Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (Tri-4C)

Enhancer looping governs gene regulatory circuitry but is challenging to detect. Here we present Tri-4C, an ultrafine mapping method for distal chromatin contacts using triple restriction enzyme (RE) digestion. Tri-4C identifies enhancer loops that are undetectable by current single RE- based methods and reveals quantitative loop strengths in enhancer interaction networks underlying dynamic gene control. This multi-RE approach may be applied to general 3C-derived methods for accurate detection of enhancer loops. Overall design: Examination of long range chromatin interaction in IFNB1 locus in IMR90 cells. Examination of long range chromatin interaction of ECAD9 in H7-derived vascular smooth muscle cells. Examination of long range chromatin interaction of IMR90 using Tri-4C with alternative (CviAII) digestion. The file "GSE119187_sample_viewpoints.xlsx" at the foot of this record includes the method (4C or Tri-4C) and the viewpoint sequence for each sample"