Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

Nature Protocols
Ryan A FlynnHoward Y Chang

Abstract

icSHAPE (in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3-modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. The entire experimental procedure can be completed in ∼5 d, and the sequencing and bioinformatics data analysis take an additional 4-5 d with no extensive computational skills required. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models.

References

Aug 29, 2000·Science·T R Cech
Mar 24, 2005·Journal of the American Chemical Society·Edward J MerinoKevin M Weeks
Dec 22, 2006·Nature Reviews. Molecular Cell Biology·Tariq M Rana
Oct 20, 2007·Nature Protocols·Pilar TijerinaRick Russell
Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·W A Ziehler, D R Engelke
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Feb 26, 2009·Cell·Thomas A CooperGideon Dreyfuss
Mar 17, 2010·BMC Bioinformatics·Jessica S Reuter, David H Mathews
May 8, 2010·Current Opinion in Structural Biology·Kevin M Weeks
Jul 6, 2010·Nature Structural & Molecular Biology·Julian KönigJernej Ule
Sep 3, 2010·Nature·Michael KerteszEran Segal
Nov 9, 2010·Nature Methods·Jason G UnderwoodDavid Haussler
Jun 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Julius B LucksAdam P Arkin
Jul 27, 2012·Cell Reports·Fan LiBrian D Gregory
Nov 28, 2012·Nature Chemical Biology·Robert C SpitaleHoward Y Chang
Sep 28, 2013·Science·Daniel B GoodmanSriram Kosuri
Oct 15, 2014·Nucleic Acids Research·Shakti IngleThomas D Tullius
Nov 21, 2014·RNA·Ryan A FlynnHoward Y Chang
Mar 3, 2015·Methods in Enzymology·Michael F Sloma, David H Mathews
Mar 25, 2015·Nature·Robert C SpitaleHoward Y Chang
Apr 30, 2015·Briefings in Bioinformatics·Youhuang BaiMing Chen
Oct 7, 2015·Trends in Cell Biology·Viviana I Risca, William J Greenleaf

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Citations

May 20, 2016·International Journal of Molecular Sciences·Rui LiYunbo Luo
Jul 22, 2016·RNA Biology·Shira Weingarten-Gabbay, Eran Segal
Feb 24, 2017·Nature Protocols·Yoichiro SugimotoJernej Ule
Oct 24, 2017·Nucleic Acids Research·Andreas ZauckerKaruna Sampath
Jan 9, 2018·Nucleic Acids Research·Kazumitsu OnizukaFumi Nagatsugi
Jun 9, 2018·Non-coding RNA·Laura J Leighton, Timothy W Bredy
Aug 5, 2017·Circulation. Cardiovascular Genetics·Elizabeth J Hennessy
Sep 19, 2017·PLoS Computational Biology·Alexey A GritsenkoEran Segal
Feb 1, 2018·Molecular Genetics and Genomics : MGG·Fei WangQing Wang
Apr 4, 2019·Nucleic Acids Research·Jasmin ChahalSelena M Sagan
Dec 3, 2016·Biochemical Society Transactions·Chun Kit Kwok
Jul 25, 2019·Journal of Molecular Cell Biology·Alisha N Jones, Michael Sattler
Jun 3, 2020·International Journal of Molecular Sciences·Omer AnHenry Yang
Jul 12, 2020·Nucleic Acids Research·Minglei YangYiliang Ding
Mar 20, 2019·Nature Structural & Molecular Biology·Lei SunQiangfeng Cliff Zhang
Jul 12, 2016·Wiley Interdisciplinary Reviews. RNA·Katrina M Kutchko, Alain Laederach
Sep 11, 2018·Frontiers in Physiology·Anna ZampetakiKathleen Steinhofel
Jul 23, 2020·Nucleic Acids Research·Takako OhyamaPiero Carninci
Jul 1, 2017·Wiley Interdisciplinary Reviews. RNA·Shawn W FoleyBrian D Gregory
Jun 28, 2018·SLAS Technology·John Lalith Charles Richard, Pieter Johan Adam Eichhorn
Sep 21, 2016·Annual Review of Genetics·Philip C BevilacquaSarah M Assmann
Dec 18, 2020·Nucleic Acids Research·Marina KalininaDmitri D Pervouchine
Oct 19, 2019·Trends in Genetics : TIG·Junjie T HuaHousheng H He
Feb 12, 2021·Methods : a Companion to Methods in Enzymology·Si-Kun GuoLing-Ling Chen
Dec 7, 2018·Methods : a Companion to Methods in Enzymology·Zhiye WangXiuren Zhang
Jan 24, 2021·Journal of Experimental Botany·Jiaying ZhuXiuren Zhang
Feb 20, 2021·Genomics, Proteomics & Bioinformatics·Gongwang YuJian-Rong Yang
Apr 18, 2021·Nature Communications·Svetlana KalmykovaDmitri Pervouchine
May 18, 2021·STAR Protocols·Lu ChenSteven E Artandi
Jul 14, 2021·Nature Cell Biology·Li-Sheng ZhangChuan He
Jul 14, 2018·Microbiology Spectrum·Alexander J Westermann
Aug 28, 2021·Biochemistry·Allison M WilliamsPhilip C Bevilacqua

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