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The regulatory impact of RNA-binding proteins on microRNA targeting

Author

Listed:
  • Sukjun Kim

    (Seoul National University)

  • Soyoung Kim

    (Seoul National University)

  • Hee Ryung Chang

    (Seoul National University)

  • Doyeon Kim

    (Seoul National University)

  • Junehee Park

    (Seoul National University)

  • Narae Son

    (Seoul National University)

  • Joori Park

    (Korea University
    Korea University)

  • Minhyuk Yoon

    (Seoul National University)

  • Gwangung Chae

    (Seoul National University)

  • Young-Kook Kim

    (Chonnam National University Medical School)

  • V. Narry Kim

    (Seoul National University
    Institute for Basic Science)

  • Yoon Ki Kim

    (Korea University
    Korea University)

  • Jin-Wu Nam

    (Hanyang University)

  • Chanseok Shin

    (Seoul National University
    Seoul National University
    Seoul National University)

  • Daehyun Baek

    (Seoul National University
    Seoul National University)

Abstract

Argonaute is the primary mediator of metazoan miRNA targeting (MT). Among the currently identified >1,500 human RNA-binding proteins (RBPs), there are only a handful of RBPs known to enhance MT and several others reported to suppress MT, leaving the global impact of RBPs on MT elusive. In this study, we have systematically analyzed transcriptome-wide binding sites for 150 human RBPs and evaluated the quantitative effect of individual RBPs on MT efficacy. In contrast to previous studies, we show that most RBPs significantly affect MT and that all of those MT-regulating RBPs function as MT enhancers rather than suppressors, by making the local secondary structure of the target site accessible to Argonaute. Our findings illuminate the unappreciated regulatory impact of human RBPs on MT, and as these RBPs may play key roles in the gene regulatory network governed by metazoan miRNAs, MT should be understood in the context of co-regulating RBPs.

Suggested Citation

  • Sukjun Kim & Soyoung Kim & Hee Ryung Chang & Doyeon Kim & Junehee Park & Narae Son & Joori Park & Minhyuk Yoon & Gwangung Chae & Young-Kook Kim & V. Narry Kim & Yoon Ki Kim & Jin-Wu Nam & Chanseok Shi, 2021. "The regulatory impact of RNA-binding proteins on microRNA targeting," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25078-5
    DOI: 10.1038/s41467-021-25078-5
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    Cited by:

    1. Hyun Jung Hwang & Hongseok Ha & Ban Seok Lee & Bong Heon Kim & Hyun Kyu Song & Yoon Ki Kim, 2022. "LC3B is an RNA-binding protein to trigger rapid mRNA degradation during autophagy," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Jun Inamo & Akari Suzuki & Mahoko Takahashi Ueda & Kensuke Yamaguchi & Hiroshi Nishida & Katsuya Suzuki & Yuko Kaneko & Tsutomu Takeuchi & Hiroaki Hatano & Kazuyoshi Ishigaki & Yasushi Ishihama & Kazu, 2024. "Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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