aurelian 0.3.2__py3-none-any.whl

aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines.md

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+Gene Ontology guidelines for transcription factor
+annotation
+
+Authors: Pascale Gaudet, Colin Logie, Ruth Lovering
+Date last updated: 2023-10-24
+
+GO has refactored the MF branch representing the activities of proteins involved in transcription.
+In addition to RNA polymerase, we defined three different types of activities involved in
+transcription and its regulation:
+
+I. GTFs: General transcription factors, the molecular machine that assembles
+with the RNA polymerase at the promoter to form the pre-initiation complex (PIC).
+II. dbTFs: Specific DNA binding transcription factors that provide genomic
+addresses and specify the cell types and the conditions under which specific
+genes are expressed. Central to dbTF function is their binding to specific DNA
+sequences (often named transcription factor binding sites (TFBS), and
+III. coTFs: Transcription coregulators (also known as transcription cofactors)
+serve multiple functions, such as bridging the GTF and the dbTFs, specifying the
+regulatory effect of DbTFs, modifying the chromatin structure to render it more or
+less accessible for transcription. coTFs normally exert their function independent
+of high affinity binding to specific DNA sequences.
+
+The present guidelines aim to help curators apply the revised transcription terms. Please use
+more specific child terms whenever possible.
+
+GTFs annotations should include, depending on the evidence available:
+
+●  MF
+
+○  GO:0140223 general transcription initiation factor activity
+
+●  BP
+
+○  GO:0006351 transcription, DNA-templated
+
+●  CC
+
+is active in GO:0000785 chromatin
+
+○
+○  part of GO:0097550 transcriptional preinitiation complex
+
+dbTFs annotations may include:
+
+●  MF
+
+○  GO:0003700 DNA binding transcription factor activity
+
+1
+
+■  GO:0001228 DNA-binding transcription activator activity, RNA
+
+polymerase II-specific
+
+■  GO:0001227 DNA-binding transcription repressor activity, RNA
+
+polymerase II-specific
+
+○  GO:0000987 cis-regulatory region sequence-specific DNA binding
+
+■  GO:0000978 RNA polymerase II cis-regulatory region sequence-specific
+
+●  BP
+
+DNA binding
+
+○  GO:0006355 regulation of transcription, DNA-templated,
+
+■  GO:0045893 positive regulation of transcription, DNA-templated children
+■  GO:0045892 negative regulation of transcription, DNA-templated children
+
+●  CC
+
+is active in GO:0000785 chromatin
+
+○
+○  part of GO:0005667 transcription factor complex
+
+coTFs annotations may include:
+
+Note that coTFs perform a wide range of functions, the common functions are listed below,
+however, this list is not exhaustive:
+
+●  MF
+
+○  GO:0003712 transcription coregulator activity
+
+■  GO:0003713 transcription coactivator activity
+■  GO:0003714 transcription corepressor activity
+
+○  GO:0140097 catalytic activity, acting on DNA
+
+■  GO:0009008 DNA-methyltransferase activity
+■  etc
+
+○  GO:0140096 catalytic activity, acting on a protein
+■  GO:0033558 protein deacetylase activity
+
+●  GO:0004407 histone deacetylase activity
+
+○  GO:0030234 enzyme regulator activity
+
+■  GO:0035034 histone acetyltransferase regulator activity
+■  GO:0035033 histone deacetylase regulator activity
+
+○  GO:0140297 DNA-binding transcription factor binding
+
+●  BP
+
+○  GO:0006355 regulation of transcription, DNA-templated
+○  GO:0031507  heterochromatin assembly
+
+■
+■
+■
+■
+
+ GO:0140719 constitutive heterochromatin assembly
+ GO:0140718 facultative heterochromatin assembly
+ GO:0071514 genomic imprinting
+ GO:0033696 heterochromatin boundary formation
+
+○  GO:0016570 histone modification
+
+2
+
+■  GO:0031056 regulation of histone modification
+
+○  GO:0006304 DNA modification
+
+■  GO:0006306 DNA methylation
+
+●  GO:0044030 regulation of DNA methylation
+
+●  CC
+
+is active in GO:0000785 chromatin
+
+○
+○  part of GO:0005667 transcription factor complex
+
+Other transcription regulator activities
+
+There are also proteins that inhibit dbTFs, for example by sequestering them in the cytoplasm or
+nucleus (‘dbTF-inhibitors’). The difference between coTFs and dbTF regulators is that the latter
+do not act at the genomic location of target regulated gene, whereas coTFs are associated with
+the transcriptional regulatory complex. Therefore, the input of the coTF is the dbTF, not the
+target gene.
+ MF
+
+●
+
+○  GO:0140416 DNA-binding transcription factor inhibitor activity
+○
+●  BP:
+
+looking for example for positive regulators
+
+○  GO:0006355 regulation of transcription, DNA-templated
+
+●  CC
+
+○  as appropriate
+
+Annotation extensions
+
+-  MF and BP: target gene of a dbTF or a coTF: has_input [dbTF]
+-  MF localization: is_active in [GO:cellular component, cell, tissue….]
+-  BP localization: occurs_in [GO:cellular component, cell, tissue….]
+
+Annotating a transcription regulator from experimental data
+
+The following annotation approach follows the strategy that we currently recommend, to ensure
+that curators use all information available, and do not restrict to annotating papers individually
+and out of the more general context. Note that the information does not necessarily need to be
+extracted from a single paper; reviewing a wide range of papers is recommended to ensure
+annotations are as accurate as possible, so that annotations are based on multiple observations
+from different articles and independent research groups.
+
+The following four questions provide a checklist to assess whether a gene can be annotated as
+a transcriptional regulator:
+
+3
+
+1.  What is the starting hypothesis: are the authors characterizing a transcription
+
+regulator? Scientific models are built by adding new data to the existing corpus of
+evidence. New data can either support or contradict existing models. The introduction
+section of research articles can be used to understand what prior knowledge the article
+builds on, and what aspect of the existing model or what new model the authors are
+assessing. The intent of the authors is essential to understand what GO term should be
+chosen, with the caveat that inconsistent terminology has been used in transcription
+research articles and therefore may not always be consistent with the GO term labels.
+Curators must look carefully at the GO term definitions and the placement of the term in
+the ontology to ensure that the meaning of the GO term corresponds to the concept
+being described in the article.
+
+2.  Does knowledge from specific protein domains or characterized orthologs
+
+support the hypothesis?
+The presence of specific domains and the existence of well characterized orthologs can
+provide useful support for interpreting experimental data. Note that domain information
+and sequence homology data should be used very carefully: not all domains have a
+single function; and only closely related orthologs whose function have been
+unambiguously characterized can be used to support the association of a gene with a
+GO term, if those are consistent with the experimental data presented in the article.
+
+a.  GTFs: GTFs have been characterized in several organisms, from bacteria, to
+yeast, to mammalian cells (PMID:25693126), and therefore orthology should
+provide strong support for the decision to associate these proteins with a child
+specific for RNA polymerase I, II or III of the MF term "GO:0140223 general
+transcription initiation factor activity". In addition, the naming of GTFs is well
+established across human and model organism nomenclature groups and can be
+used to help guide these decisions. Thus, for human GTFs the HUGO Gene
+Nomenclature Committee (HGNC, www.genenames.org) provide the gene
+symbol TAF#, for TATA-box binding protein associated factors, and GTF2#s and
+GTF3#s, for general transcription factor II and III subunits respectively, although
+a few GTFs have more specific names such as BTAF1: B-TFIID TATA-box
+binding protein associated factor 1.
+
+b.  dbTFs: Gene products associated with the GO term "GO:0003700 DNA-binding
+transcription factor activity" should have experimental evidence to confirm
+their ability to bind DNA and that this binding regulates the expression of a
+limited set of target genes. In these cases the direct target gene(s) can also be
+included in the annotation using the "has input relation". Proteins that belong to
+families of well characterized transcription factors, such as those that contain
+GATA and homeobox domains and proteins with a one-to-one ortholog already
+demonstrated to be a dbTF, weaker evidence of DNA binding, such as ChIP
+experiments is sufficient. For proteins with domains known to be associated with
+
+4
+
+functions other than DNA binding (such as zinc fingers) or proteins with
+enzymatic activity, strong evidence of DNA binding is required.
+
+In addition, in some cases, neither the protein nor a member of the protein’s
+family will have been previously associated with the dbTF activity term. In these
+cases, clear experimental evidence of sequence-specific DNA binding and gene
+transcription regulation via cognate DNA motifs located in gene-associated
+cis-regulatory modules will be required for the protein to be classified as a dbTFs.
+
+c.  coTFs: A coTF is defined as a protein that interacts specifically with a dbTF or a
+coTF at a cis-regulatory region (GO:0003712). This interaction either activates or
+represses the transcription of specific genes, often acting by altering chromatin
+structure and modifications. There are many roles that coregulators can play: for
+example, one class of transcription coregulators modifies chromatin structure
+through covalent modification of histones. A second class of coregulators
+modifies the conformation of chromatin in an ATP-dependent manner. A third
+class modulates interactions of dbTFs with other coTFs.
+
+Many coTFs have enzymatic activity and do not bind DNA. For coTFs that do
+bind DNA, many recognize very short, common DNA sequences, not sufficiently
+unique to enable the coTF to regulate the expression of a limited set of genes in
+a discrete environmental or developmental stage (for example AT-hook coTFs).
+
+The distinction between a dbTF and a coTF can be difficult to make, so a more
+exhaustive review of the literature, including looking at the characterized
+orthologs, is highly recommended before annotating a coTF.
+
+3.  Are there other GO annotations or published experimental results consistent with
+
+the hypothesis ?
+Keeping in mind the gene-by-gene/pathway-by-pathway annotation approach, it can be
+valuable to take into account results from other research articles, to make sure results
+and annotations are consistent. Curators should avoid creating annotations that are
+inconsistent with existing annotations, by either choosing a different term for annotation,
+or by reviewing and eventually disputing annotations that appear to be incorrect (see
+next section).
+
+4.  Are the experimental results consistent with the hypothesis ?
+
+The curator should carefully look at the results presented in the paper and, if those are
+consistent with the hypothesis that this is a transcription regulator, then appropriate GO
+annotations can be made.
+
+Note that DNA-binding transcription factors as well as co-regulators often act as activators or
+repressors in different promoters or dependent on the context, so annotation to both activator
+
+5
+
+and repressor is not considered inconsistent. This may be further resolved through additional
+context details, e.g. cell type, environmental conditions, etc.
+
+Reviewing existing annotations
+
+If time allows, it is very useful for the research community and for future annotation that other
+annotations associated with the gene be reviewed. If there are conflicting annotations, then the
+supporting data should be reviewed to see whether the annotations are inconsistent with the
+data, in which case annotations should be fixed.
+
+In cases where the primary data is conflicting across different papers (for example a protein is
+sometimes described as a transcription factor, and sometimes as a coregulator), then the
+literature should be reviewed carefully to decide whether:
+
+i.
+ii.
+
+iii.
+
+iv.
+
+the annotation is incorrect (bad choice of term, wrong protein annotated)
+knowledge has evolved. If necessary some (usually older) papers should
+be marked as ‘do not curate’ and the associated annotations should be
+removed.
+the protein plays multiple roles under different conditions (ie,
+acts as a DNA-binding transcription factor in certain contexts and as a
+cofactor on others), as these two molecular functions are not mutually
+exclusive.
+no clear activity has been established yet, in which case: either
+annotations to both DNA-binding transcription factor and cofactor may be
+made (if the evidence supports it), or if the data is not sufficient, do not
+annotate.
+
+GO-CAM representation of transcription
+
+GO-CAM Modeling Guidelines: DNA binding transcription factor activity
+
+Potential pitfalls
+
+The annotation of dbTFs can be challenging for multiple reasons:
+
+●  Some activities are hard to distinguish from each other, and adding to this difficulty,
+transcription regulators form complexes that are more or less fluid, so that it can be
+difficult to detect which protein in a complex is responsible for a specific activity.
+It can be difficult to distinguish certain activities, and some proteins do have multiple
+functions.
+
+●
+
+6
+
+●  Researchers use "transcription factor" loosely. It can mean a GTF, a dbTF, or a coTF.
+●  The terms "cofactor", "coactivator", and "corepressor" are also used for different
+
+activities: either as described in this document, and sometimes (especially in older
+papers), they are used to describe a dbTF that acts as a dimer.
+
+●  The complexity of the transcription process means that no single experiment is usually
+sufficient to define the function of a protein: interpretation of experimental results that
+investigate dbTFs must rely on existing knowledge.
+
+●  Many proteins presumed to function as dbTFs have never been experimentally
+
+demonstrated to bind DNA, but their role is indirectly inferred by the presence of specific
+domains and in some cases, evidence of an effect on the transcription of putative direct
+target genes.
+
+●  The presence of a DNA binding domain in a protein does not always imply the protein
+
+functions as a dbTF.
+
+________________________ADDITIONAL INFORMATION_____________________
+
+Additional information
+
+Ontology structure
+
+Molecular Function
+
+MF: GO:0140110 transcription regulator activity and children
+
+The transcription regulator activity (GO:0140110) MF branch of the GO describes the activities
+of transcription regulators: GTFs, dbTF, and coTFs (Figure 1).
+
+7
+
+Figure 1. Transcription regulator activity branch of the Gene Ontology. This part of the
+Molecular Function (MF) ontology describes the activities of transcription regulators: GTFs,
+dbTF, and coTFs. Highlighted in blue are the most specific GO terms available to describe these
+activities in eukaryotic cells (prokaryotes use a single polymerase).
+
+MF: GO:0000987 cis-regulatory region sequence-specific DNA binding
+
+The transcription regulatory region sequence-specific DNA-binding sub-tree of GO includes
+terms describing specific regulatory regions, such as the core promoter (including the TATA box
+and the transcription start site), cis-regulatory regions (bound by dbTFs), and specific types of
+cis-regulatory motifs (such as E-box and N-box). Overview of the GO structure for DNA binding
+activities is shown in Figure 1.
+
+8
+
+Figure 2. DNA binding branch of the Gene Ontology. This part of the Molecular Function
+(MF) ontology describes DNA binding. The key DNA binding terms that should be associated
+with dbTF are highlighted in blue, more specific GO terms are available to provide information
+about the DNA motifs bound by the dbTF.
+
+Biological process
+
+**NOTE THAT THIS PART OF THE ONTOLOGY IS STILL BEING REVIEWED**
+There are currently two axes of classification: by product (Figure 3) and by the RNA polymerase
+generating the transcript (Figure 4). Ideally both terms should be used; the product generated
+by the transcription event is the most meaningful biologically. We plan to remove the RNA
+polymerase-specific branch of the BP ontology. Having a single branch will ensure that
+consistent and efficient annotation can be achieved.
+
+For the 'regulation of transcription' branch ("GO:0006355 regulation of transcription,
+DNA-templated", and children; Figure 5), the 'product' axis does not currently exist. We will
+rename the polymerase-centric terms to the product-specific equivalent as appropriate. If there
+are two polymerases responsible for the same transcript, two terms will be instantiated (for
+
+9
+
+example, GO:1905380 regulation of snRNA transcription by RNA polymerase II; NEW term
+regulation of snRNA transcription by RNA polymerase III will both remain).
+
+Figure 3. Transcription branch of the Gene Ontology. This part of the BP ontology provides
+terms to describe the role of GTFs in transcription of a specific type of transcript.
+
+Figure 4. Transcription branch of the Gene Ontology. This part of the BP terms available to
+describe the role of GTFs in transcription mediated by a specific RNA polymerase.
+
+Figure 5. Regulation of transcription branch of the Gene Ontology. This part of the BP
+terms available to describe the role of dbTFs and coTFs in regulating transcription. Highlighted
+in blue are the key GO terms available to describe regulation of transcription in eukaryotic cells
+(prokaryotes use a single polymerase). The more specific child terms for the highlighted terms
+describe the role of transcription in other processes, eg "GO:1900464 negative regulation of
+cellular hyperosmotic salinity response by negative regulation of transcription from RNA
+
+10
+
+polymerase II promoter", these terms are being phased out. Instead, aside from its biochemical
+activity in the process of transcription, a transcription factor can be annotated to the biological
+process it receives input from, as a molecular signaling pathway or biomolecular sensor
+endpoint, and provides transcriptional output for through its target genes.
+
+Cellular components: Complexes and cellular locations
+
+**NOTE THAT THIS PART OF THE ONTOLOGY IS STILL BEING REVIEWED**
+
+Annotation examples from research articles
+
+Below we describe annotation work flows from a workshop held at EBI in April 2020.
+
+This is a concept, perhaps other format is needed, a landscape page may be better suited
+
+hypothesis-exampl
+e/steps
+
+GTF
+
+dbTF
+
+coTF
+
+Example article
+
+PMID:10924514
+
+PMID:26314965
+
+PMID:22783022
+
+Step 1: Hypothesis
+
+GTF2H2 is a subunit of
+the TFIIH GTF.
+
+NKX6.3 is a
+transcription
+regulator.
+
+Step 2: Database
+mining for protein
+domains and
+orthologs
+
+GTF2H2 contains a
+TFIIH subunit Ssl1/p44
+domain (IPR012170),
+described in InterPro as
+a component of the
+transcription factor
+TFIIH core.
+UniProt describes
+GTF2H2 as a
+"Component of the
+TFIID-containing RNA
+polymerase II
+pre-initiation complex"
+(https://www.uniprot.org
+/uniprot/Q13888#functi
+on).
+
+NKX6.3 contains a
+DNA binding
+homeobox domain
+(IPR020479).
+UniProt describes
+NKX6.3 as a
+"Putative
+transcription factor,
+which may be
+involved in
+patterning of central
+nervous system and
+pancreas."
+(https://www.uniprot.
+org/uniprot/A6NJ46#
+function).
+
+SIN3A (Q96ST3) is a
+transcription
+co-repressor.
+
+SIN3A contains a
+SIN3A domain
+(IPR037969), among
+others. IPR037969 is
+associated with the
+GO Molecular
+Function GO:0003714
+transcription
+corepressor activity
+(https://www.ebi.ac.uk
+/interpro/entry/InterPr
+o/IPR037969/)
+UniProt describes
+SIN3A as "Acts as a
+transcriptional
+repressor.
+Corepressor for
+
+11
+
+Step 3: GO
+annotation and
+literature mining
+
+Existing annotations
+were consistent with
+the hypothesis that the
+gene encodes a GTF:
+there are IDA
+annotations to
+GO:0016251 RNA
+polymerase II general
+transcription initiation
+factor activity and
+GO:0008353 RNA
+polymerase II CTD
+heptapeptide repeat
+kinase activity, both
+functions of GTFs
+subunits.
+
+Existing annotations
+were consistent with
+the hypothesis that
+the gene encodes a
+dbTF.
+- GO:0003700 (and
+children)
+DNA-binding
+transcription factor
+activity
+IDA, IBA, ISA, ISM
+- GO:0000978
+RNA polymerase II
+cis-regulatory region
+sequence-specific
+DNA binding
+IBA
+- GO:0043565
+sequence-specific
+DNA binding
+IDA, IBA
+
+REST."
+(https://www.uniprot.o
+rg/uniprot/Q96ST3#fu
+nction).
+
+Existing annotations
+were conflicting. After
+review of the curated
+articles, several
+annotations were
+removed, because
+many of the activities
+were those of proteins
+SIN3A interacts with,
+not its function.
+Searching PubMed
+for SIN3A, and
+filtering for reviews,
+since there is a lot of
+literature describing
+SIN3A, result in many
+articles mentioning
+epigenetics, further
+supporting the coTF
+repressor hypothesis (
+https://pubmed.ncbi.nl
+m.nih.gov/?term=Sin3
+a&filter=pubt.review).
+
+Step 4: New data
+extraction from
+publication
+
+Figure 4, compares
+wild type GTF2H2 and
+a mutant in abortive
+initiation and promoter
+escape assays. The
+results show that the
+mutant GTF2H2 is
+unable to initiate
+transcription. This data
+supports the annotation
+GO:0016251 RNA
+polymerase II general
+
+Figure 5 shows
+increased
+expression of target
+genes containing
+predicted binding
+motif sequences
+(TAAT), which was
+abolished by
+decreasing NKX6.3
+expression with an
+antisense transcript.
+Moreover, ChIP data
+confirmed that
+
+Figure 4 shows by
+ChIP assay that the
+SIN3A is found in the
+vicinity of the SOCS3
+gene, a gene
+regulated by STAT3.
+The same figure also
+shows that STAT3
+does not interact with
+the SOCS3 promoter
+in the presence of
+SIN3A, indicating a
+repressor effect of
+
+12
+
+transcription initiation
+factor activity
+
+SIN3A on STAT3's
+transcription activator
+function. This
+supports an
+annotation of SIN3A
+to:
+- GO:0003714
+transcription
+corepressor activity
+- GO:0000122
+negative regulation of
+transcription by RNA
+polymerase II
+
+NKX6.3 is bound to
+regulatory regions of
+the target genes
+(see notes above on
+the use of ChIP data
+to support an
+annotation). The
+dbTF activity
+annotation for
+NKX6.3 can
+therefore include the
+direct target genes
+information using
+the relation "has
+input".
+This supports an
+annotation of
+NKX6.3 to:
+- GO:0000978 RNA
+polymerase II
+cis-regulatory region
+sequence-specific
+DNA binding
+- GO:0001228
+DNA-binding
+transcription
+activator activity,
+RNA polymerase
+II-specific
+- GO:0001227
+DNA-binding
+transcription
+repressor activity,
+RNA polymerase
+II-specific
+- GO:0045944
+positive regulation of
+transcription by RNA
+polymerase II
+GO:0000122
+negative regulation
+
+13
+
+of transcription by
+RNA polymerase II
+
+Evidence for a GTF
+
+PMID:10924514 Studies of the function of the GTF2H2 subunit of the TFIIH GTF
+
+1.  The hypothesis is that GTF2H2 is a subunit of the TFIIH GTF.
+2.  Protein domains or characterized orthologs: GTF2H2 contains a TFIIH subunit
+
+Ssl1/p44 domain (IPR012170), described in InterPro as a component of the transcription
+factor TFIIH core.
+UniProt describes GTF2H2 as a "Component of the TFIID-containing RNA polymerase II
+pre-initiation complex" (https://www.uniprot.org/uniprot/Q13888#function).
+
+3.  Are there other GO annotations or published experimental results consistent with
+the hypothesis ? Yes, existing annotations were consistent with the hypothesis that the
+gene encodes a GTF: there are IDA annotations to GO:0016251 RNA polymerase II
+general transcription initiation factor activity and GO:0008353 RNA polymerase II CTD
+heptapeptide repeat kinase activity, both functions of GTFs subunits.
+
+4.  Are the experimental results consistent with the hypothesis ? Yes, GTF
+
+GO:0016251 RNA polymerase II general transcription initiation factor activity from Figure
+4, which  compares wild type GTF2H2 and a mutant in abortive initiation and promoter
+escape assays. The results show that the mutant GTF2H2 is unable to initiate
+transcription.
+
+Evidence for a dbTF
+
+PMID:26314965 studies the activity of the NKX6.3 (UniProt:A6NJ46) transcription factor. Going
+through the checklist shows the following:
+
+1.  The hypothesis stated by the authors is that NKX6.3 is a transcription regulator.
+2.  Protein domains or characterized orthologs: NKX6.3 contains a DNA binding
+
+homeobox domain (IPR020479). UniProt describes NKX6.3 as a "Putative transcription
+factor, which may be involved in patterning of central nervous system and pancreas."
+(https://www.uniprot.org/uniprot/A6NJ46#function).
+
+3.  Are there other GO annotations or published experimental results consistent with
+
+the hypothesis ?
+All already existing annotations were consistent with the hypothesis that the gene
+encodes a dbTF.
+
+GO ID
+
+Term label
+
+Evidence(s)
+
+Consistent with
+hypothesis?
+
+14
+
+GO:0003700
+(and children)
+
+DNA-binding transcription factor
+activity
+
+IDA, IBA, ISA, ISM
+
+Yes
+
+GO:0000978
+
+RNA polymerase II cis-regulatory
+region sequence-specific DNA binding
+
+IBA
+
+GO:0043565
+
+sequence-specific DNA binding
+
+IDA, IBA
+
+Yes
+
+Yes
+
+4.  Are the experimental results consistent with the hypothesis ? Yes, Figure 5 shows
+increased expression of target genes containing predicted binding motif sequences
+(TAAT), which was abolished by decreasing NKX6.3 expression with an antisense
+transcript. Moreover, ChIP data confirmed that NKX6.3 is bound to regulatory regions of
+the target genes (see notes above on the use of ChIP data to support an annotation).
+The dbTF activity annotation for NKX6.3 can therefore include the direct target genes
+information using the relation "has input".
+This supports an annotation of NKX6.3 to:
+
+-  GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA
+
+binding
+
+-  GO:0001228 DNA-binding transcription activator activity, RNA polymerase
+
+II-specific
+
+-  GO:0001227 DNA-binding transcription repressor activity, RNA polymerase
+
+II-specific
+
+-  GO:0045944 positive regulation of transcription by RNA polymerase II
+-  GO:0000122 negative regulation of transcription by RNA polymerase II
+
+Evidence for a coTF
+
+PMID:22783022 studies the activity of the SIN3A transcription co-activator. This paper shows
+that the transcription factor STAT3 is a target of regulation by SIN3A. Going through the
+checklist shows the following:
+
+1.  The starting hypothesis stated by the authors is that SIN3A (Q96ST3) is a transcription
+
+co-repressor.
+
+2.  Protein domains or characterized orthologs:
+
+SIN3A contains a SIN3A domain (IPR037969), among others. IPR037969 is associated
+with the GO Molecular Function GO:0003714 transcription corepressor activity
+(https://www.ebi.ac.uk/interpro/entry/InterPro/IPR037969/)
+UniProt describes SIN3A as "Acts as a transcriptional repressor. Corepressor for REST."
+(https://www.uniprot.org/uniprot/Q96ST3#function).
+
+3.  Are there other GO annotations or published experimental results consistent with
+
+the hypothesis ?
+
+a.  Existing annotations are conflicting. After review of the original articles, several
+
+annotations were removed, because many of the activities were those of proteins
+SIN3A interacts with, not its function.
+
+15
+
+b.  Searching PubMed for SIN3A, and filtering for reviews, since there is a lot of
+literature describing SIN3A, result in many articles mentioning epigenetics,
+further supporting the coTF repressor hypothesis (
+https://pubmed.ncbi.nlm.nih.gov/?term=Sin3a&filter=pubt.review).
+
+GO ID
+
+Term label
+
+Evidence(s)
+
+Consistent with
+hypothesis? /Action if
+not
+
+GO:0003714
+
+transcription corepressor activity
+
+IBA
+
+Yes
+
+GO:0003700  DNA-binding transcription factor activity
+
+IEA (Ensembl)
+
+No / Removed
+
+GO:0000976
+
+transcription regulatory region
+sequence-specific DNA binding
+
+GO:0033558
+
+protein deacetylase activity
+
+GO:0004407
+
+histone deacetylase activity
+
+GO:0000976
+
+transcription regulatory region
+sequence-specific DNA binding
+
+ISS
+
+IMP
+
+IBA
+
+ISS
+
+No / Removed
+
+No / Removed
+
+No / Removed
+
+No / Removed
+
+4.  Are the experimental results consistent with the hypothesis ?
+
+Yes, Figure 4 shows by ChIP assay that the SIN3A is found in the vicinity of the SOCS3
+gene, a gene regulated by STAT3. The same figure also shows that STAT3 does not
+interact with the SOCS3 promoter in the presence of SIN3A, indicating a repressor effect
+of SIN3A on STAT3's transcription activator function. This supports an annotation of
+SIN3A to:
+
+-  GO:0003714 transcription corepressor activity
+-  GO:0000122 negative regulation of transcription by RNA polymerase II
+
+Guidance on specific small scale experiments
+
+Experiments providing evidence for DNA binding transcription factor activity can be found in
+Tables 3 and 4 of Tripathi 2013 (PMID:27270715).
+
+Guidance on specific high-throughput experiments
+
+The strategy outlined above for the annotation of transcription regulators should be applied
+when curating high-throughput data. The guidelines below are mostly relevant to dbTFs, if the
+experimental data can be used to capture information about coTFs this will be indicated.
+
+16
+
+High-throughput data can be used to capture the ‘direct’ target of a dbTF or a coTF. The direct
+target may be the genomic coordinates and/or the target gene.
+
+HT-SELEX experiments (dbTF data)
+High throughput selection experiments such as the HT-SELEX protocol (PMID:1697402, PMID:
+2200121) yield data that provides strong experimental evidence of the DNA sequence
+recognised by a protein. This is then presented as an optimal DNA motif that represents the
+consensus of many binding observations.  Crucially, sequence-specific DNA binding does not
+necessarily imply transcription regulation function. For instance, PRMT14 has a specific DNA
+binding activity, but it is involved in meiotic recombination site determination. For annotation to
+the dbTF Mf term, it is still necessary to have evidence that at least one target gene is
+regulated.  However, often that evidence was already obtained in the course of other published
+studies. The  HT-SELEX experiments, then, provide support for annotation to:
+
+-  GO:0000987 cis-regulatory region sequence-specific DNA binding or the descendent
+GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
+However, if there is also evidence of regulation of transcription of a gene associated with the
+regulator region (either by transfection and measuring mRNA or by a reporter gene assay, etc),
+then HT-SELEX data provides support for the following annotations:
+
+-  GO:0003700 DNA-binding transcription factor activity or a child
+-  GO:0006357 regulation of transcription by RNA polymerase II (or GONEW: regulation of
+
+mRNA transcription)
+
+for the TF IDA (HT-SELEX) is one of the strongest experimental evidence types to assign as
+dbTF. Still,  further strengthens this conclusion. Eg: PRMT14 (is a meiosis factor not a TF).
+Cumulating evidence is important (Oriol Formes email of 18 February).
+
+ChIP-seq experiments (dbTF or coTF data)
+
+As ChIP-seq experiments include cross-linking of proteins to other proteins and/or DNA, on their
+own ChIP-seq experiments are inconclusive. However, if (a) the protein is known to bear a DNA
+binding domain and (b) there is evidence of regulation of transcription (either by transfection and
+measuring mRNA or by a reporter gene assay, etc), then the CHIP-seq data provides support
+for the following annotations:
+
+-  GO:0000987 cis-regulatory region sequence-specific DNA binding or the descendent
+GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
+
+-  GO:0003700 DNA-binding transcription factor activity or a child
+-  GO:0006357 regulation of transcription by RNA polymerase II (or GONEW: regulation of
+
+mRNA transcription)
+
+If (c) the protein is known to be a coTF and (b) there is evidence of regulation of transcription
+(either by transfection and measuring mRNA or by a reporter gene assay, etc), then the
+CHIP-seq data provides support for the following annotations:
+-  GO:0003712 transcription coregulator activity or a child
+
+17
+
+-  GO:0006357 regulation of transcription by RNA polymerase II (or GONEW: regulation of
+
+mRNA transcription)
+
+Bacterial 1-hybrid experiments
+
+The bacterial one-hybrid (B1H) system is a method for identifying the sequence-specific target
+site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a
+fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides
+representing potential TF target sequences are cloned into a separate vector containing the
+selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target
+site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the
+reporter genes in that clone  (https://en.wikipedia.org/wiki/Bacterial_one-hybrid_system;
+PMC1435991).
+
+18
+
+19
+