Tri-4C: Efficient and Quantitative Analysis of Enhancer Loops at Hundred Base Pair Resolution

Enhancer looping governs gene regulatory circuitry but is challenging to detect. Here we present Tri-4C, a novel targeted chromatin conformation capture method (4C) using triple restriction enzyme (RE) digestion to fine map distal chromatin contacts at unprecedented hundred base pair resolution. Tri-4C identifies enhancer loops that are undetectable by existing UMI-4C 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 enhancer loop detection with high accuracy.