m6A RNA methylation impacts fate choices during skin morphogenesis
Abstract
N6-methyladenosine is the most prominent RNA modification in mammals. Here we study mouse skin embryogenesis to tackle m6A’s functions and physiological importance. We first landscape the m6A modifications on skin epithelial progenitor mRNAs. Contrasting with in vivo ribosomal profiling, we unearth a correlation between m6A-modification in coding sequences and enhanced translation, particularly of key morphogenetic signaling pathways. Tapping physiological relevance, we show that m6A loss profoundly alters these cues and perturbs cellular fate choices and tissue architecture in all skin lineages. By single-cell transcriptomics and bioinformatics, both signaling and canonical translation pathways show significant downregulation after m6A loss. Interestingly, however, many highly m6A-modified mRNAs are markedly upregulated upon m6A loss, and they encode RNA-methylation, RNA-processing and RNA-metabolism factors. Together, our findings suggest that m6A functions to enhance translation of key morphogenetic regulators, while also destabilizing sentinel mRNAs that are primed to activate rescue pathways when m6A levels drop.
Data availability
The miCLIP and single-cell RNA-seq data that support the findings of this study have been deposited to the Gene Expression Omnibus (GEO) repository with the accession codes GSE147415, GSE147489 and GSE14749.
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Single-cell RNA-seq of embryonic day 17 (E17) mouse skin epithelial cells with or without Mettl3 knockoutNCBI Gene Expression Omnibus, GSE147415.
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miCLIP-seq of postnatal day 0 (P0) normal mouse skin epithelial cellsNCBI Gene Expression Omnibus, GSE147489.
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mouse skin epithelial cellsNCBI Gene Expression Omnibus, GSE147490.
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Epidermis-specific ribosome profiling to describe the translational landscape of SOX2NCBI Gene Expression Omnibus, GSE83332.
Article and author information
Author details
Funding
Damon Runyon Cancer Research Foundation (Dale F. and Betty Ann Frey Fellow,DRG-2263-16)
- Linghe Xi
National Institute of Health (R01-AR27883)
- Elaine Fuchs
National Institute of Health (R01-AR31737)
- Elaine Fuchs
National Institute of Health (R01-CA186702)
- Samie R Jaffrey
National Institute of Health (R21-CA224391)
- Samie R Jaffrey
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: Animal experimentation: All mouse strains were housed in an AAALAC-accredited facility and experiments were conducted according to the Rockefeller University's Institutional Animal Care and Use Committee (IACUC), and NIH guidelines for Animal Care and Use. All animal procedures used in this study are described in our #20012-H & #17091-H protocols, which had been previously reviewed and approved by the Rockefeller University IACUC.
Reviewing Editor
- Valerie Horsley, Yale University, United States
Publication history
- Received: March 17, 2020
- Accepted: August 25, 2020
- Accepted Manuscript published: August 26, 2020 (version 1)
- Version of Record published: October 5, 2020 (version 2)
Copyright
© 2020, Xi 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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Further reading
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- Developmental Biology
- Evolutionary Biology
Development of tooth shape is regulated by the enamel knot signalling centre, at least in mammals. Fgf signalling regulates differential proliferation between the enamel knot and adjacent dental epithelia during tooth development, leading to formation of the dental cusp. The presence of an enamel knot in non-mammalian vertebrates is debated given differences in signalling. Here, we show the conservation and restriction of fgf3, fgf10, and shh to the sites of future dental cusps in the shark (Scyliorhinus canicula), whilst also highlighting striking differences between the shark and mouse. We reveal shifts in tooth size, shape, and cusp number following small molecule perturbations of canonical Wnt signalling. Resulting tooth phenotypes mirror observed effects in mammals, where canonical Wnt has been implicated as an upstream regulator of enamel knot signalling. In silico modelling of shark dental morphogenesis demonstrates how subtle changes in activatory and inhibitory signals can alter tooth shape, resembling developmental phenotypes and cusp shapes observed following experimental Wnt perturbation. Our results support the functional conservation of an enamel knot-like signalling centre throughout vertebrates and suggest that varied tooth types from sharks to mammals follow a similar developmental bauplan. Lineage-specific differences in signalling are not sufficient in refuting homology of this signalling centre, which is likely older than teeth themselves.
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- Developmental Biology
- Evolutionary Biology
The tooth shape of sharks and mice are regulated by a similar signaling center despite their teeth having very different geometries.