RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro
- The University of Texas Health Science Center at San Antonio, United States
- New England Biolabs, United States
Abstract
Methyltransferase like-3 (METTL3) and METTL14 complex transfers a methyl group from S-adenosyl-L-methionine to N6 amino group of adenosine bases in RNA (m6A) and DNA (m6dA). Emerging evidence highlights a role of METTL3-METTL14 in the chromatin context, especially in processes where DNA and RNA are held in close proximity. However, a mechanistic framework about specificity for substrate RNA/DNA and their interrelationship remain unclear. By systematically studying methylation activity and binding affinity to a number of DNA and RNA oligos with different propensities to form inter- or intra-molecular duplexes or single-stranded molecules in vitro, we uncover an inverse relationship for substrate binding and methylation and show that METTL3-METTL14 preferentially catalyzes the formation of m6dA in single-stranded DNA (ssDNA), despite weaker binding affinity to DNA. In contrast, it binds structured RNAs with high affinity, but methylates the target adenosine in RNA (m6A) much less efficiently than it does in ssDNA. We also show that METTL3-METTL14-mediated methylation of DNA is largely restricted by structured RNA elements prevalent in long noncoding and other cellular RNAs.
Data availability
The information about coding sequences of human METTL3 (NCBI reference sequence GI: 33301371) and METTL14 (NCBI reference sequence GI: 172045930) used in this study is available at NCBI. Source data are provided as a separate Source Data file. Correspondence and requests for material should be addressed to Y.K.G. (guptay@uthscsa.edu).
Article and author information
Author details
Funding
Max and Minnie Tomerlin Voelcker Fund
- Yogesh K Gupta
San Antonio Area Foundation
- Yogesh K Gupta
IIMS/CTSA pilot award
- Yogesh K Gupta
Greehey Children's Cancer Research Institute
- Shan Qi
- Yogesh K Gupta
University of Texas System
- Yogesh K Gupta
National Institute of Allergy and Infectious Diseases (1R01AI161363)
- Yogesh K Gupta
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Shozeb Haider, University College London, United Kingdom
Version history
- Received: February 2, 2021
- Preprint posted: January 9, 2022 (view preprint)
- Accepted: January 20, 2022
- Accepted Manuscript published: January 21, 2022 (version 1)
- Version of Record published: February 9, 2022 (version 2)
- Version of Record updated: April 4, 2022 (version 3)
Copyright
© 2022, Qi et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro
eLife 11:e67150.
https://doi.org/10.7554/eLife.67150
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