TY - JOUR TI - Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts AU - Bell, Jason C AU - Jukam, David AU - Teran, Nicole A AU - Risca, Viviana I AU - Smith, Owen K AU - Johnson, Whitney L AU - Skotheim, Jan M AU - Greenleaf, William James AU - Straight, Aaron F A2 - Dekker, Job VL - 7 PY - 2018 DA - 2018/04/12 SP - e27024 C1 - eLife 2018;7:e27024 DO - 10.7554/eLife.27024 UR - https://doi.org/10.7554/eLife.27024 AB - 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. Using Drosophila 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. KW - RNA KW - chromatin KW - dosage compensation KW - transcription KW - genomics KW - non-coding RNA JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -