Hi everyone - I've got a list of genes that I am interested in identifying the enhancers that regulate their expression. I've got the BED file for the enhancers within my cell line of interest generated by intersecting ChIP-Seq peaks of different histone markers. How can I identify which enhancers regulate this list of genes (one of them is around 3000 genes) so I'd prefer something that doesn't need to be done manually one by one, unless there's none, I can then do so manually for a couple of them to test my hypothesis.
I also have another question, the BED files for the enhancers that I have are generated using hg19 as the reference genome. I did a liftOver to convert it to hg38 however, when I open both BED files on IGV, the regions representing the enhancers are quite different between both files. I used https://genome.ucsc.edu/cgi-bin/hgLiftOver to do the LiftOver with all default settings. Is there anything I could have missed?
Thank you.
From my understanding of the data you have at hand, I believe the best you could do is basically just show distances between enhancers and genes.
Depending on if your histone marks define active/poised with gene expression data, you could maybe show which active enhancers are close to the genes in your list (i.e. which enhancers from your list are within 100kb of the genes in your list). If you have expression changes or histone marker changes, you could also try to correlate these. These would be indirect evidence of course.
There may also be published 3d chromatin assays for a related cell line, where you could identify putative relationships by crossing your active enhancers with known enhancers and seeing if they have identified gene associations
What exactly do you mean by different? The reference sequence is totally different or the annotations are totally different, or ...?
Hello, I apologize for the late reply.
So you mean any enhancers (active) that are within 100kb of a gene would be considered as enhancers that regulate the expression of that gene? But then most likely there are other genes that are within those 100 kb window...
By saying they're different I meant that it does not correspond to the same region between both genome versions.
Yes, without some sort of direct enhancer / gene evidence, it would be simply associative. It's entirely possible the enhancer can regulate other nearby genes. You could also just find the enhancers that are closest to your genes of interest. You may even consider generating a list of enhancers close to your genes, then compare to the enhancers found close to a different set of genes.
All of this can be context specific though, so I would carefully consider what question you want to answer. For example, it will be hard to say definitively if an enhancer actually regulates your gene, but if you are asking a question to identify candidates for follow-up, this is one way to do that. Or, if you want to show these active enhancers found in a certain cell type are enriched in certain cell type specific genes, you could show that they are closer to the cell-type genes than to genes from other cell types.
How do you know they are not the same region?