RNA duplex map in living cells reveals higher-order transcriptome structure

Zhipeng Lu, Qiangfeng Cliff Zhang, Byron Lee, Ryan A. Flynn, Martin A. Smith, James T. Robinson, Chen Davidovich, Anne R. Gooding, Karen J. Goodrich, John S. Mattick, Jill P. Mesirov, Thomas R. Cech, Howard Y. Chang

Research output: Contribution to journalArticleResearchpeer-review

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.
Original languageEnglish
Pages (from-to)1267-1279
Number of pages13
JournalCell
Volume165
Issue number5
DOIs
Publication statusPublished - 19 May 2016

Cite this

Lu, Z., Zhang, Q. C., Lee, B., Flynn, R. A., Smith, M. A., Robinson, J. T., ... Chang, H. Y. (2016). RNA duplex map in living cells reveals higher-order transcriptome structure. Cell, 165(5), 1267-1279. https://doi.org/10.1016/j.cell.2016.04.028
Lu, Zhipeng ; Zhang, Qiangfeng Cliff ; Lee, Byron ; Flynn, Ryan A. ; Smith, Martin A. ; Robinson, James T. ; Davidovich, Chen ; Gooding, Anne R. ; Goodrich, Karen J. ; Mattick, John S. ; Mesirov, Jill P. ; Cech, Thomas R. ; Chang, Howard Y. / RNA duplex map in living cells reveals higher-order transcriptome structure. In: Cell. 2016 ; Vol. 165, No. 5. pp. 1267-1279.
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title = "RNA duplex map in living cells reveals higher-order transcriptome structure",
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.",
author = "Zhipeng Lu and Zhang, {Qiangfeng Cliff} and Byron Lee and Flynn, {Ryan A.} and Smith, {Martin A.} and Robinson, {James T.} and Chen Davidovich and Gooding, {Anne R.} and Goodrich, {Karen J.} and Mattick, {John S.} and Mesirov, {Jill P.} and Cech, {Thomas R.} and Chang, {Howard Y.}",
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Lu, Z, Zhang, QC, Lee, B, Flynn, RA, Smith, MA, Robinson, JT, Davidovich, C, Gooding, AR, Goodrich, KJ, Mattick, JS, Mesirov, JP, Cech, TR & Chang, HY 2016, 'RNA duplex map in living cells reveals higher-order transcriptome structure' Cell, vol. 165, no. 5, pp. 1267-1279. https://doi.org/10.1016/j.cell.2016.04.028

RNA duplex map in living cells reveals higher-order transcriptome structure. / Lu, Zhipeng; Zhang, Qiangfeng Cliff; Lee, Byron; Flynn, Ryan A.; Smith, Martin A.; Robinson, James T.; Davidovich, Chen; Gooding, Anne R.; Goodrich, Karen J.; Mattick, John S.; Mesirov, Jill P.; Cech, Thomas R.; Chang, Howard Y.

In: Cell, Vol. 165, No. 5, 19.05.2016, p. 1267-1279.

Research output: Contribution to journalArticleResearchpeer-review

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Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT et al. RNA duplex map in living cells reveals higher-order transcriptome structure. Cell. 2016 May 19;165(5):1267-1279. https://doi.org/10.1016/j.cell.2016.04.028