase II promoter
    • GO:0003709 RNA polymerase III transcription factor activity
      merge into BP term:
      • GO:0006383 transcription from RNA polymerase III promoter
  • Six terms relating to transcription elongation
    - The first three of these


  • GO:0016943 MF RNA polymerase I transcription elongation factor activity
  • GO:0016944 MF RNA polymerase II transcription elongation factor activity
  • GO:0016945 MF RNA polymerase III transcription elongation factor activity
  • GO:0003715 MF transcription termination factor activity
  • GO:0003716 MF RNA polymerase I transcription termination factor activity
  • GO:0003717 MF RNA polymerase II transcription termination factor activity
  • GO:0003718 MF RNA polymerase III transcription termination factor activity
  • GO:0016986 MF transcription initiation factor activity
  • GO:0030401 MF transcription antiterminator activity


    • GO:0042156 zinc-mediated transcriptional activator activity
      Def: Initiates or upregulates transcription in the presence of zinc.
      Brief look at PMID:10952993 indicates that they show MTF-1 binds DNA in the presence of zinc (EMSA), not sure if this shows direct binding to zinc, or if we care
      only existing term for any kind of regulation of transcription in relation to zinc is not appropriate
      • regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation (GO:0034225)
      convert to BP term?
      • positive regulation of DNA-dependent transcription in response to zinc


??


  • GO:0003706 MF ligand-regulated transcription factor activity

def includes binding


  • GO:0016988 MF transcription initiation factor antagonist activity


related regulation terms


  • GO:0090046 regulation of transcription regulator activity
  • GO:0090047 positive regulation of transcription regulator activity
  • GO:0090048 negative regulation of transcription regulator activity

Supporting information

Annotation counts

via GOOSE (Berkeley BOP) on 3/30/2011

=== Summary of GO annotation counts, by source ===

Source............      non-IEA IEA     Grand Total
..............ASAP      9       -       9
.............AspGD      17      51      68
...............CGD      71      35      106
.........dictyBase      36      33      69
............EcoCyc      337     30      367
.........EcoliWiki      146     40      186
...........Ensembl      -       208     208
................FB      374     126     500
GeneDB_Pfalciparum      4       -       4
.....GeneDB_Spombe      56      7       63
....GeneDB_Tbrucei      4       -       4
........GR_protein      306     -       306
..........JCVI_CMR      314     -       314
...............MGI      888     345     1233
..............NCBI      2       -       2
...............PDB      4       753     757
.........PseudoCAP      142     -       142
............RefSeq      -       129     129
...............RGD      763     478     1241
...............SGD      186     54      240
...............SGN      1       -       1
..............TAIR      315     79      394
..........TIGR_CMR      299     -       299
.........UniProtKB      1650    93884   95534
................WB      36      167     203
..............ZFIN      61      576     637
Grand Total.......      6021    96995   103016
=== Summary of GO annotation counts, by term ===

GO Term......................................................   aspect  non-IEA IEA     Grand Total
.............................transcription regulator activity   MF      1238    62032   63270

.............................transcription activator activity   MF      2354    6847    9201
.............zinc-mediated transcriptional activator activity   MF      10      7       17
.............................transcription repressor activity   MF      1554    9353    10907

...............RNA polymerase I transcription factor activity   MF      32      12      44
..............RNA polymerase II transcription factor activity   MF      383     3913    4296
.............RNA polymerase III transcription factor activity   MF      49      13      62

..................transcription elongation regulator activity   MF      69      8348    8417
............negative transcription elongation factor activity   MF      12      7       19
............positive transcription elongation factor activity   MF      23      150     173
....RNA polymerase I transcription elongation factor activity   MF      -       -       -
...RNA polymerase II transcription elongation factor activity   MF      54      125     179
..RNA polymerase III transcription elongation factor activity   MF      -       -       -

....................transcription termination factor activity   MF      80      5011    5091
...RNA polymerase I transcription termination factor activity   MF      17      4       21
..RNA polymerase II transcription termination factor activity   MF      5       3       8
.RNA polymerase III transcription termination factor activity   MF      2       -       2

.....................transcription initiation factor activity   MF      39      699     738
........................transcription antiterminator activity   MF      43      420     463

...............ligand-regulated transcription factor activity   MF      39      33      72

..........transcription initiation factor antagonist activity   MF      3       4       7

.............. regulation of transcription regulator activity   BP      -       -       -
......positive regulation of transcription regulator activity   BP      15      14      29
......negative regulation of transcription regulator activity   BP      -       -       -

Grand Total..................................................           6021    96995   103016

Subsets

All subsets for "transcription regulator activity"

  • Prokaryotic GO subset
  • Candida GO slim
  • GOA and proteome slim
  • PIR GO slim
  • Plant GO slim
  • Yeast GO slim

Prokaryotic GO subset

  • GO:0030528 - transcription regulator activity
  • GO:0016563 - transcription activator activity
  • GO:0016564 - transcription repressor activity
  • GO:0016986 - transcription initiation factor activity
  • GO:0016988 - transcription initiation factor antagonist activity
  • GO:0003711 - transcription elongation regulator activity
  • GO:0003715 - transcription termination factor activity
  • GO:0030401 - transcription antiterminator activity

Terms not in subsets

  • GO:0042156 zinc-mediated transcriptional activator activity
  • GO:0003701 - RNA polymerase I transcription factor activity
  • GO:0003702 - RNA polymerase II transcription factor activity
  • GO:0003709 - RNA polymerase III transcription factor activity
  • GO:0008159 - positive transcription elongation factor activity
  • GO:0008148 - negative transcription elongation factor activity
  • GO:0016943 - RNA polymerase I transcription elongation factor activity
  • GO:0016944 - RNA polymerase II transcription elongation factor activity
  • GO:0016945 - RNA polymerase III transcription elongation factor activity
  • GO:0003716 - RNA polymerase I transcription termination factor activity
  • GO:0003717 - RNA polymerase II transcription termination factor activity
  • GO:0003718 - RNA polymerase III transcription termination factor activity
  • GO:0090046 - regulation of transcription regulator activity
  • GO:0090047 - positive regulation of transcription regulator activity
  • GO:0090048 - negative regulation of transcription regulator activity


Sample of existing annotations to transcription regulator activity

downloaded from SGD April 2011

Manual annotations for S. cerevisiae genes

Gene                            Annot
Name    Evidence        Date    Source  Description
BRE2    ISS             4/2/03  SGD     Subunit of COMPASS (Set1C) complex, which methylates Lys4 of histone H3 and functions in silencing at telomeres
ASK10   TAS             3/11/03 SGD     Component of RNA polymerase II holoenzyme, phosphorylated in response to oxidative stress
RLF2    IMP             2/16/05 SGD     Largest subunit (p90) of the Chromatin Assembly Complex (CAF-1) with Cac2p and Msi1p that assembles newly synthesized histones onto recently replicated DNA
DEP1    IMP             2/9/06  SGD     Transcriptional modulator involved in regulation of structural phospholipid biosynthesis genes and metabolically unrelated genes, as well as maintenance of telomeres, mating efficiency, and sporulation
BDF1    ISS|IMP         3/11/03 SGD     Protein involved in transcription initiation at TATA-containing promoters
UME6    IMP|IDA         2/26/02 SGD     Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p
UME6    IMP|IDA         2/26/02 SGD     Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p
IME1    TAS             3/11/03 SGD     Master regulator of meiosis that is active only during meiotic events, activates transcription of early meiotic genes through interaction with Ume6p, degraded by the 26S proteasome following phosphorylation by Ime2p
MSI1    IMP             2/16/05 SGD     Subunit of chromatin assembly factor I (CAF-1), negative regulator of the RAS/cAMP pathway via sequestration of Npr1p kinase
LAP3    IDA             9/30/02 SGD     Cysteine aminopeptidase with homocysteine-thiolactonase activity
SUS1    IDA             2/17/09 SGD     Protein involved in mRNA export coupled transcription activation and elongation
GTS1    IDA|IPI         4/14/08 SGD     Arf3p GTPase Activating Protein (GAP) that localizes to endocytic patches
RTG2    IDA             5/8/03  SGD     Sensor of mitochondrial dysfunction
LRE1    IDA             10/1/02 SGD     Protein involved in control of cell wall structure and stress response
CAC2    IMP             2/16/05 SGD     Component of the chromatin assembly complex (with Rlf2p and Msi1p) that assembles newly synthesized histones onto recently replicated DNA, required for building functional kinetochores, conserved from yeast to humans

Computational annotations for S. cerevisiae genes

Gene                                                                    Annot
Name    Ev Code With (or) From                                  Date    Source          Description
YOX1    IEA     EBI:IPR017970                                   1/10/11 InterPro        Homeodomain-containing transcriptional repressor, binds to Mcm1p and to early cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed in M/G1 phase
YHP1    IEA     EBI:IPR017970                                   1/10/11 InterPro        One of two homeobox transcriptional repressors (see also Yox1p), that bind to Mcm1p and to early cell cycle box (ECB) elements of cell cycle regulated genes, thereby restricting ECB-mediated transcription to the M/G1 interval
PHO2    IEA     EBI:IPR017970                                   1/10/11 InterPro        Homeobox transcription factor
RPA12   IEA     EBI:IPR001222                                   1/10/11 InterPro        RNA polymerase I subunit A12.2
RPB9    IEA     EBI:IPR001222                                   1/10/11 InterPro        RNA polymerase II subunit B12.6
TYE7    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Serine-rich protein that contains a basic-helix-loop-helix (bHLH) DNA binding motif
MAF1    IEA     EBI:IPR017152                                   1/10/11 InterPro        Negative regulator of RNA polymerase III
INO2    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Component of the heteromeric Ino2p/Ino4p basic helix-loop-helix transcription activator that binds inositol/choline-responsive elements (ICREs), required for derepression of phospholipid biosynthetic genes in response to inositol depletion
HAP4    IEA     EBI:IPR018287                                   1/10/11 InterPro        Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression
HMRA1   IEA     EBI:IPR017970                                   1/10/11 InterPro        Silenced copy of a1 at HMR
DST1    IEA     EBI:IPR001222|EBI:IPR010990                     1/10/11 InterPro        General transcription elongation factor TFIIS, enables RNA polymerase II to read through blocks to elongation by stimulating cleavage of nascent transcripts stalled at transcription arrest sites
HIR1    IEA     EBI:IPR011494|EBI:IPR019015                     1/10/11 InterPro        Subunit of the HIR complex, a nucleosome assembly complex involved in regulation of histone gene transcription
YAP7    IEA     EBI:IPR018287                                   1/10/11 InterPro        Putative basic leucine zipper (bZIP) transcription factor
PHO4    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Basic helix-loop-helix (bHLH) transcription factor of the myc-family
CDC36   IEA     EBI:IPR007282                                   1/10/11 InterPro        Component of the CCR4-NOT complex, which has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs by deadenylation
RTG1    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Transcription factor (bHLH) involved in interorganelle communication between mitochondria, peroxisomes, and nucleus
YKR023W IEA     EBI:IPR009349                                   1/10/11 InterPro        Putative protein of unknown function
RPL7A   IEA     EBI:IPR005998                                   1/10/11 InterPro        Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins
HIR2    IEA     EBI:IPR011494                                   1/10/11 InterPro        Subunit of the HIR complex, a nucleosome assembly complex involved in regulation of histone gene transcription
NOT5    IEA     EBI:IPR007282|EBI:IPR007207|EBI:IPR012270       1/10/11 InterPro        Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation
RTG3    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor that forms a complex with another bHLH/Zip protein, Rtg1p, to activate the retrograde (RTG) and TOR pathways
RPL7B   IEA     EBI:IPR005998                                   1/10/11 InterPro        Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Ap and has similarity to E. coli L30 and rat L7 ribosomal proteins
HMS1    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Basic helix-loop-helix (bHLH) protein with similarity to myc-family transcription factors
CBF1    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Helix-loop-helix protein that binds the motif CACRTG, which is present at several sites including MET gene promoters and centromere DNA element I (CDEI)
TAF5    IEA     EBI:IPR007582                                   1/10/11 InterPro        Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification
INO4    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Transcription factor required for derepression of inositol-choline-regulated genes involved in phospholipid synthesis
RPC11   IEA     EBI:IPR001222                                   1/10/11 InterPro        RNA polymerase III subunit C11
NOT3    IEA     EBI:IPR007282|EBI:IPR007207|EBI:IPR012270       1/10/11 InterPro        Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation
SUA7    IEA     EBI:IPR000812                                   1/10/11 InterPro        Transcription factor TFIIB, a general transcription factor required for transcription initiation and start site selection by RNA polymerase II
BRF1    IEA     EBI:IPR000812                                   1/10/11 InterPro        TFIIIB B-related factor, one of three subunits of RNA polymerase III transcription initiation factor TFIIIB, binds TFIIIC and TBP and recruits RNA pol III to promoters, amino-terminal half is homologous to TFIIB