IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-59457-z.html
   My bibliography  Save this article

Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells

Author

Listed:
  • Sunfengda Song

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Haiyang Xie

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Qingwen Wang

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Xinyi Sun

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Jiasu Xu

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Rui Chen

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Yuankang Zhu

    (Shanghai Jiao Tong University)

  • Lai Jiang

    (Shanghai Jiao Tong University)

  • Xianting Ding

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

Abstract

Liquid-liquid phase separations (LLPS) are membraneless organelles driven by biomolecule assembly and are implicated in cellular physiological activities. However, spatiotemporal deciphering of the dynamic proteome in living cells during LLPS formation remains challenging. Here, we introduce the Composition of LLPS proteome Assembly by Proximity labeling-assisted Mass spectrometry (CLAPM). We demonstrate that CLAPM can instantaneously label and monitor the FUS interactome shifts within intracellular droplets undergoing spatiotemporal LLPS. We report 129, 182 and 822 proteins specifically present in the LLPS droplets of HeLa, HEK 293 T and neuronal cells respectively. CLAPM further categorizes spatiotemporal dynamic proteome in droplets for living neuronal cells and identifies 596 LLPS-aboriginal proteins, 226 LLPS-dependent proteins and 58 LLPS-sensitive proteins. For validation, we uncover 11 previously unknown LLPS proteins in vivo. CLAPM provides a versatile tool to decipher proteins involved in LLPS and enables the accurate characterization of dynamic proteome in living cells.

Suggested Citation

  • Sunfengda Song & Haiyang Xie & Qingwen Wang & Xinyi Sun & Jiasu Xu & Rui Chen & Yuankang Zhu & Lai Jiang & Xianting Ding, 2025. "Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59457-z
    DOI: 10.1038/s41467-025-59457-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-59457-z
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-59457-z?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. Pablo Gracia & David Polanco & Jorge Tarancón-Díez & Ilenia Serra & Maruan Bracci & Javier Oroz & Douglas V. Laurents & Inés García & Nunilo Cremades, 2022. "Molecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Hermann Broder Schmidt & Ariana Barreau & Rajat Rohatgi, 2019. "Phase separation-deficient TDP43 remains functional in splicing," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    3. Sayaka Yasuda & Hikaru Tsuchiya & Ai Kaiho & Qiang Guo & Ken Ikeuchi & Akinori Endo & Naoko Arai & Fumiaki Ohtake & Shigeo Murata & Toshifumi Inada & Wolfgang Baumeister & Rubén Fernández-Busnadiego &, 2020. "Stress- and ubiquitylation-dependent phase separation of the proteasome," Nature, Nature, vol. 578(7794), pages 296-300, February.
    4. Susmitha Ambadipudi & Jacek Biernat & Dietmar Riedel & Eckhard Mandelkow & Markus Zweckstetter, 2017. "Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    5. Diana M. Mitrea & Jaclyn A. Cika & Christopher B. Stanley & Amanda Nourse & Paulo L. Onuchic & Priya R. Banerjee & Aaron H. Phillips & Cheon-Gil Park & Ashok A. Deniz & Richard W. Kriwacki, 2018. "Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    6. Pilong Li & Sudeep Banjade & Hui-Chun Cheng & Soyeon Kim & Baoyu Chen & Liang Guo & Marc Llaguno & Javoris V. Hollingsworth & David S. King & Salman F. Banani & Paul S. Russo & Qiu-Xing Jiang & B. Tra, 2012. "Phase transitions in the assembly of multivalent signalling proteins," Nature, Nature, vol. 483(7389), pages 336-340, March.
    7. Mylene C. Ferrolino & Diana M. Mitrea & J. Robert Michael & Richard W. Kriwacki, 2018. "Compositional adaptability in NPM1-SURF6 scaffolding networks enabled by dynamic switching of phase separation mechanisms," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    8. Elsje G. Otten & Emma Werner & Ana Crespillo-Casado & Keith B. Boyle & Vimisha Dharamdasani & Claudio Pathe & Balaji Santhanam & Felix Randow, 2021. "Ubiquitylation of lipopolysaccharide by RNF213 during bacterial infection," Nature, Nature, vol. 594(7861), pages 111-116, June.
    9. Samsuzzoha Mondal & Karthik Narayan & Samuel Botterbusch & Imania Powers & Jason Zheng & Honey Priya James & Rui Jin & Tobias Baumgart, 2022. "Multivalent interactions between molecular components involved in fast endophilin mediated endocytosis drive protein phase separation," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    10. Amy R. Strom & Alexander V. Emelyanov & Mustafa Mir & Dmitry V. Fyodorov & Xavier Darzacq & Gary H. Karpen, 2017. "Phase separation drives heterochromatin domain formation," Nature, Nature, vol. 547(7662), pages 241-245, July.
    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. Furqan Dar & Samuel R. Cohen & Diana M. Mitrea & Aaron H. Phillips & Gergely Nagy & Wellington C. Leite & Christopher B. Stanley & Jeong-Mo Choi & Richard W. Kriwacki & Rohit V. Pappu, 2024. "Biomolecular condensates form spatially inhomogeneous network fluids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Xiaocen Jin & Hikari Tanaka & Meihua Jin & Kyota Fujita & Hidenori Homma & Maiko Inotsume & Huang Yong & Kenichi Umeda & Noriyuki Kodera & Toshio Ando & Hitoshi Okazawa, 2023. "PQBP5/NOL10 maintains and anchors the nucleolus under physiological and osmotic stress conditions," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    3. Manisha Poudyal & Komal Patel & Laxmikant Gadhe & Ajay Singh Sawner & Pradeep Kadu & Debalina Datta & Semanti Mukherjee & Soumik Ray & Ambuja Navalkar & Siddhartha Maiti & Debdeep Chatterjee & Jyoti D, 2023. "Intermolecular interactions underlie protein/peptide phase separation irrespective of sequence and structure at crowded milieu," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    4. Andres R. Tejedor & Ignacio Sanchez-Burgos & Maria Estevez-Espinosa & Adiran Garaizar & Rosana Collepardo-Guevara & Jorge Ramirez & Jorge R. Espinosa, 2022. "Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Zheng Shen & Daxiao Sun & Adriana Savastano & Sára Joana Varga & Maria-Sol Cima-Omori & Stefan Becker & Alf Honigmann & Markus Zweckstetter, 2023. "Multivalent Tau/PSD-95 interactions arrest in vitro condensates and clusters mimicking the postsynaptic density," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Emanuele Zippo & Dorothee Dormann & Thomas Speck & Lukas S. Stelzl, 2025. "Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    7. Xianle Shi & Yanjing Li & Hongwei Zhou & Xiukun Hou & Jihong Yang & Vikas Malik & Francesco Faiola & Junjun Ding & Xichen Bao & Miha Modic & Weiyu Zhang & Lingyi Chen & Syed Raza Mahmood & Effie Apost, 2024. "DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    8. Taehyun Kim & Jaeyoon Yoo & Sungho Do & Dong Soo Hwang & YongKeun Park & Yongdae Shin, 2023. "RNA-mediated demixing transition of low-density condensates," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    9. Ellen H. Brumbaugh-Reed & Yang Gao & Kazuhiro Aoki & Jared E. Toettcher, 2024. "Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    10. Pan Jia & Xiang Li & Xuelei Wang & Liangjiao Yao & Yingying Xu & Yu Hu & Wenwen Xu & Zhe He & Qifan Zhao & Yicong Deng & Yi Zang & Meiyu Zhang & Yan Zhang & Jun Qin & Wei Lu, 2021. "ZMYND8 mediated liquid condensates spatiotemporally decommission the latent super-enhancers during macrophage polarization," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    11. Simon M Lichtinger & Adiran Garaizar & Rosana Collepardo-Guevara & Aleks Reinhardt, 2021. "Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence," PLOS Computational Biology, Public Library of Science, vol. 17(8), pages 1-28, August.
    12. Yongqi Huang & Jitao Wen & Lisa-Marie Ramirez & Eymen Gümüşdil & Pravin Pokhrel & Viet H. Man & Haiqiong Ye & Yue Han & Yunfei Liu & Ping Li & Zhengding Su & Junmei Wang & Hanbin Mao & Markus Zweckste, 2023. "Methylene blue accelerates liquid-to-gel transition of tau condensates impacting tau function and pathology," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    13. Daniel C. Carrettiero & Maria C. Almeida & Andrew P. Longhini & Jennifer N. Rauch & Dasol Han & Xuemei Zhang & Saeed Najafi & Jason E. Gestwicki & Kenneth S. Kosik, 2022. "Stress routes clients to the proteasome via a BAG2 ubiquitin-independent degradation condensate," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    14. Richoo B. Davis & Anushka Supakar & Aishwarya Kanchi Ranganath & Mahdi Muhammad Moosa & Priya R. Banerjee, 2024. "Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    15. Shuangcheng Alivia Wu & Chenchen Shen & Xiaoqiong Wei & Xiawei Zhang & Siwen Wang & Xinxin Chen & Mauricio Torres & You Lu & Liangguang Leo Lin & Huilun Helen Wang & Allen H. Hunter & Deyu Fang & Shen, 2023. "The mechanisms to dispose of misfolded proteins in the endoplasmic reticulum of adipocytes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    16. Beatrice Ramm & Dominik Schumacher & Andrea Harms & Tamara Heermann & Philipp Klos & Franziska Müller & Petra Schwille & Lotte Søgaard-Andersen, 2023. "Biomolecular condensate drives polymerization and bundling of the bacterial tubulin FtsZ to regulate cell division," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
    17. Xiaofan Yang & Xiaotong Zhu & Junli Sheng & Yuling Fu & Dingnai Nie & Xiaolong You & Yitian Chen & Xiaodan Yang & Qiao Ling & Huili Zhang & Xiaomin Li & Shengfeng Hu, 2024. "RNF213 promotes Treg cell differentiation by facilitating K63-linked ubiquitination and nuclear translocation of FOXO1," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    18. Yifeng Qi & Bin Zhang, 2021. "Chromatin network retards nucleoli coalescence," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    19. Raluca Groza & Kita Valerie Schmidt & Paul Markus Müller & Paolo Ronchi & Claire Schlack-Leigers & Ursula Neu & Dmytro Puchkov & Rumiana Dimova & Claudia Matthaeus & Justin Taraska & Thomas R. Weikl &, 2024. "Adhesion energy controls lipid binding-mediated endocytosis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    20. Ting Peng & Yingping Hou & Haowei Meng & Yong Cao & Xiaotian Wang & Lumeng Jia & Qing Chen & Yang Zheng & Yujie Sun & Hebing Chen & Tingting Li & Cheng Li, 2023. "Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions," Nature Communications, Nature, vol. 14(1), pages 1-15, 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_s41467-025-59457-z. 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.