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  • Review Article
  • Published:

Gene expression regulation mediated through reversible m6A RNA methylation

Nature Reviews Genetics volume 15, pages 293–306 (2014)Cite this article

Subjects

Key Points

  • RNA modifications may post-transcriptionally regulate RNA stability, localization, transport, splicing and translation.

  • METTL3 and METTL14 catalyse N6-methyladenosine (m6A) methylation of mRNA (and other types of nuclear RNA) both in vitro and in vivo. Wilms' tumour 1-associating protein (WTAP) is another crucial component of this methyltransferase complex.

  • α-ketoglutarate-dependent dioxygenases FTO and ALKBH5 are m6A demethylases of mRNA (and other types of nuclear RNA) that affect biological processes such as development, energy homeostasis and spermatogenesis.

  • Genome-wide mapping of m6A in mRNA reveals that m6A localizes around stop codons and at 3′ untranslated regions in mammals and yeast. The methylation is dynamic and seems to have regulatory roles.

  • The YTHDF domain family proteins preferentially bind to m6A in mRNA. The recognition of m6A in mRNA and other polyadenylated RNA by YTHDF2 reduces the half-lives of its substrate RNAs through processing-body-mediated degradation.

  • RNA methylation directly affects the cell circadian cycle, embryonic stem cell differentiation and yeast meiosis.

  • We propose that the reversible RNA methylation pathway has evolved to regulate processes that involve rapid expression changes of large groups of genes and proteins.

Abstract

Cellular RNAs carry diverse chemical modifications that used to be regarded as static and having minor roles in 'fine-tuning' structural and functional properties of RNAs. In this Review, we focus on reversible methylation through the most prevalent mammalian mRNA internal modification, N6-methyladenosine (m6A). Recent studies have discovered protein 'writers', 'erasers' and 'readers' of this RNA chemical mark, as well as its dynamic deposition on mRNA and other types of nuclear RNA. These findings strongly indicate dynamic regulatory roles that are analogous to the well-known reversible epigenetic modifications of DNA and histone proteins. This reversible RNA methylation adds a new dimension to the developing picture of post-transcriptional regulation of gene expression.

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Figure 1: Reversible chemical modifications that regulate the flow of genetic information.
Figure 2: Profiling of m6A in RNA by m6A RNA immunoprecipitation.
Figure 3: Reversible m6A methylation of mRNA and other types of nuclear RNA.
Figure 4: Functions of the reader (that is, effector) proteins of m6A.
Figure 5: RNA methylation could affect various aspects of RNA metabolism and mRNA translation, and regulate protein expression post-transcrptionally.

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Acknowledgements

The authors apologize to colleagues whose work was not cited owing to space limitation. They thank T. Pan, X. Wang, Y. Yue and J. Liu for discussion. C.H. is supported by the US National Institutes of Health grants GM071440 and the EUREKA grant GM088599. This work was also supported partly by grants from the Israel Science Foundation, the Flight Attendant Medical Research Institute (FAMRI) and the Israeli Centers of Research Excellence. S.F. Reichard contributed to editing of this manuscript.

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Authors and Affiliations

  1. Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, 60637, Illinois, USA

    Ye Fu, Dan Dominissini & Chuan He

  2. Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, 52621, Israel

    Dan Dominissini & Gideon Rechavi

  3. Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel

    Dan Dominissini & Gideon Rechavi

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  1. Ye Fu
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Correspondence to Chuan He.

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Glossary

Epigenetic modifications

Reversible chemical modifications on DNA and histones that regulate gene expression independently of the genome sequences and that are heritable through cell division.

'Writers', 'erasers' and 'readers'

Enzymes or proteins that add, remove or preferentially bind to the chemical modifications at designated DNA or RNA nucleotides and amino acid residues of histones.

Methyltransferase

An enzyme that transfers a methyl group to its substrate. Most methyltransferases use S-adenosyl-l-methionine (SAM) as the methyl donor.

Two-dimensional thin layer chromatography

A technique to separate and identify nucleosides on cellulose plates according to their differential migration patterns in two different solvents. The nucleoside is typically radiolabelled for detection.

High-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry

(HPLC–QqQ-MS/MS). A liquid chromatography method coupled with triple-quadrupole tandem mass spectrometry, which can quantitatively and simultaneously monitor multiple molecular species according to their fragmentation patterns.

m6A RNA immunoprecipitation

An immunoprecipitation method to selectively enrich for N6-methyladenosine (m6A)-containing RNA using an m6A-targeted antibody.

Nuclear speckles

Nuclear domains located in the interchromatin regions of the nucleoplasm and enriched with pre-mRNA processing factors.

Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation

(PAR–CLIP). A biochemical method that takes advantage of incorporated photoreactive ribonucleoside analogues to identify the binding sites of RNA-binding proteins in cells.

Yeast two-hybrid screens

A method in which one protein is fused to the GAL4 activation domain and the other to the GAL4 DNA-binding domain, and both fusion proteins are introduced into yeast. Expression of a GAL4-regulated reporter gene indicates that the two proteins physically interact.

Demethylase

An enzyme that removes a methyl group from its substrate.

Oxidative demethylation

A chemical reaction in which the C–H bond of a methyl group attached to a nitrogen or an oxygen atom is oxidized to –OH by demethylases, and the intermediate decomposes to release the methyl group as formaldehyde.

Ribosome profiling

Qualitative and quantitative sequencing of the RNA attached to ribosomes as a signature of genes that are expressed.

Processing bodies

(P-bodies). Distinct foci in the cytoplasm that are enriched with RNA degradation factors.

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Fu, Y., Dominissini, D., Rechavi, G. et al. Gene expression regulation mediated through reversible m6A RNA methylation. Nat Rev Genet 15, 293–306 (2014). https://doi.org/10.1038/nrg3724

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