Methods to Study RNA–Chromatin Interactions

RNA plays a fundamental role in the organization of chromatin as well as the regulation of gene expression. Although the chromatin is pervasively attached by both coding and noncoding RNAs, the impact of these chromatin-associated RNAs (caRNAs) on gene expression and cellular functions and their underlying mechanisms have just begun to be unraveled. One approach to understand the potential mechanism of gene regulation by caRNAs is to identify the caRNA-associated genomic regions. Several groups have developed methods to capture RNA-chromatin interactions in either one RNA vs the whole genome, i.e., "one-to-all" or all RNAs vs the whole genome, i.e., "all-to-all" manner. In this chapter, we discuss several state-of-the-art methods highlighting the principles behind them, the experimental procedures, the advantages and limitations, and their applications. Our goal is to provide an overview and guide to researchers interested in exploring caRNAs using these techniques.