NTR: Fiber-seq

[jenjou]

Preferred Term: m6A-MTase sequencing assay Synonyms: Fiber-seq Definition: A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MTase) and then sequenced using single-molecule circular consensus sequencing to identify regions of accessible DNA at nucleotide resolution. Relevant info: https://pubmed.ncbi.nlm.nih.gov/32587015/ Parent Term: OBI:0001266 DNA methylation profiling by high throughput sequencing assay

[ddooley]

Discussing Sept 9th. @jenjou thanks for the paper reference. That the label references enzyme being used sounds like a stable way to reference this kind of sequencing. We are wondering if assay ultimately is intended to identify accessible regions or the methyl group location? Perhaps the paper reveals this?

We'd like further information about this distinction to show in label and definition and parent class. OBI may need to add a parent, say "chromatin accessibility assay".

[jenjou]

I asked one of the labs I work with who is utilizing this assay, and they told me that they primarily see it as an assay to identify accessible regions. So, although the assay involves methylation, I think my originally proposed parent term might not be the best option, as you suggested. "Chromatin accessibility assay" seems reasonable to me.

[jenjou]

Hello, I noticed there has been no recent activity on this request. Is there any info I can provide that would help regarding this term?

[sebastianduesing]

Apologies, this fell off my radar. Thanks for the reminder. I'll put together a pull request either today or tomorrow for you to review.

[mgiglio99]

A quick note for this... We already have OBI:0002039 'assay for transposase-accessible chromatin using sequencing' (alt term ATAC-seq) as a direct child of 'assay'. Seems like the new term requested here and the ATAC-seq term should be siblings under the proposed 'chromatin accessibility assay' term. There might be other related terms lurking around as well. Best, Michelle

[sebastianduesing]

@mgiglio99 Thanks for noting that. Do you have any suggestions on how to define 'chromatin accessibility assay'?

[bpeters42]

Maybe:

An assay that determines which regions of DNA in chromatin are able to make direct physical contact (=are accessible) with other factors.

On Thu, Nov 7, 2024 at 2:44 PM Sebastian Duesing @.***> wrote:

@mgiglio99 https://github.com/mgiglio99 Thanks for noting that. Do you have any suggestions on how to define 'chromatin accessibility assay'?

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[mgiglio99]

Maybe we can use the words euchromatin and heterochromatin in there somewhere? How about: An assay that determines which regions of a DNA molecule are in the form of euchromatin and thus able to make direct physical contact with (i.e. are accessible to) other molecules such as RNA polymerase, transcription factors, etc.

[sebastianduesing]

Got it, thank you both! I'll use that for the PR.