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RNA duplex map in living cells reveals higher order transcriptome structure


RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here we develop PARIS, a method based on reversible psoralen- crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long- range structures, higher order architectures, and RNA:RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on a single molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures, and discovered conserved long-range and alternative structures. XIST, a lncRNA essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome.

Type Journal
Authors Lu, Z.; Zhang, Q.C.; Lee, B.; Flynn, R.A.; Smith, M.A.; Robinson, J.T.; Davidovich, C.; Gooding, A.R.; Goodrich, K.J.; Mattick, J.S.; Mesirov, J.P.; Cech, T.R.; Chang, H.Y.;
Publisher Name CELL
Published Date 2016-05-19
Published Volume 165
Published Issue 5
Published Pages 1267-79
Status Published in-print
DOI 10.1016/j.cell.2016.04.028
URL link to publisher's version
OpenAccess link to author's accepted manuscript version