This request follows from the annotation conference call held on 26th July 2011
http://wiki.geneontology.org/index.php/Transcription_jamboree
Firstly need to establish what transcription repressor relevant terms exist.
GO:0003714 transcription corepressor activity
Definition Interacting selectively and
covalently with a repressing
transcription factor and also with the
transcription machinery in order to
prevent, or reduce the frequency, rate
transcription. Cofactors generally do
DNA, but rather mediate proteininteractions between repressive
transcription factors and the basal
transcription machinery.
nonbasal
stop,
or extent of
not bind
protein
Has_part child:
GO:0070491 repressing transcription
binding
factor
Definition Interacting selectively and
covalently with a transcription
any protein whose activity is required
or downregulate transcription.
nonrepressor,
to prevent
Is_ a child
GO:0001103 RNA polymerase II
transcription factor binding
repressing
Definition Interacting selectively and non-covalently with an RNA polymerase II
transcription repressing factor, a protein involved in negative regulation of transcription.
Sorry I know this is going to be a complex email so I am numbering each point.
1. Because there is no actual GO term for transcription repressing factor activity it is
difficult to know how to interpret these co-repressor terms. From the definition in the 3
terms above I think that a co-repressor can also be described as a ‘repressing
transcription factor’, which seems to be defined as ‘any protein whose activity is required
to prevent or downregulate transcription’ ie a repressor or a co-repressor or histone
deacetylase.
In which case if an experiment shows 2 proteins which downregulate mRNA transcription
bind each other then we can annotate both proteins with
GO:0001103 RNA polymerase II repressing transcription factor binding.
However, if we can annotate protein A binds protein B with a such a specific binding term,
based on the fact that protein B has a particular activity, then we should also be able to
annotate protein B as having that particular activity. So in this case we would like to be
able to use the term “RNA polymerase II repressing transcription factor activity” to describe
a protein that negatively regulates transcription by binding a regulatory region of DNA.
2. I have several problems with the definition for
GO:0003714 transcription corepressor activity
Definition Interacting selectively and non-covalently with a repressing transcription factor
and also with the basal transcription machinery in order to stop, prevent, or reduce the
frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather
mediate protein-protein interactions between repressive transcription factors and the basal
transcription machinery.
a) Interacting selectively and non-covalently with a repressing transcription factor
(which seems to be defined as ‘any protein whose activity is required to prevent or
downregulate transcription’, ie a repressor or a co-repressor or histone deacetylase).
a. I think this is fine, although I am not sure that repressing TF is meant to be
this broad? Having a term and a def for repressing TF activity will help with
this.
b) Interacting selectively and non-covalently with the basal transcription machinery
a. Very few papers describing human proteins with co-repressor activity will
demonstrate that the protein interacts selectively and non-covalently with the
basal transcription machinery. This therefore substantially reduces the
number of human proteins which can be described as being co-repressors.
b. The term GO:0003712 transcription cofactor activity also includes this
statement and therefore the only GO terms available for proteins which do
not have evidence that they bind basal transcription machinery is
GO:0000989 transcription factor binding transcription factor activity, which is
used for both activators and repressors.
c. It would be helpful to have a GO term for basal transcription machinery
(presumably the RNA polymerase preinitiation complex), the best I could find
was in the GO term GO:0001098 basal transcription machinery binding;
Definition Interacting selectively and non-covalently with the basal
transcription machinery which is composed of the RNA polymerase core
enzyme and the basal transcription factor(s), the minimal set of factors
required for formation of the preinitiation complex (PIC) by the RNA
polymerase.
c) Interacting selectively and non-covalently with a repressing transcription factor,
therefore presumably we can do IPI annotations to this term?
d) Cofactors generally do not bind DNA,
a. So if the protein binds DNA we cannot annotate it to GO:0003714
transcription corepressor activity?
b. Or could this sentence be modified to: Some cofactors bind DNA, but in
general cofactors mediate protein-protein interactions between repressive
transcription factors and the basal transcription machinery.
3. How are we going to capture information about the following hypothetical proteins,
which are members of well characterised TF repressor or TF co-repressor families?
a) binds DNA, represses transcription, is not shown to bind basal transcription
machinery or any other proteins? Ie a co-repressor (or repressor) without repressing TF
binding basal transcription machinery binding evidence.
b) binds DNA, represses transcription, binds another protein which also represses
transcription but is not shown to bind basal transcription machinery? Ie a co-repressor (or
repressor) without basal transcription machinery binding evidence.
c) represses transcription, binds another protein which also represses transcription
but is not shown to bind DNA or basal transcription machinery? Ie a co-repressor without
basal transcription machinery binding evidence.
4. The suggestion has been made that we need a more general repressor activity term
such as:
RNA polymerase II repressing transcription factor activity
Definition: a protein that negatively regulates transcription by binding a specific sequence
within a regulatory region of DNA.
AND
sequence-specific DNA binding, transcription factor activity, co-repressor recruiting,
involved in negative regulation of transcription
Definition: a protein that negatively regulates transcription by binding a specific sequence
within a regulatory region of DNA and recruiting co-repressors to this region.
Example paper that has been annotated
PMID: 19162039 Hepatoma-derived growth factor represses SET and MYND domain
containing 1 gene expression through interaction with C-terminal binding protein.
Abstract (edited)
Hepatoma Derived Growth Factor (HDGF) is a nuclear protein. Oligonucleotide microarray
analysis was used to gain insights into HDGF function. Adenoviral expression of HDGF
significantly (≥ 2 fold) downregulated a large group (66) of genes, and increased
expression of a relatively small number of genes (9). In a one-hybrid system, GBD-HDGF
significantly repressed reporter gene activity in a dose dependent manner. This
demonstrated that HDGF has transcriptional repressive activity. Moreover, in G-7 myoblast
cells, overexpression of a GFP-HDGF fusion specifically downregulated SMYD1 mRNA
expression and the activity of the human SMYD1 promoter. HDGF repressed SMYD1
gene transcription through interaction with a transcriptional corepressor C-terminal binding
protein (CtBP). Overexpressing of CtBP potentiated the trans-repressive activity of HDGF;
on the other hand, knocking down CtBP attenuated the trans-repressive effect of HDGF.
HDGF binds CtBP through a non-canonical binding motif (PKDLF) within the PWWP
domain, as substitutional mutation of DL to AS abolished HDGF and CtBP interaction and
diminished the trans-repressive effect of HDGF without affecting DNA binding. Finally,
fluorescent microscopy studies showed that HDGF induced the nuclear accumulation of
CtBP suggesting that HDGF forms a transcriptional complex with CtBP. Taken together,
our data demonstrate that HDGF functions as a transcriptional repressor of the SMYD1
gene, through interaction with the transcriptional corepressor CtBP.
Annotations created:
I have annotated HDGF as having transcription corepressor activity, but the authors
suggest it has transcription repressor activity.
CTBP1 is described by authors as a transcription corepressor, and has no repressing
activity alone, only represses transcription when HDGF is present.
I have also annotated CTBP1 as binding a repressing transcription factor (HDGF)
And HDGF as binding a transcription corepressor (CTBP1)
We should be able to annotate to repressing transcription factor activity if we can annotate
a protein as binding a repressing transcription factor.
Note that the species source for some of the constructs in the paper are not available.