Abstract
N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), and plays important roles in cell differentiation and tissue development. It regulates multiple steps throughout the RNA life cycle including RNA processing, translation, and decay, via the recognition by selective binding proteins. In the cytoplasm, m6A binding protein YTHDF1 facilitates translation of m6A-modified mRNAs, and YTHDF2 accelerates the decay of m6A-modified transcripts. The biological function of YTHDF3, another cytoplasmic m6A binder of the YTH (YT521-B homology) domain family, remains unknown. Here, we report that YTHDF3 promotes protein synthesis in synergy with YTHDF1, and affects methylated mRNA decay mediated through YTHDF2. Cells deficient in all three YTHDF proteins experience the most dramatic accumulation of m6A-modified transcripts. These results indicate that together with YTHDF1 and YTHDF2, YTHDF3 plays critical roles to accelerate metabolism of m6A-modified mRNAs in the cytoplasm. All three YTHDF proteins may act in an integrated and cooperative manner to impact fundamental biological processes related to m6A RNA methylation.
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Acknowledgements
We thank Professor T Pan (The University of Chicago) for kindly providing the polysome profiling instrument. We thank Dr J Tauler (The University of Chicago) for editing the manuscript. We also thank Institutes of Biomedical Sciences at Fudan University for the protein mass spectrometry experiments. The work was supported by the National Institutes of Health grants GM071440 and GM113194 to CH. CH is an investigator of the Howard Hughes Medical Institute (HHMI). HS is supported by the Gustavus F Swift Fellowship from the Chemistry Department at University of Chicago. HM is supported by the Postdoctoral International Exchange Program of the China Postdoctoral Council (CPC). The Mass Spectrometry Facility of the University of Chicago is funded by the National Science Foundation (CHE-1048528).
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Supplementary information
Supplementary information, Figure S1
Analyses of YTHDF3 PAR-CLIP data. (PDF 271 kb)
Supplementary information, Figure S2
Ribosome profiling and polysome profiling of HeLa cells depleted of YTHDF3 (A-J), and protein and mRNA levels of reporters in the double tethering assay (K). (PDF 210 kb)
Supplementary information, Figure S3
YTHDF3 and YTHDF1 co-immunoprecipitate and share protein partners. (PDF 103 kb)
Supplementary information, Figure S4
YTHDF3 regulates binding specificity and affinity of THDF1 and YTHDF2 towards target RNAs. (PDF 114 kb)
Supplementary information, Figure S5
Temporal order of YTHDFs' interaction with m6A-modified transcripts. (PDF 126 kb)
Supplementary information, Table S1
Target transcripts of YTHDF3 and Comparison of YTHDF1-3 targets (XLSX 25543 kb)
Supplementary information, Table S2
YTHDF3 protein interactome and Comparison of YTHDF1 and YTHDF3 protein partners (XLSX 39 kb)
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Shi, H., Wang, X., Lu, Z. et al. YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. Cell Res 27, 315–328 (2017). https://doi.org/10.1038/cr.2017.15
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DOI: https://doi.org/10.1038/cr.2017.15
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