Systematic Mapping of RNA-Chromatin Interactions In Vivo

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 unperturb...

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Bibliographic Details
Published in:Current biology 2017-02, Vol.27 (4), p.602-609
Main Authors: Sridhar, Bharat, Rivas-Astroza, Marcelo, Nguyen, Tri C., Chen, Weizhong, Yan, Zhangming, Cao, Xiaoyi, Hebert, Lucie, Zhong, Sheng
Format: Article
Language:English
Subjects:
chromatin
chromatin-associated RNA
proximity ligation
RNA
RNA-chromatin interactions
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Summary: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. [Display omitted] •MARGI globally profiles native RNA-chromatin interactions•Two variations of MARGI interrogate proximity-based and direct interactions•The majority of transcription start sites are associated with interacting RNAs•RNA attachment is positively correlated with active histone marks in promoters Sridhar et al. develop a technology to map global RNA-chromatin interactions in unperturbed cells. They discover hundreds of chromatin-associated RNAs. They find that the majority of known transcription start sites are associated with chromatin-associated RNAs, suggesting that this phenomenon is more widespread than previously thought.
ISSN:0960-9822
1879-0445
DOI:10.1016/j.cub.2017.01.011