HiCAR analysis of zebrafish fin regeneration identifies cis-regulatory chromatin reorganization in response to injury

HiCAR (Hi-C on accessible regulatory DNA), which is a genome-wide profiling of chromatin accessibility and open chromatin anchored cis-regulatory element (cRE) interactions, identified 28690 calling loops from zebrafish caudal fins at three different time points (0, 1 and 4 day(s) post amputation (dpa)) including 5022 regeneration-responsive loops (17.5%). 10 caudal fins each of adult wild type zebrafish at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing HiCAR DNA libraries 10 caudal fins each of adult wild type zebrafish at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing HiCAR DNA libraries to find regeneration-responsive loops only in 1 and/or 4 dpa regenerating fins not in 0 dpa uninjured control fins..