Question: Determining the relationship between putative enhancer activity and it's associated gene activity
gravatar for Sinji
4.8 years ago by
UT Southwestern Medical Center
Sinji3.0k wrote:

I am looking for links to similar studies that I can learn from, for questions that I should consider answering, and bioinformatic analysis I should / could conduct in order to help answer a question. I realize these kinds of posts are looked down upon by this community because it might look like I want you guys to solve my problem, but I have limited access to bioinformatic mentors at my institute and as the only computational biologist in my lab, I am only one view, and I have hit a wall on how to continue moving forward on my project.

The details:

I have ChIP data on a transcription factor that I identified to be found in intergenic regions. After overlaying this TF with a broad range of histone markers, I learned that a large subset of these intergenic TF peaks correlated nicely with known enhancer markers. I annotated these enhancer regions to their nearest gene (side question: Is there a more sophisticated method for associating enhancers to genes?).

I obtained some GRO-seq data from another lab in my cell line, and I am now interested in determining whether there is any relationship / correlation between eRNA activity in my enhancer regions and their associated gene transcription activity.

Preliminary analysis shows me that the majority of the associated genes are active, and only a small subset of enhancer regions show transcriptional activity (which I am assuming are eRNA's). I don't visually see any higher amounts of expression at genes that are associated with enhancers that show transcriptional activity.

What other analysis could I run to determine whether their is a relationship here, or not? What other wet lab studies should be conducted to identify if my TF actually has an effect on the associated gene and to what affect (RNA-seq, ChIP-seq of KO's of my TF?). I am more interested in papers that attempt to associated enhancers with associated genes.

Any and all help is appreciated.

PS: If this post is not allowed, please feel free to close.

ADD COMMENTlink modified 4.8 years ago by jotan1.2k • written 4.8 years ago by Sinji3.0k
gravatar for jotan
4.8 years ago by
jotan1.2k wrote:

This is one technique you might want to consider if you're really interested in enhancer/promoter interactions:

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

It's a modified Hi-C type technique where you design probes to capture your promoters of interest (usually cell-type specific) and then sequence outwards from the promoters to identify potential enhancers.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by jotan1.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1303 users visited in the last hour