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Cell. 2016 May 19;165(5):1267-1279. doi: 10.1016/j.cell.2016.04.028. Epub 2016 May 12.

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

Author information

1
Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
2
Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
3
RNA Biology and Plasticity Group, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Medicine, NSW 2052, Australia.
4
Department of Medicine and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
5
HHMI and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia; EMBL Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, VIC 3800, Australia.
6
HHMI and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA.
7
Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA. Electronic address: howchang@stanford.edu.

Abstract

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 an individual-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 long noncoding RNA (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. VIDEO ABSTRACT.

PMID:
27180905
PMCID:
PMC5029792
DOI:
10.1016/j.cell.2016.04.028
[Indexed for MEDLINE]
Free PMC Article

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