Enhancer distance cutoff

Question

[sysbiocoder]

How far can be the enhancer peaks (H3K27ac) associated with TSS of the protein coding gene. As enhancer can act at long distance, I want to concentrate on Cis-acting enhancers and use it for Geneset enrichment analysis

Answer 1

[Kristoffer Vitting-Seerup]

That is a question we cannot answer as there is no max distance. We even know of enhancers that act on different chromosomes - but those are naturally rare events.

From a more practical orientation a possible cold be features within the same TAD (topological associated domain) or features within +/-2e5 nucleotides. Generally I would not suggest going larger than that.

Hope this helps.

Kristoffer