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RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro

Shan Qi1,2, Javier Mota1, Siu-Hong Chan3

  • 1Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, United States.

Elife
|January 21, 2022
PubMed

Insights

The METTL3-METTL14 complex methylates RNA and DNA. It preferentially methylates single-stranded DNA (ssDNA) over structured RNA, despite binding RNA more strongly.

Area of Science:

  • Epigenetics
  • Molecular Biology
  • Biochemistry

Background:

  • The Methyltransferase like-3 (METTL3) and METTL14 complex is known to methylate adenosine bases in RNA (m⁶A) and DNA (m⁶dA).
  • This complex plays a role in chromatin regulation, particularly where DNA and RNA interact.
  • The precise mechanisms governing substrate specificity and the interplay between DNA and RNA methylation by METTL3-METTL14 remain incompletely understood.

Purpose of the Study:

  • To elucidate the substrate specificity of the METTL3-METTL14 complex for both DNA and RNA.
  • To investigate the relationship between substrate binding affinity and methylation activity for DNA and RNA.
  • To understand how nucleic acid structure influences METTL3-METTL14-mediated methylation.

Main Methods:

  • In vitro analysis of METTL3-METTL14 methylation activity and binding affinity.
  • Systematic testing using DNA and RNA oligonucleotides with varying structures (single-stranded, duplex, structured).
  • Assessment of methylation efficiency across different substrates and structural contexts.

Main Results:

  • An inverse correlation was observed between substrate binding affinity and methylation activity for the METTL3-METTL14 complex.
  • METTL3-METTL14 preferentially catalyzes m⁶dA formation in single-stranded DNA (ssDNA), despite lower binding affinity compared to RNA.
  • While binding structured RNAs with high affinity, METTL3-METTL14 exhibits significantly lower m⁶A methylation efficiency in RNA compared to ssDNA.
  • Structured RNA elements were found to restrict METTL3-METTL14-mediated DNA methylation.

Conclusions:

  • The METTL3-METTL14 complex demonstrates distinct substrate preferences based on nucleic acid structure and methylation efficiency.
  • Single-stranded DNA is a preferred substrate for methylation by METTL3-METTL14, contrasting with its higher affinity for structured RNAs.
  • Cellular RNA structures can act as regulators, limiting the METTL3-METTL14 complex's access to DNA substrates.
Keywords:
DNA methylationRNA methylationRNA/DNA bindingRNA/DNA modificationsbiochemistrychemical biologychemical modificationhumanmedicinesam-dependent methyltransferase

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