Transcription jamboree
Examples for discussion at electronic Transcription Jamboree
Resources for curators
- Karen's curation manual
How much evidence is needed to make MF annotations
i) PMID 11486045 [VK] - Fig 2
How much evidence is needed to make MF annotations
i) PMID 11486045 [VK] - Fig 2 - this data would have been previously annotated to the now obsolete term GO:0016564 transcription repressor activity.
- can we can we annotate to anything more than the biological process: 'GO:00045892; negative regulation of transcription, DNA-dependent', and 'DNA binding' as the molecular function?
- There is no indication anymore in the available MF terms of a proteins repressor activity, concerns about losing this information.
- if we can discribe the binding of a protein as activating transcription in the molecular function ontology (GO 0001102 RNA polymerase II activating transcription factor binding ), why are we no longer able state that a transcription factor is activating or repressing in its activity?
Annotation to promoter/DNA binding terms
- Could we use one of the diagram of the promoter/regulatory regions which bind proteins - and identify the protein things that bind to distinct regions? - DNA binding or binds to a region of the DNA in particular - so curators can more easily identify a proximal region (is this region 5' or 3' located)
- if a curator is trying to describe the up-regulation of a protein-encoding gene, then is it correct to assume that regulation of expression would necessarily be via the RNA polymerase II. We shouldn't need direct evidence demonstrating the involvement of RNA polymerase II?
gene product i) PMID 12270142 [VK]
Based on figs 1 and 2 have annotated to
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
Based on fig 3 have annotated to
GO:2000679 positive regulation of transcription regulatory region DNA binding
Is this correct or are there other terms that should have been used instead?
ii) PMID 17332325 [VK]
Is Fig 3 sufficient to support the following annotations?
GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity
GO:0070888 E-box binding
iii) PMID 19342457 [YAF]
Based on Figs 1 and 3 I have annotated REST_HUMAN (Q13127) to:
GO:0000987 core promoter proximal region sequence-specific DNA binding
GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
Not sure if these are correct.
iv) PMID 17130167 [YAF]
Based on Figs 2, 5 and 6, I have tentatively annotated to
GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
GO:0045892 negative regulation of transcription, DNA-dependent
v) PMID 17984088 [YAF]
Based on Fig 1 I have annotated REST_H Q13127 to
GO:0001047 core promoter binding
GO:0045892 negative regulation of transcription, DNA-dependent
GO:0045893 positive regulation of transcription, DNA-dependent
and based on Fig 4 I have annotated BRM_H P51531 to
GO:0045893 positive regulation of transcription, DNA-dependent
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0044212 transcription regulatory region DNA binding
vi) PMID 20590529 [RH]
Based on Fig. 3 (p240) have annotated MEF2A (Q02078) and MEF2D (Q14814) to;
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
(may not be enough evidence for the second annotation; extract: "we performed a time-course analysis of c-Jun expression in PMA-differentiated cells.MEF2A and MEF2D proteins were induced within 2 h of treatment, before c-Jun, whose up-regulation was seen after 4 h (Figure 3B). These data support the idea that c-Jun is regulated by MEF2 in HL60 cells."
Possible full papers for jamboree
PMID 18062917 [VK]