Hello everyone! Recently, I have been worrying about identifying the target genes regulated by enhancers, because there seems to be no better identification method at present, such as identifying enhancers to regulate target genes by distance, but I accidentally found that hic describes the interaction between chromosomes, so I want to use hic .Is it feasible to directly identify the target gene regulated by the element? For example, if an enhancer region is known, the interaction matrix of this region is extracted by juicer dump. After the interaction matrix is extracted, the R package biomaRt is used to obtain all target genes. But the hic interaction matrix is followed by the value of the interaction strength, do I need to consider it? Whether to filter out areas with low interaction strength.** eg:
chr start end chr start end value
chr11 1056892 2365830 chr11 1078962 1126548 5
chr11 1042352 2563830 chr11 1045822 1135628 4
The former region (if it is an enhancer region) interacts with the latter region, then the gene in the latter region is the target gene regulated by the enhancer, is this ok?
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I am not a HiC expert by any means but isn't HiC far too low-resolution to identify direct target genes unless you sequence it super deep with multiple experimental replicates? Look at your coordinates, these are 50kb and larger resolutions, thats longer than many genes as a whole.
I'm glad for your reply, that coordinate above is just an example. So if the resolution is lowered, is it better to identify the target gene? For example, the resolution is 1000.
You will have a hard time finding HiC data with 1kb resolution (are there any at all?) for exactly the celltype you workon as these interactions are celltype-specific.
Do you mean that the hic data found must be fixed to a certain cell line? For example, lung adenocarcinoma, there is hic data of A549, can I apply this data to H522 cell line, which is also lung adenocarcinoma, because I am exposed to hic for the first time, not very clear。