Question: histone mark associated with enhancers
1
gravatar for na.cna30
5.0 years ago by
na.cna300
na.cna300 wrote:

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.

histone marks enhancer • 4.9k views
ADD COMMENTlink modified 5.0 years ago by Ming Tang2.5k • written 5.0 years ago by na.cna300
3
gravatar for Ming Tang
5.0 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

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

ADD COMMENTlink written 5.0 years ago by Ming Tang2.5k

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? 

ADD REPLYlink written 5.0 years ago by na.cna300
1

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 degree ( 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 http://www.pnas.org/content/107/50/21931.abstract

 enhancers with both H3K4me and H3k27ac are active enhancers.

 

ADD REPLYlink written 5.0 years ago by Ming Tang2.5k
1
gravatar for aditi.qamra
5.0 years ago by
aditi.qamra260
Toronto
aditi.qamra260 wrote:

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.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by aditi.qamra260

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 many literatures but they are varied and there is no consensus as far as I understand. 

ADD REPLYlink written 5.0 years ago by na.cna300
2

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 dont you start reading from here ( incase you haven't already ) - http://hmg.oxfordjournals.org/content/18/R2/R195.full

ADD REPLYlink written 5.0 years ago by aditi.qamra260

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 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?

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by na.cna300
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