NTR: [positive regulation of nucleosome disassembly]

robnash commented 2 years ago

Please provide as much information as you can:

Suggested term label:

positive regulation of nucleosome disassembly

Definition (free text)

Any process that activates or increases the frequency, rate or extent of the controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

Reference, in format PMID:#######

https://pubmed.ncbi.nlm.nih.gov/34471130/ https://pubmed.ncbi.nlm.nih.gov/35308047/

Gene product name and ID to be annotated to this term

CLB5-CDC28 kinase complex (S. cerevisiae) aka CPX-1702

Parent term(s)

GO:0006337 nucleosome disassembly

Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?

none

Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)

none

Cross-references
For enzymes, please provide RHEA and/or EC numbers.
Can also provide MetaCyc, KEGG, Wikipedia, and other links.
Any other information

robnash commented 2 years ago

anyone able to add this one for me?

robnash commented 2 years ago

anyone able to add this one for me?

pgaudet commented 2 years ago

Hi @robnash

Thanks for the ping. We are actively working in this area, there has been many recent changes in the ontology. This complex (as well the the chaperone it regulates) can be annotated to 'GO:0006335 DNA replication-dependent chromatin assembly' (see https://github.com/geneontology/go-ontology/issues/22130 for relevant changes).

We could create a MF histone chaperone regulator activity if you think this is needed.

@colinlog other suggestions?

Thanks, Pascale

robnash commented 2 years ago

In the paper I have been trying to annotate, Yta7p is shown to disrupt chromatin by disassembling nucleosomes, and this facilitates progression of the replisome through a chromatin template, preventing replicative stress. The S phase CDK complex (CLB5-CDC28 kinase complex (CPX-1702)) stimulates the the ATPase activity and the chromatin segregase function of Yta7p resulting in nucleosome disassembly. So the term "GO:0006335 DNA replication-dependent chromatin assembly" would not be correct here as its not assembly, rather disassembly.

So far I have captured the remodeling activity and chose " ATP-dependent chromatin remodeler activity" as it is not referred to it as a histone chaperone, and used as part of nucleosome disassembly, and as part of DNA replication:

YTA7 GO:0140658 ATP-dependent chromatin remodeler activity (IDA, IMP); part of GO:0006337 nucleosome disassembly (IDA, IMP); part of: GO:0006261 DNA-templated DNA replication (IDA, IMP); is located on: GO:0000785 chromatin (IDA)

and the stimulation of ATPase activity by the CDK complex as:

CLB5-CDC28 kinase complex (CPX-1702) GO:0004693 cyclin-dependent protein serine/threonine kinase activity (IDA), has input: YTA7; part of: GO:0032781 positive regulation of ATP-dependent activity, has input: YTA7 (IDA)

what I need to capture is the stimulation of segregase activity, so was proposing:

CLB5-CDC28 kinase complex (CPX-1702) GO:0004693 cyclin-dependent protein serine/threonine kinase activity (IDA), has input: YTA7; regulates NTR: GO:XXXXXXX positive regulation of nucleosome disassembly, has input: YTA7 (IDA)

So if this is not possible, I need another way to capture this stimulation of segregase activity (nucleosome disassembly). So if I bypass the inclusion of the kinase activity, regulating the process, I suppose I could annotate a complex function directly using a new term to describe this regulator of "ATP-dependent chromatin remodeler activity (GO:0140658)". So am thinking something like "ATP-dependent chromatin remodeler regulator activity" although the wording sounds a bit awkward

pgaudet commented 2 years ago

After discussion with @colinlog We will create 'positive regulation of nucleosome disassembly' and a sibling to 'GO:0006335 DNA replication-dependent chromatin assembly', DNA replication-dependent chromatin disassembly.

Note that for the CLB5-CDC28 complex:

CLB5-CDC28 kinase complex (CPX-1702) GO:0004693 cyclin-dependent protein serine/threonine kinase activity (IDA), has input: YTA7; regulates NTR: GO:XXXXXXX positive regulation of nucleosome disassembly, has input: YTA7 (IDA)

it is not correct to have YTA7 as the input; the input would be the nucleosome (or the histones composing it), which is already in the term label, so you don't need an input here.

pgaudet commented 2 years ago

+[Term] +id: GO:0140887 +name: positive regulation of nucleosome disassembly +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA." [PMID:34471130, PMID:35308047] +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006334 ! nucleosome assembly +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23229 xsd:anyURI +created_by: pg +creation_date: 2022-07-11T16:56:42Z

+[Term] +id: GO:0140889 +name: DNA replication-dependent chromatin disassembly +namespace: biological_process +namespace: The disruption of nucleosomes during DNA replication to allow the replication machinery to access the DNA. {xref="PMID:35308047", xref="PMID:34471130"} +is_a: GO:0006325 ! chromatin organization +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23229 xsd:anyURI +created_by: pg +creation_date: 2022-07-11T19:41:22Z +

robnash commented 2 years ago

Thanks Colin and Pascale for taking a look and creating the new terms. Much appreciated!

pgaudet commented 2 years ago

I still have a doubt about the regulation of the nucleosome assembly - I think (but I am not sure) that CLB5-CDC28 regulates replication, and that all the steps nucleosome disassembly /reassembly, DNA polymerase activity, etc et, are part of DNA replication.

So I think the correct model is

CLB5-CDC28 regulates YTA7 activity (and its 200 other substrates)
YTA7 _part_of nucleosome disassemby
CLB5-CDC28 acts upstream of, positive effect nucleosome disassemby (via YTA7)

Anyhow, I'll leave it like this for now, but just to say, we may revisit this when we look at DNA replication/cell cycle progression more closely.

Thanks,

Pascale

ValWood commented 2 years ago

I'm still struggling to understand these terms.

This activity seems to be part of the overall pathway of removing and adding nucleosomes during replication. But the process term to represent this process covers only the reassembly/ de novo assembly part GO:0006335 DNA replication-dependent chromatin assembly

I'm also still struggling also with the distinction between "nucleosome assembly" and "chromatin assembly".

~I'm also struggling with where the "regulation" should be represented (but this is a more general issue I have lots of examples of this, not just in the chromatin area -I will raise questions on Slack and then on an annotation call, hopefully in the next few weeks).~ Note this is a more general issue about my struggles with regulation, not specific to this ticket

geneontology / go-ontology

NTR: [positive regulation of nucleosome disassembly] #23229