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METTL3 modulates chromatin and transcription dynamics during cell fate transition

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Abstract

Transcriptional programming plays a key role in determining the cell state. Timely reconfiguration of chromatin structure and attenuation of pluripotent genes are required for efficient embryonic stem cell (ESC) differentiation. Here, we identify METTL3, a core N6-methyladenosine (m6A) catalyzing enzyme, as a crucial modulator of dynamic transcription and chromatin accessibility upon ESC-derived cardiac differentiation. Genome-wide analysis of chromatin-associated RNAs revealed that depletion of METTL3 failed to dramatically attenuate the transcription of pluripotent genes, as well as activate nascent cardiomyocyte-specific transcripts upon differentiation. Consistently, ATAC-seq analysis showed that loss of METTL3 markedly attenuated the dynamic alteration of chromatin accessibility at both promoters and gene bodies, resulting in reduced sensitivity of ESC chromatin structure to cardiac differentiation signal. Furthermore, we found that METTL3 negatively regulated the histone modifications H3K4me3 and H3K36me3, which are involved in METTL3-modulated dynamic chromatin architecture during cell state transition. Unexpectedly, using chromatin-associated m6A sequencing, we found that nuclear m6A underwent a dramatic increase upon differentiation, which correlates with the decrease of chromatin accessibility. Collectively, our findings reveal that METTL3 and nuclear m6A epitranscriptome couple with chromatin state to ensure transcriptional regulation of cell fate transition.

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Data availability

The ChrRNA-seq, ATAC-seq, and Chrm6A-seq data generated for this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE190083. ChIP-seq for histone modifications used in this study has been reanalyzed from published sequencing data (GSE120376).

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Acknowledgements

The authors are grateful to Howard Y. Chang at Stanford University for kindly providing Mettl3 knockout ES cells, and Roman Spektor at Cornell University for the assistance with ATAC-seq library preparation. They are also grateful to Cornell University Life Sciences Core Laboratory Center for sequencing support.

Funding

This work was supported by US National Institutes of Health (R21CA227917), HHMI Faculty Scholar (55108556), and National Natural Science Foundation of China (32070868, 81974527), as well as Natural Science Foundation of Jiangsu Province, China (BK20211219, BK20190533).

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  1. Xiao-Min Liu and Yuanhui Mao have contributed equally to this work.

Authors and Affiliations

  1. School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China

    Xiao-Min Liu, Shen Wang & Jun Zhou

  2. Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA

    Yuanhui Mao & Shu-Bing Qian

  3. Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China

    Yuanhui Mao

  4. Field of Genetics, Genomics, and Development, Cornell University, Ithaca, NY, 14853, USA

    Shu-Bing Qian

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  1. Xiao-Min Liu
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Contributions

XML and SBQ conceived the project and wrote the manuscript. XML performed the majority of experiments. YM conducted the majority of data analysis. SW conducted protein blotting and cell differentiation assay with support from JZ. All the authors discussed the results and edited the manuscript.

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Correspondence to Xiao-Min Liu or Shu-Bing Qian.

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Liu, XM., Mao, Y., Wang, S. et al. METTL3 modulates chromatin and transcription dynamics during cell fate transition. Cell. Mol. Life Sci. 79, 559 (2022). https://doi.org/10.1007/s00018-022-04590-x

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