Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification
Top Cited Papers
- 22 January 2015
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 137 (5), 2107-2115
- https://doi.org/10.1021/ja513080v
Abstract
N6-Methyladenosine (m6A) modification is hypothesized to control processes such as RNA degradation, localization, and splicing. However, the molecular mechanisms by which this occurs are unclear. Here, we measured structures of an RNA duplex containing m6A in the GGACU consensus, along with an unmodified RNA control, by 2D NMR. The data show that m6A–U pairing in the double-stranded context is accompanied by the methylamino group rotating from its energetically preferred syn geometry on the Watson–Crick face to the higher-energy anti conformation, positioning the methyl group in the major groove. Thermodynamic measurements of m6A in duplexes reveal that it is destabilizing by 0.5–1.7 kcal/mol. In contrast, we show that m6A in unpaired positions base stacks considerably more strongly than the unmodified base, adding substantial stabilization in single-stranded locations. Transcriptome-wide nuclease mapping of methylated RNA secondary structure from human cells reveals a structural transition at methylated adenosines, with a tendency to single-stranded structure adjacent to the modified base.Keywords
Funding Information
- Swiss National Science Foundation
- National Human Genome Research Institute (P50-HG007735, R01-HG004361)
- National Institute of General Medical Sciences (GM067201, GM068122)
This publication has 36 references indexed in Scilit:
- ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse FertilityMolecular Cell, 2013
- Complementarity of End Regions Increases the Lifetime of Small RNAs in Mammalian CellsPLOS ONE, 2012
- N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTONature Chemical Biology, 2011
- Association of Obesity-related Genetic Variants With Endometrial Cancer Risk: A Report From the Shanghai Endometrial Cancer Genetics StudyAmerican Journal of Epidemiology, 2011
- The role of the fat mass and obesity associated gene (FTO) in breast cancer riskBMC Medical Genetics, 2011
- Comprehensive comparative analysis of strand-specific RNA sequencing methodsNature Methods, 2010
- TopHat: discovering splice junctions with RNA-SeqBioinformatics, 2009
- The Obesity-AssociatedFTOGene Encodes a 2-Oxoglutarate-Dependent Nucleic Acid DemethylaseScience, 2007
- Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cellsJournal of Molecular Biology, 1977
- Conformation of N 6 -Methyladenine, a Base Involved in DNA Modification: Restriction ProcessesScience, 1973