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A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation

Author

Listed:
  • Christopher P. Watkins

    (Department of Biochemistry and Molecular Biology)

  • Wen Zhang

    (University of Chicago)

  • Adam C. Wylder

    (University of Chicago)

  • Christopher D. Katanski

    (Department of Biochemistry and Molecular Biology)

  • Tao Pan

    (Department of Biochemistry and Molecular Biology)

Abstract

Small RNAs include tRNA, snRNA, micro-RNA, tRNA fragments and others that constitute > 90% of RNA copy numbers in a human cell and perform many essential functions. Popular small RNA-seq strategies limit the insights into coordinated small RNA response to cellular stress. Small RNA-seq also lacks multiplexing capabilities. Here, we report a multiplex small RNA-seq library preparation method (MSR-seq) to investigate cellular small RNA and mRNA response to heat shock, hydrogen peroxide, and arsenite stress. Comparing stress-induced changes of total cellular RNA and polysome-associated RNA, we identify a coordinated tRNA response that involves polysome-specific tRNA abundance and synergistic N3-methylcytosine (m3C) tRNA modification. Combining tRNA and mRNA response to stress we reveal a mechanism of stress-induced down-regulation in translational elongation. We also find that native tRNA molecules lacking several modifications are biased reservoirs for the biogenesis of tRNA fragments. Our results demonstrate the importance of simultaneous investigation of small RNAs and their modifications in response to varying biological conditions.

Suggested Citation

  • Christopher P. Watkins & Wen Zhang & Adam C. Wylder & Christopher D. Katanski & Tao Pan, 2022. "A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30261-3
    DOI: 10.1038/s41467-022-30261-3
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    References listed on IDEAS

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    1. Dan Dominissini & Sigrid Nachtergaele & Sharon Moshitch-Moshkovitz & Eyal Peer & Nitzan Kol & Moshe Shay Ben-Haim & Qing Dai & Ayelet Di Segni & Mali Salmon-Divon & Wesley C. Clark & Guanqun Zheng & T, 2016. "The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA," Nature, Nature, vol. 530(7591), pages 441-446, February.
    2. Xiao Wang & Zhike Lu & Adrian Gomez & Gary C. Hon & Yanan Yue & Dali Han & Ye Fu & Marc Parisien & Qing Dai & Guifang Jia & Bing Ren & Tao Pan & Chuan He, 2014. "N6-methyladenosine-dependent regulation of messenger RNA stability," Nature, Nature, vol. 505(7481), pages 117-120, January.
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