Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

Molecular Cell
Erin E DuffyMatthew D Simon

Abstract

We describe a chemical method to label and purify 4-thiouridine (s(4)U)-containing RNA. We demonstrate that methanethiosulfonate (MTS) reagents form disulfide bonds with s(4)U more efficiently than the commonly used HPDP-biotin, leading to higher yields and less biased enrichment. This increase in efficiency allowed us to use s(4)U labeling to study global microRNA (miRNA) turnover in proliferating cultured human cells without perturbing global miRNA levels or the miRNA processing machinery. This improved chemistry will enhance methods that depend on tracking different populations of RNA, such as 4-thiouridine tagging to study tissue-specific transcription and dynamic transcriptome analysis (DTA) to study RNA turnover.

References

May 21, 1998·Nucleic Acids Research·E G MuellerJ L Paulson
May 18, 2007·Annual Review of Genomics and Human Genetics·Tsung-Cheng Chang, Joshua T Mendell
Sep 21, 2007·Bioinformatics·Mark D Robinson, Gordon K Smyth
Oct 9, 2008·Proceedings of the National Academy of Sciences of the United States of America·Cindy Y Jao, Adrian Salic
Mar 4, 2009·Nature Cell Biology·Julia WinterSven Diederichs
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 30, 2010·RNA·Sophie BailMegerditch Kiledjian
Mar 31, 2011·Nucleic Acids Research·Michael P GantierBryan R G Williams
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 21, 2012·Briefings in Bioinformatics·Helga ThorvaldsdóttirJill P Mesirov
Aug 28, 2012·Trends in Biochemical Sciences·Stefan Rüegger, Helge Großhans
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
Jun 5, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·Gunnar Jeschke
Oct 29, 2013·Nucleic Acids Research·Paul Julian KerseyDaniel Michael Staines
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Aug 28, 2014·RNA·Benjamin NeymotinDavid Gresham
Feb 6, 2015·Nucleic Acids Research·Yanwen GuoJun Lu

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Citations

Apr 14, 2016·Cell Reports·Yang ZhangLing-Ling Chen
May 6, 2016·Annual Review of Genomics and Human Genetics·Michael Rutenberg-SchoenbergMatthew D Simon
Nov 22, 2016·Nature Structural & Molecular Biology·Neelanjan MukherjeeUwe Ohler
Feb 1, 2017·Journal of the American Chemical Society·Kim NguyenRobert C Spitale
Mar 7, 2017·Bioconjugate Chemistry·Katharina SchmidMark Helm
Jun 24, 2017·Nucleic Acids Research·Naoki HidaMichael D Cleary
Feb 14, 2018·RNA·Andrew LugowskiOlivia S Rissland
Sep 26, 2017·Nature Methods·Veronika A HerzogStefan L Ameres
Oct 19, 2017·Molecular and Cellular Biology·Rafal Donczew, Steven Hahn
Jan 26, 2018·Wiley Interdisciplinary Reviews. Developmental Biology·Michael D Cleary
Jul 10, 2018·Nucleic Acids Research·Erin E DuffyMatthew D Simon
Jul 17, 2018·Nucleic Acids Research·Maria G IacovellaPeter De Wulf
Jan 23, 2018·Nature Methods·Jeremy A SchofieldMatthew D Simon
Nov 28, 2018·The EMBO Journal·Saša ŠvikovićJulian E Sale
Aug 8, 2019·PLoS Computational Biology·Alexey UvarovskiiChristoph Dieterich
Aug 9, 2019·Wiley Interdisciplinary Reviews. RNA·Nils MuthmannAndrea Rentmeister
Dec 8, 2016·Current Protocols in Chemical Biology·Erin E Duffy, Matthew D Simon
Jan 10, 2020·Nature Protocols·Lea H GregersenJesper Q Svejstrup
Feb 6, 2020·Cold Spring Harbor Symposia on Quantitative Biology·Paulina PawlicaJoan A Steitz
Dec 3, 2016·RNA Biology·Matthias Heiss, Stefanie Kellner
Apr 19, 2018·Nucleic Acids Research·Choudhary Shoaib AhmedCatherine L Jopling
Oct 28, 2019·Genome Research·Sascha H DuttkeChristopher Benner
Sep 15, 2019·Genome Research·Elena R Kingston, David P Bartel
Feb 6, 2020·Nature Methods·Sarah NainarRobert C Spitale
Nov 23, 2016·Wiley Interdisciplinary Reviews. RNA·Tara AlpertKarla M Neugebauer
Jun 10, 2017·Genome Research·Miha MilekMarkus Landthaler
Mar 14, 2017·Frontiers in Microbiology·Robert KnüppelSébastien Ferreira-Cerca
Dec 12, 2018·Quantitative Biology·Nicole M Martinez, Wendy V Gilbert
Jun 28, 2019·Nature Protocols·Wayo MatsushimaEric A Miska
Apr 15, 2020·Nature Biotechnology·Junyue CaoJay Shendure
Sep 7, 2016·Chembiochem : a European Journal of Chemical Biology·Sarah NainarRobert C Spitale
Aug 3, 2019·Cold Spring Harbor Perspectives in Biology·Karla M Neugebauer
Feb 13, 2018·Genes & Development·Joshua D EatonSteven West
Feb 22, 2017·Nature Reviews. Genetics·Mark Helm, Yuri Motorin

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