IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-51258-0.html
   My bibliography  Save this article

Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts

Author

Listed:
  • Kotaro Tomuro

    (RIKEN Cluster for Pioneering Research
    The University of Tokyo)

  • Mari Mito

    (RIKEN Cluster for Pioneering Research)

  • Hirotaka Toh

    (RIKEN Cluster for Pioneering Research)

  • Naohiro Kawamoto

    (RIKEN Cluster for Pioneering Research)

  • Takahito Miyake

    (Kyoto University, Sakyō-ku)

  • Siu Yu A. Chow

    (The University of Tokyo)

  • Masao Doi

    (Kyoto University, Sakyō-ku)

  • Yoshiho Ikeuchi

    (The University of Tokyo
    The University of Tokyo
    The University of Tokyo)

  • Yuichi Shichino

    (RIKEN Cluster for Pioneering Research)

  • Shintaro Iwasaki

    (RIKEN Cluster for Pioneering Research
    The University of Tokyo)

Abstract

Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of “Ribo-FilterOut”, which is based on the separation of footprints from ribosome subunits by ultrafiltration, and “Ribo-Calibration”, which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.

Suggested Citation

  • Kotaro Tomuro & Mari Mito & Hirotaka Toh & Naohiro Kawamoto & Takahito Miyake & Siu Yu A. Chow & Masao Doi & Yoshiho Ikeuchi & Yuichi Shichino & Shintaro Iwasaki, 2024. "Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51258-0
    DOI: 10.1038/s41467-024-51258-0
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-51258-0
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-51258-0?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Shintaro Iwasaki & Stephen N. Floor & Nicholas T. Ingolia, 2016. "Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor," Nature, Nature, vol. 534(7608), pages 558-561, June.
    2. Shiho Makino & Tomoko Kawamata & Shintaro Iwasaki & Yoshinori Ohsumi, 2021. "Selectivity of mRNA degradation by autophagy in yeast," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    3. Kazuhiro Kashiwagi & Yuichi Shichino & Tatsuya Osaki & Ayako Sakamoto & Madoka Nishimoto & Mari Takahashi & Mari Mito & Friedemann Weber & Yoshiho Ikeuchi & Shintaro Iwasaki & Takuhiro Ito, 2021. "eIF2B-capturing viral protein NSs suppresses the integrated stress response," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Hironori Saito & Yuma Handa & Mingming Chen & Tilman Schneider-Poetsch & Yuichi Shichino & Mari Takahashi & Daniel Romo & Minoru Yoshida & Alois Fürstner & Takuhiro Ito & Kaori Fukuzawa & Shintaro Iwa, 2024. "DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Antonios Apostolopoulos & Naohiro Kawamoto & Siu Yu A. Chow & Hitomi Tsuiji & Yoshiho Ikeuchi & Yuichi Shichino & Shintaro Iwasaki, 2024. "dCas13-mediated translational repression for accurate gene silencing in mammalian cells," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    3. Yifei Gu & Yuanhui Mao & Longfei Jia & Leiming Dong & Shu-Bing Qian, 2021. "Bi-directional ribosome scanning controls the stringency of start codon selection," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Ramona Weber & Leon Kleemann & Insa Hirschberg & Min-Yi Chung & Eugene Valkov & Cátia Igreja, 2022. "DAP5 enables main ORF translation on mRNAs with structured and uORF-containing 5′ leaders," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Kazuhiro Kashiwagi & Yuichi Shichino & Tatsuya Osaki & Ayako Sakamoto & Madoka Nishimoto & Mari Takahashi & Mari Mito & Friedemann Weber & Yoshiho Ikeuchi & Shintaro Iwasaki & Takuhiro Ito, 2021. "eIF2B-capturing viral protein NSs suppresses the integrated stress response," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Chisa Shiraishi & Akinobu Matsumoto & Kazuya Ichihara & Taishi Yamamoto & Takeshi Yokoyama & Taisuke Mizoo & Atsushi Hatano & Masaki Matsumoto & Yoshikazu Tanaka & Eriko Matsuura-Suzuki & Shintaro Iwa, 2023. "RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    7. Alla D. Fedorova & Stephen J. Kiniry & Dmitry E. Andreev & Jonathan M. Mudge & Pavel V. Baranov, 2022. "Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    8. Fajin Li & Jianhuo Fang & Yifan Yu & Sijia Hao & Qin Zou & Qinglin Zeng & Xuerui Yang, 2023. "Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51258-0. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.