A potentially abundant junctional RNA motif stabilized by m6A and Mg2.

Nature Communications
Bei LiuHashim M Al-Hashimi

Abstract

N6-Methyladenosine (m6A) is an abundant post-transcriptional RNA modification that influences multiple aspects of gene expression. In addition to recruiting proteins, m6A can modulate RNA function by destabilizing base pairing. Here, we show that when neighbored by a 5' bulge, m6A stabilizes m6A-U base pairs, and global RNA structure by ~1 kcal mol-1. The bulge most likely provides the flexibility needed to allow optimal stacking between the methyl group and 3' neighbor through a conformation that is stabilized by Mg2+. A bias toward this motif can help explain the global impact of methylation on RNA structure in transcriptome-wide studies. While m6A embedded in duplex RNA is poorly recognized by the YTH domain reader protein and m6A antibodies, both readily recognize m6A in this newly identified motif. The results uncover potentially abundant and functional m6A motifs that can modulate the epitranscriptomic structure landscape with important implications for the interpretation of transcriptome-wide data.

References

Nov 1, 1979·FEBS Letters·H A Geerdes, C W Hilbers
Oct 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·R DesrosiersF Rottman
Sep 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·S HorowitzF M Rottman
Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
Nov 24, 1999·The Journal of Biological Chemistry·G M WilsonG Brewer
Mar 7, 2008·Nature·Marc Parisien, François Major
Feb 20, 2010·The Journal of Biological Chemistry·Zhaiyi ZhangStefan Stamm
Mar 17, 2010·BMC Bioinformatics·Jessica S Reuter, David H Mathews
Mar 5, 2011·Nature Protocols·Ana M Rossi, Colin W Taylor
Oct 18, 2011·Nature Chemical Biology·Guifang JiaChuan He
May 12, 2012·Nature·Dan DominissiniGideon Rechavi
Aug 30, 2012·Nature Methods·Caroline A SchneiderKevin W Eliceiri
Dec 10, 2013·Nature Chemical Biology·Jianzhao LiuChuan He
Sep 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Shukun Luo, Liang Tong
Sep 23, 2014·Nature Chemical Biology·Chao XuJinrong Min
Jan 23, 2015·Journal of the American Chemical Society·Caroline RoostEric T Kool
Mar 25, 2015·Nature·Robert C SpitaleHoward Y Chang
Jun 30, 2015·Nature Methods·Bastian LinderSamie R Jaffrey
Aug 4, 2015·Chemistry : a European Journal·Sandro NeunerRonald Micura
Nov 26, 2015·Cell·Kate D MeyerSamie R Jaffrey
Jan 12, 2016·Nature Structural & Molecular Biology·Junhong ChoiJoseph D Puglisi
Feb 16, 2016·Molecular Cell·Wen XiaoYun-Gui Yang
Mar 24, 2016·Proceedings of the National Academy of Sciences of the United States of America·Chuanzhao ZhangGregg L Semenza
Apr 28, 2016·Cell Host & Microbe·Edward M KennedyBryan R Cullen
Apr 28, 2016·Molecular Cell·Shuibin LinRichard I Gregory
Aug 31, 2016·Nature Microbiology·Gianluigi LichinchiTariq M Rana
Oct 25, 2016·Cell Host & Microbe·Nandan S GokhaleStacy M Horner
Nov 4, 2016·Nature Reviews. Molecular Cell Biology·Boxuan Simen ZhaoChuan He
Dec 30, 2016·Nature Methods·Xiaoyu LiChengqi Yi
Jun 18, 2017·Cell·Ian A RoundtreeChuan He
Jun 18, 2017·EMBO Reports·Lin HuangDavid Mj Lilley

❮ Previous
Next ❯

Citations

Jul 10, 2019·Annual Review of Virology·Graham D WilliamsStacy M Horner
Jan 22, 2020·Wiley Interdisciplinary Reviews. RNA·Joshua D JonesKristin S Koutmou
Mar 21, 2019·Biological Chemistry·Paria Asadi-AtoiStefanie Kellner
Jun 27, 2019·RNA Biology·Saira AshrafDavid M J Lilley
Apr 22, 2020·Scientific Reports·Alexa B R McIntyreChristopher E Mason
Nov 14, 2019·International Journal of Molecular Sciences·Phillip J McCownJessica A Brown
Jul 1, 2020·Stem Cells·James M W R McElhinneyAbdulrahim A Sajini
Sep 19, 2020·Chemical Society Reviews·Ronald Micura, Claudia Höbartner
Oct 27, 2020·Nucleic Acids Research·Hala Abou AssiHashim M Al-Hashimi
Sep 12, 2020·The Journal of Biological Chemistry·Yu XuHashim M Al-Hashimi
Feb 27, 2020·Cell Reports·Laura R GanserHashim M Al-Hashimi
Dec 15, 2020·Trends in Biochemical Sciences·Michael J McFadden, Stacy M Horner
Dec 13, 2019·Journal of the American Chemical Society·Honglue ShiHashim M Al-Hashimi
Nov 23, 2018·Journal of the American Chemical Society·Clark Templeton, Ron Elber
Dec 5, 2018·Biochemistry·Christopher S Eubanks, Amanda E Hargrove
Aug 19, 2021·Immunological Reviews·Matthew G ThompsonStacy M Horner
Dec 8, 2021·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Lina WorpenbergJean-Yves Roignant

❮ Previous
Next ❯

Datasets Mentioned

BETA
AB047639

Methods Mentioned

BETA
NMR
immunoprecipitation
pulldown
dot blot
size exchange chromatography

Software Mentioned

Mathematica
RNAstructure
ImageJ
RNAstructure package
Fold
SPARKY
NMRpipe
RNAstrutcure
MC
Python

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Translational Research : the Journal of Laboratory and Clinical Medicine
Nian Liu, Tao Pan
Proceedings of the National Academy of Sciences of the United States of America
Hasan ImamAleem Siddiqui
© 2022 Meta ULC. All rights reserved