IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-64848-3.html
   My bibliography  Save this article

Systematic characterization of the composition and dynamics of processing body-associated mRNAs

Author

Listed:
  • Zhiyuan Sun

    (Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology)

  • Xiaozhen Wen

    (Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology)

  • Yanping Li

    (Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology)

  • Xiaoxin Xie

    (Southern University of Science and Technology)

  • Peng Dong

    (Southern University of Science and Technology)

  • Yi Shu

    (Southern University of Science and Technology)

  • Shuye Tian

    (Southern University of Science and Technology)

  • Jiao Yang

    (Southern University of Science and Technology)

  • Yangfan Lin

    (Southern University of Science and Technology)

  • Mengran Wang

    (Southern University of Science and Technology)

  • Feifei Jiang

    (Southern University of Science and Technology)

  • Qionghua Zhu

    (Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology)

  • Huanhuan Cui

    (Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology)

  • Jixian Zhai

    (Southern University of Science and Technology)

  • Yuhui Hu

    (Southern University of Science and Technology)

  • Liang Fang

    (Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology)

  • Wei Chen

    (Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology
    Southern University of Science and Technology)

Abstract

Processing bodies (PBs) are dynamic, membraneless organelles consisting of RNAs and proteins. While PB proteins have been extensively characterized, the methods for systematically profiling PB-associated RNAs are limited. To address this, we developed PB-TRIBE-STAMP, a tool based on two orthogonal RNA editing enzymes. Simultaneously applying APOBEC1-DDX6 and LSM14A-ADAR2dd, PB-TRIBE-STAMP identified 1,639 and 2,577 PB-associated mRNAs in HCT116 and HEK293T cells, respectively. Further biochemical isolation of PBs followed by RNA-seq validated that edited transcripts of these mRNAs were indeed enriched in PBs. Integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails. Many mRNA 3’ UTR isoforms exhibited isoform-specific PB association patterns. Moreover, we established a TRIBE-ID-based tool to characterize the mRNA-LSM14A/PB association at high temporal resolution and unveiled a higher splicing efficiency of LSM14A-associated XBP1 transcripts during unfolded protein response (UPR). Finally, based on single-cell LSM14A-TRIBE-ID (sc-LSM14A-TRIBE-ID), we demonstrated the dynamic pattern of mRNA-LSM14A/PB association during cell cycle progression.

Suggested Citation

  • Zhiyuan Sun & Xiaozhen Wen & Yanping Li & Xiaoxin Xie & Peng Dong & Yi Shu & Shuye Tian & Jiao Yang & Yangfan Lin & Mengran Wang & Feifei Jiang & Qionghua Zhu & Huanhuan Cui & Jixian Zhai & Yuhui Hu &, 2025. "Systematic characterization of the composition and dynamics of processing body-associated mRNAs," Nature Communications, Nature, vol. 16(1), pages 1-22, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-64848-3
    DOI: 10.1038/s41467-025-64848-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-64848-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-64848-3?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. Lauren A. Blake & Leslie Watkins & Yang Liu & Takanari Inoue & Bin Wu, 2024. "A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Charlotte A. Cialek & Gabriel Galindo & Tatsuya Morisaki & Ning Zhao & Taiowa A. Montgomery & Timothy J. Stasevich, 2022. "Imaging translational control by Argonaute with single-molecule resolution in live cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Xiangbin Ruan & Kaining Hu & Xiaochang Zhang, 2023. "PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Hugo C. Medina-Munoz & Eric Kofman & Pratibha Jagannatha & Evan A. Boyle & Tao Yu & Krysten L. Jones & Jasmine R. Mueller & Grace D. Lykins & Andrew T. Doudna & Samuel S. Park & Steven M. Blue & Brodi, 2024. "Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies," Nature Communications, Nature, vol. 15(1), pages 1-17, 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. Luis A. Ortiz-Rodríguez & Hadi Yassine & Ali Hatami & Vidhyadhar Nandana & Christopher A. Azaldegui & Jiayu Cheng & Yingxi Zhu & Jared M. Schrader & Julie S. Biteen, 2025. "Stress changes the material state of a bacterial biomolecular condensate and shifts its function from mRNA decay to storage," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    2. Ziguo Song & Junfan Guo & Zhanqing Fan & Shuhong Huang & Guanglei Li & Zichang Zhao & Bingchun Chen & Shisheng Huang & Wenxin Zheng & Yinghui Wei & Yulin Chen & Xingxu Huang & Jianghuai Liu & Lina Wu , 2025. "Noncanonical target-strand cytosine base editing via engineered Un1Cas12f1 platform," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    3. Qishan Liang & Tao Yu & Eric Kofman & Pratibha Jagannatha & Kevin Rhine & Brian A. Yee & Kevin D. Corbett & Gene W. Yeo, 2024. "High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Phillipp Torkler & Marina Sauer & Uwe Schwartz & Selim Corbacioglu & Gunhild Sommer & Tilman Heise, 2024. "LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    5. Lauren A. Blake & Leslie Watkins & Yang Liu & Takanari Inoue & Bin Wu, 2024. "A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    6. Ryan P. Hildebrandt & Kathryn R. Moss & Aleksandra Janusz-Kaminska & Luke A. Knudson & Lance T. Denes & Tanvi Saxena & Devi Prasad Boggupalli & Zhuangyue Li & Kun Lin & Gary J. Bassell & Eric T. Wang, 2023. "Muscleblind-like proteins use modular domains to localize RNAs by riding kinesins and docking to membranes," Nature Communications, Nature, vol. 14(1), pages 1-19, 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:16:y:2025:i:1:d:10.1038_s41467-025-64848-3. 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.