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

By Jason C. Bell, David Jukam, Nicole A. Teran, Viviana I Risca, Owen K Smith, Whitney L Johnson, Jan Skotheim, William J. Greenleaf, Aaron F. Straight

Posted 20 Mar 2017
bioRxiv DOI: 10.1101/118786 (published DOI: 10.7554/elife.27024)

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 Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. 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.

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