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Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly

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  • Fenghua Yang

    (Fudan University
    Westlake University; Institute of Biology, Westlake Institute for Advanced Study
    Westlake Laboratory of Life Sciences and Biomedicine)

  • Tong Bian

    (Fudan University
    Westlake University; Institute of Biology, Westlake Institute for Advanced Study
    Westlake Laboratory of Life Sciences and Biomedicine)

  • Xiechao Zhan

    (Westlake University; Institute of Biology, Westlake Institute for Advanced Study
    Westlake Laboratory of Life Sciences and Biomedicine)

  • Zhe Chen

    (School of Basic Medical Sciences, Xinjiang Medical University)

  • Zhihan Xing

    (Westlake University; Institute of Biology, Westlake Institute for Advanced Study
    Westlake Laboratory of Life Sciences and Biomedicine)

  • Nicolas A. Larsen

    (Foghorn Therapeutics)

  • Xiaofeng Zhang

    (Westlake University; Institute of Biology, Westlake Institute for Advanced Study
    Westlake Laboratory of Life Sciences and Biomedicine)

  • Yigong Shi

    (Westlake University; Institute of Biology, Westlake Institute for Advanced Study
    Westlake Laboratory of Life Sciences and Biomedicine)

Abstract

Three RNA helicases – DDX42, DDX46 and DHX15 – are found to be associated with human U2 snRNP, but their roles and mechanisms in U2 snRNP and spliceosome assembly are insufficiently understood. Here we report the cryo-electron microscopy (cryo-EM) structures of the DDX42-SF3b complex and a putative assembly precursor of 17S U2 snRNP that contains DDX42 (DDX42-U2 complex). DDX42 is anchored on SF3B1 through N-terminal sequences, with its N-plug occupying the RNA path of SF3B1. The binding mode of DDX42 to SF3B1 is in striking analogy to that of DDX46. In the DDX42-U2 complex, the N-terminus of DDX42 remains anchored on SF3B1, but the helicase domain has been displaced by U2 snRNA and TAT-SF1. Through in vitro assays, we show DDX42 and DDX46 are mutually exclusive in terms of binding to SF3b. Cancer-driving mutations of SF3B1 target the residues in the RNA path that directly interact with DDX42 and DDX46. These findings reveal the distinct roles of DDX42 and DDX46 in assembly of 17S U2 snRNP and provide insights into the mechanisms of SF3B1 cancer mutations.

Suggested Citation

  • Fenghua Yang & Tong Bian & Xiechao Zhan & Zhe Chen & Zhihan Xing & Nicolas A. Larsen & Xiaofeng Zhang & Yigong Shi, 2023. "Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36489-x
    DOI: 10.1038/s41467-023-36489-x
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    References listed on IDEAS

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    1. Zhenwei Zhang & Norbert Rigo & Olexandr Dybkov & Jean-Baptiste Fourmann & Cindy L. Will & Vinay Kumar & Henning Urlaub & Holger Stark & Reinhard Lührmann, 2021. "Structural insights into how Prp5 proofreads the pre-mRNA branch site," Nature, Nature, vol. 596(7871), pages 296-300, August.
    2. Constantin Cretu & Patricia Gee & Xiang Liu & Anant Agrawal & Tuong-Vi Nguyen & Arun K. Ghosh & Andrew Cook & Melissa Jurica & Nicholas A. Larsen & Vladimir Pena, 2021. "Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    3. Chengcheng Wang & Zhouyan Guo & Xiechao Zhan & Fenghua Yang & Mingxuan Wu & Xiaofeng Zhang, 2020. "Structure of the yeast Swi/Snf complex in a nucleosome free state," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
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