Chromatin isolation by RNA purification (ChIRP) and its applications

Chromatin isolation by RNA purification (ChIRP) is a valuable method to map the genomic binding profile of chromatin-associated RNAs, such as long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). ChIRP was initially designed by Chu and colleagues to investigate RNA bound DNA using affinity-probes to a target RNA, and its application has been recently extended to also identify RNAs and proteins that interact with the target RNA. Since its original development in 2011, ChIRP has been increasingly used in various fields of biological research which has, in turn, resulted in an enhanced understanding of the dynamics of RNA-chromatin interactions and their roles in health and diseases. This chapter describes the methodology and applications of ChIRP.