Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.

Abstract

RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called <b>Ch</b>romatin-<b>A</b>ssociated <b>R</b>NA <b>seq</b>uencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using <i>Drosophila</i> cells, we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.