Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing

  1. Li Zhang
  2. Ngoc-Tung Tran
  3. Hairui Su
  4. Rui Wang
  5. Yuheng Lu
  6. Haiping Tang
  7. Sayura Aoyagi
  8. Ailan Guo
  9. Alireza Khodadadi-Jamayran
  10. Dewang Zhou
  11. Kun Qian
  12. Todd Hricik
  13. Jocelyn Côté
  14. Xiaosi Han
  15. Wenping zhou
  16. Suparna Laha
  17. Omar Abdel-Wahab
  18. Ross L Levine
  19. Glen Raffel
  20. Yanyan Liu
  21. Dongquan Chen
  22. Haitao Li
  23. Tim Townes
  24. Hengbin Wang
  25. Haiteng Deng
  26. Yujun George Zheng
  27. Christina Leslie
  28. Minkui Luo
  29. Xinyang Zhao  Is a corresponding author
  1. The University of Alabama at Birmingham, United States
  2. Memorial Sloan Kettering Cancer Center, United States
  3. Tsinghua University, China
  4. Cell Signaling Technology, Inc., United States
  5. The University of Georgia, United States
  6. University of Ottawa, Canada
  7. Zhengzhou - Henan Cancer Hospital, China
  8. University of Massachusetts Medical School, United States
  9. Tsinghua University, United States

Abstract

RBM15, an RNA binding protein, determines cell-fate specification of many tissues including blood. We demonstrate that RBM15 is methylated by protein arginine methyltransferase 1 (PRMT1) at residue R578 leading to its degradation via ubiquitylation by an E3 ligase (CNOT4). Overexpression of PRMT1 in acute megakaryocytic leukemia cell lines blocks megakaryocyte terminal differentiation by downregulation of RBM15 protein level. Restoring RBM15 protein level rescues megakaryocyte terminal differentiation blocked by PRMT1 overexpression. At the molecular level, RBM15 binds to pre-mRNA intronic regions of genes important for megakaryopoiesis such as GATA1, RUNX1, TAL1 and c-MPL. Furthermore, preferential binding of RBM15 to specific intronic regions recruits the splicing factor SF3B1 to the same sites for alternative splicing. Therefore, PRMT1 regulates alternative RNA splicing via reducing RBM15 protein concentration. Targeting PRMT1 may be a curative therapy to restore megakaryocyte differentiation for acute megakaryocytic leukemia.

Article and author information

Author details

  1. Li Zhang

    Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Ngoc-Tung Tran

    Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Hairui Su

    Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Rui Wang

    Program of Molecular Pharmacology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Yuheng Lu

    Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Haiping Tang

    School of Life Sciences, Tsinghua University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Sayura Aoyagi

    Cell Signaling Technology, Inc., Danvers, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Ailan Guo

    Cell Signaling Technology, Inc., Danvers, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Alireza Khodadadi-Jamayran

    Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Dewang Zhou

    Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Kun Qian

    Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Todd Hricik

    Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Jocelyn Côté

    Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
    Competing interests
    The authors declare that no competing interests exist.
  14. Xiaosi Han

    Department of Neurology, Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Wenping zhou

    Department of Internal Medicine, Zhengzhou - Henan Cancer Hospital, Zhengzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  16. Suparna Laha

    Division of Hematology and Oncology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Omar Abdel-Wahab

    Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Ross L Levine

    Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  19. Glen Raffel

    Division of Hematology and Oncology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  20. Yanyan Liu

    Department of Internal Medicine, Zhengzhou - Henan Cancer Hospital, Zhengzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  21. Dongquan Chen

    Division of Preventive Medicine, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  22. Haitao Li

    School of Life Sciences, Tsinghua University, Beijing, United States
    Competing interests
    The authors declare that no competing interests exist.
  23. Tim Townes

    Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  24. Hengbin Wang

    Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, United States
    Competing interests
    The authors declare that no competing interests exist.
  25. Haiteng Deng

    School of Life Sciences, Tsinghua University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  26. Yujun George Zheng

    Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, United States
    Competing interests
    The authors declare that no competing interests exist.
  27. Christina Leslie

    Computational Biology Program, Sloan Kettering Institute,, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  28. Minkui Luo

    Program of Molecular Pharmacology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  29. Xinyang Zhao

    Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
    For correspondence
    zhaox88@uab.edu
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2015, Zhang 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.

Metrics

  • 5,165
    views
  • 1,465
    downloads
  • 127
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Li Zhang
  2. Ngoc-Tung Tran
  3. Hairui Su
  4. Rui Wang
  5. Yuheng Lu
  6. Haiping Tang
  7. Sayura Aoyagi
  8. Ailan Guo
  9. Alireza Khodadadi-Jamayran
  10. Dewang Zhou
  11. Kun Qian
  12. Todd Hricik
  13. Jocelyn Côté
  14. Xiaosi Han
  15. Wenping zhou
  16. Suparna Laha
  17. Omar Abdel-Wahab
  18. Ross L Levine
  19. Glen Raffel
  20. Yanyan Liu
  21. Dongquan Chen
  22. Haitao Li
  23. Tim Townes
  24. Hengbin Wang
  25. Haiteng Deng
  26. Yujun George Zheng
  27. Christina Leslie
  28. Minkui Luo
  29. Xinyang Zhao
(2015)
Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing
eLife 4:e07938.
https://doi.org/10.7554/eLife.07938

Share this article

https://doi.org/10.7554/eLife.07938

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Jie Luo, Jeff Ranish
    Tools and Resources

    Dynamic conformational and structural changes in proteins and protein complexes play a central and ubiquitous role in the regulation of protein function, yet it is very challenging to study these changes, especially for large protein complexes, under physiological conditions. Here, we introduce a novel isobaric crosslinker, Qlinker, for studying conformational and structural changes in proteins and protein complexes using quantitative crosslinking mass spectrometry. Qlinkers are small and simple, amine-reactive molecules with an optimal extended distance of ~10 Å, which use MS2 reporter ions for relative quantification of Qlinker-modified peptides derived from different samples. We synthesized the 2-plex Q2linker and showed that the Q2linker can provide quantitative crosslinking data that pinpoints key conformational and structural changes in biosensors, binary and ternary complexes composed of the general transcription factors TBP, TFIIA, and TFIIB, and RNA polymerase II complexes.

    1. Biochemistry and Chemical Biology
    2. Stem Cells and Regenerative Medicine
    Alejandro J Brenes, Eva Griesser ... Angus I Lamond
    Research Article

    Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. In this study, we characterise the proteomes of multiple hiPSC and hESC lines derived from independent donors and find that while they express a near-identical set of proteins, they show consistent quantitative differences in the abundance of a subset of proteins. hiPSCs have increased total protein content, while maintaining a comparable cell cycle profile to hESCs, with increased abundance of cytoplasmic and mitochondrial proteins required to sustain high growth rates, including nutrient transporters and metabolic proteins. Prominent changes detected in proteins involved in mitochondrial metabolism correlated with enhanced mitochondrial potential, shown using high-resolution respirometry. hiPSCs also produced higher levels of secreted proteins, including growth factors and proteins involved in the inhibition of the immune system. The data indicate that reprogramming of fibroblasts to hiPSCs produces important differences in cytoplasmic and mitochondrial proteins compared to hESCs, with consequences affecting growth and metabolism. This study improves our understanding of the molecular differences between hiPSCs and hESCs, with implications for potential risks and benefits for their use in future disease modelling and therapeutic applications.