RNA structure probing reveals the structural basis of Dicer binding and cleavage.

Nature Communications
Qing-Jun LuoQiangfeng Cliff Zhang

Abstract

It is known that an RNA's structure determines its biological function, yet current RNA structure probing methods only capture partial structure information. The ability to measure intact (i.e., full length) RNA structures will facilitate investigations of the functions and regulation mechanisms of small RNAs and identify short fragments of functional sites. Here, we present icSHAPE-MaP, an approach combining in vivo selective 2'-hydroxyl acylation and mutational profiling to probe intact RNA structures. We further showcase the RNA structural landscape of substrates bound by human Dicer based on the combination of RNA immunoprecipitation pull-down and icSHAPE-MaP small RNA structural profiling. We discover distinct structural categories of Dicer substrates in correlation to both their binding affinity and cleavage efficiency. And by tertiary structural modeling constrained by icSHAPE-MaP RNA structural data, we find the spatial distance measuring as an influential parameter for Dicer cleavage-site selection.

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Citations

Aug 28, 2021·International Journal of Molecular Sciences·Anna Wypijewska Del NogalL Marcus Wilhelmsson

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Software Mentioned

CLIP
FARFAR
Sklearn
Map
VARNAv3
Rosetta
in
RNAStructure
Fold
house Perl script

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