Chip-seq data and Hi C data

Question

[tarek.mohamed]

Dear All,

I have analyzed a chip-seq data from which I identified a peak that is located about 10 kb upstream of an interesting gene. I want to see if this binding site is located in an enhancer region. How can I use Hi-C data to confirm this distal binding site?

Thanks Tarek

Answer 1

[igor]

I want to see if this binding site is located in an enhancer region.

To see if it's an enhancer region, you need to have at least H3K27ac ChIP-seq data.

How can I use Hi-C data to confirm this distal binding site?

Are you trying to see if that site interacts with the gene? When you do Hi-C, you should end up with an interaction matrix that will have interactions for all regions against all others. You just need to look up the region of interest. However, most Hi-C is done at 40kb resolution. Even if you find high-quality 10kb resolution Hi-C, that is still way too coarse in your case.

[tarek.mohamed]

Hi Igor,

Thank you for your reply. My chip-seq experiment was done using human heart samples, so I have to use HI-C data from the same tissue type. I am not familiar with Hi C data sets. Is there a database where I can pull down an experiment that fits my chip-seq? Also, what software/package do you recommend for such analysis. My chip-seq was analyzed as follows, FASTQ files were aligned to GRCh38 using bowtie , Peaks were called using MACS2, ChIPseek package and R to annotate the peaks.

Thanks Tarek

[igor]

WashU EpiGenome Browser has some public datasets already loaded: http://epigenomegateway.wustl.edu/browser/

That's probably the easiest place to start.