FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA

Nucleic Acids Research
Jean-Michel CarterShobbir Hussain

Abstract

Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNA, and in yeast is found at position U54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. Here we developed a genome-wide single-nucleotide resolution mapping method, Fluorouracil-Induced-Catalytic-Crosslinking-Sequencing (FICC-Seq), in order to identify the relevant enzymatic targets. We demonstrate that TRMT2A is responsible for the majority of m5U present in human RNA, and that it commonly targets U54 of cytosolic tRNAs. By comparison to current methods, we show that FICC-Seq is a particularly robust method for accurate and reliable detection of relevant enzymatic target sites. Our associated finding of extensive irreversible TRMT2A-tRNA crosslinking in vivo following 5-Fluorouracil exposure is also intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of Fluorouracil-mediated cytotoxicity.

References

Jan 1, 1994·Biochimie·J T KealeyD V Santi
Dec 10, 1999·Proceedings of the National Academy of Sciences of the United States of America·X GuD V Santi
May 2, 2003·Nature Reviews. Cancer·Daniel B LongleyPatrick G Johnston
Jan 20, 2004·RNA·Christopher J Spedaliere, Eugene G Mueller
Jan 12, 2007·Molecular Biology of the Cell·Shiho Sakita-SutoMasaaki Tatsuka
May 3, 2008·Proceedings of the National Academy of Sciences of the United States of America·Akram AlianJanet Finer-Moore
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Jul 6, 2010·Nature Structural & Molecular Biology·Julian KönigJernej Ule
Nov 5, 2010·PLoS Biology·Zhen WangJernej Ule
Apr 23, 2013·Nature Biotechnology·Vahid Khoddami, Bradley R Cairns
May 17, 2014·Nucleic Acids Research·Takeo Suzuki, Tsutomu Suzuki
Aug 19, 2014·Nucleic Acids Research·Stefanie KellnerMark Helm
Dec 18, 2015·Nucleic Acids Research·Patricia P Chan, Todd M Lowe
Dec 30, 2016·Nature Methods·Xiaoyu LiChengqi Yi
Nov 7, 2017·Nucleic Acids Research·Pietro BoccalettoJanusz M Bujnicki
May 22, 2018·Journal of the American Chemical Society·Vanja StojkovićDanica Galonić Fujimori
Oct 12, 2018·Methods : a Companion to Methods in Enzymology·Shobbir Hussain
Dec 7, 2018·Biochemical and Biophysical Research Communications·Yu-Hsin ChangSatoru Takahashi
Jan 31, 2019·Nucleic Acids Research·Valérie de Crécy-LagardJanusz M Bujnicki

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Citations

Jan 18, 2020·RNA Biology·Christopher A Powell, Michal Minczuk
Apr 18, 2020·Wiley Interdisciplinary Reviews. RNA·Phillip J McCownJessica A Brown
Aug 9, 2020·Frontiers in Genetics·M Isabel G Lopez SanchezJoanna Rorbach
Oct 1, 2020·Cells·Ivan LaptevPetr Sergiev
Dec 18, 2020·Nucleic Acids Research·Tommaso SelmiMichaela Frye
Jan 30, 2021·The FEBS Journal·Takeshi Chujo, Kazuhito Tomizawa
Nov 25, 2020·Molecular Therapy. Nucleic Acids·Jie JiangJia Meng
Apr 30, 2020·Trends in Cancer·Shobbir Hussain
Apr 4, 2021·International Journal of Molecular Sciences·Marisa PereiraAna R Soares
Apr 22, 2021·Science China. Life Sciences·Jing LiRu-Juan Liu
Apr 22, 2021·Methods : a Companion to Methods in Enzymology·Pengmian Feng, Wei Chen
Sep 25, 2021·Nature Chemical Biology·Wei DaiRalph E Kleiner

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Datasets Mentioned

BETA
GSE109183

Methods Mentioned

BETA
iCLIP
immunoprecipitations
PCR
UV-iCLIP

Software Mentioned

R packages
ENSEMB
Agilent MassHunter
ChIP
SE
R package corrplot
bowtie
Bedtools
tRNAscan
R

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