DNMT3A-coordinated splicing governs the stem state switch towards differentiation in embryonic and haematopoietic stem cells

Raghav Ramabadran, Jarey H. Wang, Jaime M. Reyes, Anna G. Guzman, Sinjini Gupta, Carina Rosas, Lorenzo Brunetti, Michael C. Gundry, Ayala Tovy, Hali Long, Tianpeng Gu, Sean M. Cullen, Siddhartha Tyagi, Danielle Rux, Jean J. Kim, Steven M. Kornblau, Michael Kyba, Fabio Stossi, Rachel E. Rau, Koichi TakahashiThomas F. Westbrook, Margaret A. Goodell

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

Upon stimulation by extrinsic stimuli, stem cells initiate a programme that enables differentiation or self-renewal. Disruption of the stem state exit has catastrophic consequences for embryogenesis and can lead to cancer. While some elements of this stem state switch are known, major regulatory mechanisms remain unclear. Here we show that this switch involves a global increase in splicing efficiency coordinated by DNA methyltransferase 3α (DNMT3A), an enzyme typically involved in DNA methylation. Proper activation of murine and human embryonic and haematopoietic stem cells depends on messenger RNA processing, influenced by DNMT3A in response to stimuli. DNMT3A coordinates splicing through recruitment of the core spliceosome protein SF3B1 to RNA polymerase and mRNA. Importantly, the DNA methylation function of DNMT3A is not required and loss of DNMT3A leads to impaired splicing during stem cell turnover. Finally, we identify the spliceosome as a potential therapeutic target in DNMT3A-mutated leukaemias. Together, our results reveal a modality through which DNMT3A and the spliceosome govern exit from the stem state towards differentiation.

Original languageEnglish (US)
Pages (from-to)528-539
Number of pages12
JournalNature Cell Biology
Volume25
Issue number4
DOIs
StatePublished - Apr 2023

Bibliographical note

Funding Information:
We thank A. Jain, A. Malovannaya and S. Jung at the proteomics core at Baylor College of Medicine; J. Sederstrom in the flow cytometry core; T. Chen at M.D. Anderson for providing Dnmt3a KO J1 6aa mouse ESCs and S. Kornblau at M.D. Anderson, Department of Leukemia for access to AML patient samples. This work was supported by NIH grants DK092883, CA183252, AG036695, F31DK113705, CA215226, CA186784 and CA125123. Also supporting this work were CPRIT (RP160884), the CDMPR/DOD Breast Cancer Research Program (1W81XWH1810573), the McNair Medical Institute, the Edward P. Evans Foundation and the American Federation of Aging Research. BCM Mass Spectrometry Proteomics Core is supported by the Dan L. Duncan Comprehensive Cancer Center NIH award (P30 CA125123), CPRIT Core Facility Award (RP210227) and NIH High End Instrument award (S10 OD026804). In addition, this project was supported by the Cytometry and Cell Sorting Core at Baylor College of Medicine with funding from the CPRIT Core Facility Support Award (CPRIT-RP180672) and the NIH (CA125123 and RR024574).

Funding Information:
We thank A. Jain, A. Malovannaya and S. Jung at the proteomics core at Baylor College of Medicine; J. Sederstrom in the flow cytometry core; T. Chen at M.D. Anderson for providing Dnmt3a KO J1 6aa mouse ESCs and S. Kornblau at M.D. Anderson, Department of Leukemia for access to AML patient samples. This work was supported by NIH grants DK092883, CA183252, AG036695, F31DK113705, CA215226, CA186784 and CA125123. Also supporting this work were CPRIT (RP160884), the CDMPR/DOD Breast Cancer Research Program (1W81XWH1810573), the McNair Medical Institute, the Edward P. Evans Foundation and the American Federation of Aging Research. BCM Mass Spectrometry Proteomics Core is supported by the Dan L. Duncan Comprehensive Cancer Center NIH award (P30 CA125123), CPRIT Core Facility Award (RP210227) and NIH High End Instrument award (S10 OD026804). In addition, this project was supported by the Cytometry and Cell Sorting Core at Baylor College of Medicine with funding from the CPRIT Core Facility Support Award (CPRIT-RP180672) and the NIH (CA125123 and RR024574).

Publisher Copyright:
© 2023, The Author(s), under exclusive licence to Springer Nature Limited.

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