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bioRxiv · 10.1101/2025.04.15.648887

M6A reader protein YTHDF3 regulates cardiomyocyte death and atrophy by modulating the alternative splicing program

Gaur, A.·Chaudhary, S.·Sharma, R. K.·Kundu, S.·E, G.·Kumari, R.·Singh, S.·Prakash, S.·Mitra, K.·Kumar, S.·Gupta, S. K.
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Abstract

BackgroundThe functional impact of m6A modifications on RNA is governed by reader proteins that read the m6A marks and process the RNA accordingly. Recent studies have highlighted the importance of m6A reader proteins in the heart. However, the function of a reader protein Ythdf3 in the heart remains completely unknown. ObjectiveWe aim to uncover the function of Ythdf3 in the hearts. Methods& ResultsHere, we show that Ythdf3 is indispensable for the heart, and its knockdown leads to cardiac cachexia evident by cardiomyocyte atrophy, death, and less dense myofibrils visualized by electron microscopy. We also found downregulation of Ythdf3 in response to doxorubicin, and its overexpression rescues doxorubicin-induced cardiomyocyte atrophy and death. Contrary to primarily cytoplasmic localization, we found that Ythdf3 localizes in the cardiomyocyte nucleus. Furthermore, using co-immunoprecipitation coupled with LC-MS/MS, we show that Ythdf3 interacts with splicing proteins like DDX5 and HNRNPU and regulates alternative splicing in the heart. Mechanistically, we found that Ythdf3 regulates the splicing of CaMKII{delta}, and its knockdown leads to an increase in CaMKII{delta}A and CaMKII{delta}C isoforms while a decrease in CaMKII{delta}9 isoform. ConclusionCollectively, Ythdf3 knockdown in the adult heart leads to cardiac cachexia due to the alteration of the splicing program.

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Gaur, A., Chaudhary, S., Sharma, R. K., Kundu, S., E, G., Kumari, R., Singh, S., Prakash, S., Mitra, K., Kumar, S., Gupta, S. K.. 2025-04-16. M6A reader protein YTHDF3 regulates cardiomyocyte death and atrophy by modulating the alternative splicing program. https://doi.org/10.1101/2025.04.15.648887

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