Question: Exploring H3K27me3 loss in cancer
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gravatar for Researcher
11 days ago by
Researcher40
Researcher40 wrote:

Hi All,

I am looking for some insights for my question interest.

I have Chip-Seq data for histone marks from 3 different subtypes of a cancer which have different levels of aggressiveness. I am interested to see if there is any association between the tumor aggressiveness and H3K27me3 loss.

Towards this I am planning to compare the coordinates that has less binding for H3K27me3 but are more bound with any of the activation marks like H3K27ac, H3K4me1 or H3K4me3 in one of the subtype compared to other.

I am not sure whether it will be a correct approach to find out these loss of H3K27me3 marks or it should be addressed differently?

Any suggestions will be highly appreciated.

Thanks

ADD COMMENTlink modified 10 days ago • written 11 days ago by Researcher40

I thought so, as I read it somewhere that H3K27ac shares a location with H3K27me3 and often seen interacting with H3K4me3 in bivalent domains. Any suggestion or insight will highly be appreciated.

Thanks

ADD REPLYlink written 10 days ago by Researcher40

what exactly is the question?

ADD REPLYlink modified 10 days ago • written 10 days ago by steve2.3k

Hi steve, I want to find out sites that have lost H3K27me3 (repressive) signal but have gained H3K27ac (or any other activation mark) in one cancer subtype compared to other and find out some pattern. But I am a bit confused whether it is recommended to compare the exact coordinates between loss of H3K27me3 and gain of H3K27ac or should I check the whole promoters or enhancers around the same gene.

Any suggestions will be appreciated.

ADD REPLYlink modified 10 days ago • written 10 days ago by Researcher40

I would not use exact overlap, but allow for a 'buffer' window of a few thousand base-pairs.

ADD REPLYlink written 9 days ago by Kevin Blighe48k

Hi Kevin Thank you for your reply. I have a follow-up question, will you also suggest to find these pattern only around TSS?

ADD REPLYlink written 8 days ago by Researcher40

Hey, which patterns? - in biology, everything is possible. H3K27me3 is found elevated at active promoters and TSS, as far as I know (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC409923/ )

ADD REPLYlink written 8 days ago by Kevin Blighe48k

Hello Researcher!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/124618/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 10 days ago by ATpoint23k

Ya I am looking for some suggestion from any of forum, will remove it from there. Thanks for pointing.

ADD REPLYlink modified 10 days ago • written 10 days ago by Researcher40

No problem. While not forbidden we generally discourage people from cross-posting as many users are active in both communities and information are preferred to be concentrated in a single thread. BioC is good for tool-related questions as many developers are active there while I personally prefer Biostars for more general questions.

ADD REPLYlink modified 10 days ago • written 10 days ago by ATpoint23k

Sure will keep a note. Thanks! Do you have a suggestion for my question?

ADD REPLYlink modified 10 days ago • written 10 days ago by Researcher40
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