title: Systematic Mapping of RNA-Chromatin Interactions In Vivo.
abstract: RNA molecules can attach to chromatin. It remains difficult to know what RNAs are associated with chromatin and where the genomic target loci of these RNAs are. Here, we present MARGI (mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNAs (caRNAs) with their target genomic sequences by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to a sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for human embryonic stem cells (ESCs) and human embryonic kidney (HEK) cells. MARGI revealed hundreds of caRNAs, including previously known XIST, SNHG1, NEAT1, and MALAT1, as well as each caRNA's genomic interaction loci. Using a cross-species experiment, we estimated that approximately 2.2% of MARGI-identified interactions were false positives. In ESCs and HEK cells, the RNA ends of more than 5% of MARGI read pairs were mapped to distal or inter-chromosomal locations as compared to the locations of their corresponding DNA ends. The majority of transcription start sites are associated with distal or inter-chromosomal caRNAs. Chromatin-immunoprecipitation-sequencing (ChIP-seq)-reported H3K27ac and H3K4me3 levels are positively correlated, while H3K9me3 is negatively correlated, with MARGI-reported RNA attachment levels. The MARGI technology should facilitate revealing novel RNA functions and their genomic target regions.
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Bharat
authors.initials: B
authors.lastname: Sridhar
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Marcelo
authors.initials: M
authors.lastname: Rivas-Astroza
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Tri C
authors.initials: TC
authors.lastname: Nguyen
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Weizhong
authors.initials: W
authors.lastname: Chen
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Zhangming
authors.initials: Z
authors.lastname: Yan
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Cao
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Lucie
authors.initials: L
authors.lastname: Hebert
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: szhong@ucsd.edu.
authors.forename: Sheng
authors.initials: S
authors.lastname: Zhong
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000235:genetics*; D002874:Chromosome Mapping; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D057809:HEK293 Cells; D000066449:Human Embryonic Stem Cells; D006801:Humans; D012313:RNA / Q000235:genetics*
chemical_list: D002843:Chromatin; D012313:RNA
keywords: RNA; RNA-chromatin interactions; chromatin; chromatin-associated RNA; proximity ligation