Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

Tri C. Nguyen, Xiaoyi Cao, Pengfei Yu, Shu Xiao, Jia Lu, Fernando H. Biase, Bharat Sridhar, Norman Huang, Kang Zhang and Sheng Zhong ()
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Tri C. Nguyen: University of California, San Diego
Xiaoyi Cao: University of California, San Diego
Pengfei Yu: University of California, San Diego
Shu Xiao: University of California, San Diego
Jia Lu: University of California, San Diego
Fernando H. Biase: University of California, San Diego
Bharat Sridhar: University of California, San Diego
Norman Huang: University of California, San Diego
Kang Zhang: University of California, San Diego
Sheng Zhong: University of California, San Diego

Nature Communications, 2016, vol. 7, issue 1, 1-12

Abstract: Abstract The pervasive transcription of our genome presents a possibility of revealing new genomic functions by investigating RNA interactions. Current methods for mapping RNA–RNA interactions have to rely on an ‘anchor’ protein or RNA and often require molecular perturbations. Here we present the MARIO (Mapping RNA interactome in viv o) technology to massively reveal RNA–RNA interactions from unperturbed cells. We mapped tens of thousands of endogenous RNA–RNA interactions from mouse embryonic stem cells and brain. We validated seven interactions by RNA antisense purification and one interaction using single-molecule RNA–FISH. The experimentally derived RNA interactome is a scale-free network, which is not expected from currently perceived promiscuity in RNA–RNA interactions. Base pairing is observed at the interacting regions between long RNAs, including transposon transcripts, suggesting a class of regulatory sequences acting in trans. In addition, MARIO data reveal thousands of intra-molecule interactions, providing in vivo data on high-order RNA structures.

Date: 2016
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DOI: 10.1038/ncomms12023

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