NTR: Nucleosome_occupancy

[aboyd003]

What is this request referring to?
Defining regions of nucleosome occupancy

What is the name you would like SO to give the term?
Nucleosome_occupancy

What is the definition that you would like for this term?
Nucleosome_occupancy would be used to indicate the entry in the GFF is related to the nucleosome occupancy of the specified region.

Synonyms
Nucleosome_coverage, Nucleosome_element

Parent Term
I was unable to identify a parent term as the only epigenetic terms returned during my search relate to modifications. There were no search results for nucleosome. These searches were performed on the sequence ontology browser.

Relevant Publications
The following are examples of publications where having the "atlas" in GFF format would be beneficial and enable individuals to better able use this work.
Lee, W., Tillo, D., Bray, N. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39, 1235–1244 (2007). https://doi.org/10.1038/ng2117
Kai Zhang, James D. Hocker, Michael Miller, Xiaomeng Hou, Joshua Chiou, Olivier B. Poirion, Yunjiang Qiu, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren,
A single-cell atlas of chromatin accessibility in the human genome,
Cell,
Volume 184, Issue 24,
2021,
Pages 5985-6001.e19,
ISSN 0092-8674,
https://doi.org/10.1016/j.cell.2021.10.024.

[egchristensen]

The sequence feature that we would add to the sequence ontology needs to be mappable to the sequence itself (usually via genomic coordinates). I think a term nucleosome_occupancy would be one or two levels up in abstraction from where we need to start modeling for the sequence ontology and may be out of scope.

I noticed that Lee et al. mention "nucleosome-depleted regions" (NDR). This may be a synonym or potential child term of accessible_DNA_region (SO:0002331) which is defined as "a biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification."

I presume that counts within a nucleosome-depleted region are used to calculate/describe nucleosome occupancy? Does that track with your experience? Are there other sequence regions used to calculate/describe nucleosome occupancy or nucleosome positioning?

A couple other related terms that might be relevant to nucleosome occupancy include:

• chromatin_regulatory_region (SO:0002306): "A region of a chromosome where regulatory events occur, including epigenetic modifications. These epigenetic modifications can include nucleosome modifications and post-replicational DNA modifications."
• epigenetically_modified_region (SO:0001720): "A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification."

By the way, for easier browsing and searching of the sequence ontology, I'd recommend downloading Protégé and opening the ontology files with "File" > "Open from URL..." > and then entering this URL: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/so.obo