UNDERSTANDING CHROMATIN INTERACTIONS FROM 1-DIMENSIONAL EPIGENETIC MARKS AND DNA SEQUENCES

Abstract

Chromatin interactions play important roles in regulating gene expression. They bridge distal regulatory elements to genes to regulate gene transcription and are involved in creating insulated domains to constrain the reach of cis-regulatory elements. We try to get better understanding of chromatin interactions from two aspects: 1) through their association with stretched cis-regulatory elements such as super-enhancers and broad H3K4me3 domains that are important in cell identity maintenance; 2) through predicting chromatin interactions from 1-dimentional epigenetic marks and DNA sequences, respectively, and investigate the epigenetic marks and DNA sequence features that are important for accurate prediction. Stretched regulatory elements showed high association with chromatin interactions and can confer higher cell-type specificities of target genes through chromatin interactions. We examined the problems of current state-of-art computational methods for predicting chromatin interactions and demonstrated that chromatin interactions can be accurately predicted from epigenetic marks as well as from pure DNA sequences.