histone mark associated with enhancers

Question

[na.cna30]

Hello:

I explore between studies about associated histone mark in enhancer locations and the result is very diverse and confusing. I am looking for enhancer STAT1. I would like to know the histone marks associated with it?

thanks.

Answer 1

[Ming Tommy Tang]

H3K4me and H3k27ac are histone marks for enhancers. p300 (a histone acetyl transferase) is also found at enhancers.

[na.cna30]

Thanks. All H3K4me are applicable? me1,me2 and me3? In this case, peak (higher score of each of them) shows active enhancer? Or some of them (like me3) should have less score?

[Ming Tommy Tang]

You might need to read some basics. H3 is the histone 3 (one component of the nucleosome), K is lysine and can be methylated to different degrees (Me, Me2 and Me3). H3K4me2 is also found at some enhancers, but I would use H3K4me as a conventional mark. H3K4me3 is a mark for promoters. According to this paper, enhancers with both H3K4me and H3k27ac are active enhancers.

Answer 2

[aditi.qamra]

Hi na.cna330 - I noticed you have multiple questions around the same central question. My strong suggestion to you would be to go through the existing literature than post every single doubt you have, here. Specifically to this question, this is not really a bioinformatics question rather a theoretical biology question easily answered had you done a quick google search of the same than posting it here.

[na.cna30]

Thanks for replying. My major is AI so I am not really familiar with biology. First I need proper data to implement AI techniques, but choosing proper data needs good understanding of biology. Anyway, I did review a lot of literature but they are varied and there is no consensus as far as I understand.

[aditi.qamra]

Hi.. In that case you could have posted the question as a specific doubt to confirm your understanding of the literature review instead of an umbrella question. Why don't you start reading from here (in case you haven't already)

[na.cna30]

Thanks for your help. One question: According to http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2769248/, each of H2A.Z, H3K4me1, H3K4me2, H3K4me3, H3K9me1 and H3K18ac are associated with enhancers. But according to http://nar.oxfordjournals.org/content/40/10/e77.long, top-ranked predictors are H3K4Ac, H3K4Me3 and H2BK5Ac. Does it mean it depends on cell-line?