ChIP-based methods for the identification of long-range chromatin interactions

Abstract

Chromatin immunoprecipitation (ChIP) is an important technique for studying protein-DNA interactions. Whole genome ChIP methods have enjoyed much success, but are limited in that they cannot uncover important long-range chromatin interactions. Chromosome conformation capture (3C) and related methods are capable of detecting remote chromatin interactions, but are tedious, have low signal-to-noise ratios, and are not genome-wide. Although the addition of ChIP to 3C (ChIP-3C) would conceivably reduce noise and increase specificity for chromatin interaction detection, there are concerns that simple mixing of the ChIP and 3C protocols would lead to high levels of false positives. In this essay, we dissect current ChIP- and 3C-based methodologies, discuss the models of specific as opposed to non-specific chromatin interactions, and suggest approaches to separate specific chromatin complexes from non-specific chromatin fragments. We conclude that the combination of sonication-based chromatin fragmentation, ChIP-based enrichment, chromatin proximity ligation and Paired-End Tag ultra-highthroughput sequencing will be a winning implementation for genome-wide, unbiased and de novo discovery of long-range chromatin interactions, which will help to establish an emerging field for studying human chromatin interactomes and genome regulation networks in three-dimensional spaces. © 2009 Wiley-Liss, Inc.