How to get enhancer regions

Question

[Faiza]

I need to know whether Snp is on enhancer region and why this Snp can regulate gene expression of that target gene.

For this I have two questions:

1st question: I need enhancer regions file for CD4+T cells from publicly available data ,e.g ENCODE. From ENCODE, I typed enhancers then selected CD4 + T cells, in result I got candidate enhancers file in bed format. Here the description of output file is Enhancer-like regions using H3K27ac-only. Does it means they just use H3k27ac mark for enhancers? My Question is "How did they defined enhancer regions?" they just mentioned the target histone mark, and give the histone chip-seq pipeline but they did not actually described how did they define the Enhancer regions . Also if i am doing something wrong, please help me how can I get enhancer regions from publicly available data and how did they define these enhancer regions. 

2nd question: from some research papers I got that enhancers are present certain distance away from TSS. but when I tried to visualize that enhancer file which I got from ENCODE on IGV visualization tool these regions overlap with intron regions of Refseq Genes, does this means enhancer regions also present on gene body??   thank you

Answer 1

[Ming Tommy Tang]

1. yes, H3K27ac ChIP-seq peaks are defined as enhancers when excluded the regions overlapping promoters.
2. yes, enhancers can be located in introns and even exons. https://www.nature.com/articles/s41576-019-0207-2

[i.sudbery]

Hmmm....

ENCODE might define H3K27ac peaks minus promoters as Enhancers, but personally I think thats a pretty shoddy definition. I like using something like chromHMM to define enhancers, taking into account multiple histone marks. But all ways of defining enhancers have their issues.

[Faiza]

thanks for replying . i donot have promoters file . How can i get promoters and then how can i minus H3K27ac peaks from promoters in order to get enhancer regions ? Thank you

[Ming Tommy Tang]

you can first get the promoters using bioconductor packages by using the promoter function or get it from gtf file using command line tricks. then use bedtools intersect to exclude promoter.bed from the H3K27ac_peaks.bed

[Ming Tommy Tang]

for chromHMM you need multiple histone ChIP-seq data. If you only have H3K27ac, then go with this...

[i.sudbery]

I'm pretty sure that roadmap epigenomics has chromHMM annotations for CD4+ T cells. You can get their state annotaitons here: https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html#core_15state

[Faiza]

thanks for your response. Since you mentioned that H3K27ac ChIP-seq peaks are defined as enhancers when excluded the regions overlapping promoters. Encode contain H3K27ac bigwig file which is Signal p value and bed (broadPeak),(NarrowPeaks) which contains peaks . My Question is which file should i use bigwig or (broadPeak),(NarrowPeaks) from ENCODE to define the enhnacer regions ?, and how can i define the enhancer regions from that file?

Also how can i exclude the regions from that file overlapping promoters? Iam going to use IGV tool to visualize that whether snps overlap with enhancer regions, so which file format and data is useful .