Literature DB >> 33885174

Paraspeckles are constructed as block copolymer micelles.

Tomohiro Yamazaki1, Tetsuya Yamamoto2, Hyura Yoshino3, Sylvie Souquere4, Shinichi Nakagawa5, Gerard Pierron6, Tetsuro Hirose1,3.   

Abstract

Paraspeckles are constructed by NEAT1_2 architectural long noncoding RNAs. Their characteristic cylindrical shapes, with highly ordered internal organization, distinguish them from typical liquid-liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. Using the soft matter physics, we then applied a theoretical framework to understand the principles that determine NEAT1_2 organization as well as shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through a type of microphase separation, micellization. This work provides an experiment-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding biomolecular condensates with optimal sizes and structures in cells.
© 2021 The Authors.

Entities:  

Keywords:  biomolecular condensate; block copolymer; long noncoding RNA; micellization; microphase separation

Mesh:

Substances:

Year:  2021        PMID: 33885174      PMCID: PMC8204865          DOI: 10.15252/embj.2020107270

Source DB:  PubMed          Journal:  EMBO J        ISSN: 0261-4189            Impact factor:   14.012


  71 in total

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Authors:  Clifford P Brangwynne; Christian R Eckmann; David S Courson; Agata Rybarska; Carsten Hoege; Jöbin Gharakhani; Frank Jülicher; Anthony A Hyman
Journal:  Science       Date:  2009-05-21       Impact factor: 47.728

Review 2.  RNA contributions to the form and function of biomolecular condensates.

Authors:  Christine Roden; Amy S Gladfelter
Journal:  Nat Rev Mol Cell Biol       Date:  2020-07-06       Impact factor: 94.444

Review 3.  The liquid nucleome - phase transitions in the nucleus at a glance.

Authors:  Amy R Strom; Clifford P Brangwynne
Journal:  J Cell Sci       Date:  2019-11-21       Impact factor: 5.285

4.  RIC-seq for global in situ profiling of RNA-RNA spatial interactions.

Authors:  Zhaokui Cai; Changchang Cao; Lei Ji; Rong Ye; Di Wang; Cong Xia; Sui Wang; Zongchang Du; Naijing Hu; Xiaohua Yu; Juan Chen; Lei Wang; Xianguang Yang; Shunmin He; Yuanchao Xue
Journal:  Nature       Date:  2020-05-06       Impact factor: 49.962

5.  RNA transcription modulates phase transition-driven nuclear body assembly.

Authors:  Joel Berry; Stephanie C Weber; Nilesh Vaidya; Mikko Haataja; Clifford P Brangwynne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-08       Impact factor: 11.205

6.  The long noncoding RNA Neat1 is required for mammary gland development and lactation.

Authors:  Laura Standaert; Carmen Adriaens; Enrico Radaelli; Alexandra Van Keymeulen; Cedric Blanpain; Tetsuro Hirose; Shinichi Nakagawa; Jean-Christophe Marine
Journal:  RNA       Date:  2014-10-14       Impact factor: 4.942

7.  Elastic ripening and inhibition of liquid-liquid phase separation.

Authors:  Kathryn A Rosowski; Tianqi Sai; Estefania Vidal-Henriquez; David Zwicker; Robert W Style; Eric R Dufresne
Journal:  Nat Phys       Date:  2020-01-27       Impact factor: 20.034

Review 8.  RNA toxicity in non-coding repeat expansion disorders.

Authors:  Bart Swinnen; Wim Robberecht; Ludo Van Den Bosch
Journal:  EMBO J       Date:  2019-11-13       Impact factor: 11.598

9.  Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture.

Authors:  Yizhu Lin; Brigitte F Schmidt; Marcel P Bruchez; C Joel McManus
Journal:  Nucleic Acids Res       Date:  2018-04-20       Impact factor: 16.971

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  12 in total

1.  CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis.

Authors:  Souvik Ghosh; Meric Ataman; Maciej Bak; Anastasiya Börsch; Alexander Schmidt; Katarzyna Buczak; Georges Martin; Beatrice Dimitriades; Christina J Herrmann; Alexander Kanitz; Mihaela Zavolan
Journal:  Nucleic Acids Res       Date:  2022-04-08       Impact factor: 16.971

2.  Statistical Thermodynamics Approach for Intracellular Phase Separation.

Authors:  Tomohiro Yamazaki; Tetsuya Yamamoto
Journal:  Methods Mol Biol       Date:  2022

3.  Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat.

Authors:  Akihiro Yamada; Hikaru Toya; Mayuko Tanahashi; Misuzu Kurihara; Mari Mito; Shintaro Iwasaki; Satoshi Kurosaka; Toru Takumi; Archa Fox; Yoshimi Kawamura; Kyoko Miura; Shinichi Nakagawa
Journal:  RNA       Date:  2022-06-02       Impact factor: 5.636

Review 4.  A conceptual framework for understanding phase separation and addressing open questions and challenges.

Authors:  Tanja Mittag; Rohit V Pappu
Journal:  Mol Cell       Date:  2022-06-07       Impact factor: 19.328

5.  Function moves biomolecular condensates in phase space.

Authors:  Marina Feric; Tom Misteli
Journal:  Bioessays       Date:  2022-03-03       Impact factor: 4.653

6.  RNA at the surface of phase-separated condensates impacts their size and number.

Authors:  Audrey Cochard; Marina Garcia-Jove Navarro; Leonard Piroska; Shunnichi Kashida; Michel Kress; Dominique Weil; Zoher Gueroui
Journal:  Biophys J       Date:  2022-03-29       Impact factor: 3.699

7.  Promyelocytic leukemia nuclear body-like structures can assemble in mouse oocytes.

Authors:  Osamu Udagawa; Ayaka Kato-Udagawa; Seishiro Hirano
Journal:  Biol Open       Date:  2022-06-06       Impact factor: 2.643

8.  Paraspeckles are constructed as block copolymer micelles.

Authors:  Tomohiro Yamazaki; Tetsuya Yamamoto; Hyura Yoshino; Sylvie Souquere; Shinichi Nakagawa; Gerard Pierron; Tetsuro Hirose
Journal:  EMBO J       Date:  2021-04-22       Impact factor: 14.012

Review 9.  Compartment-Specific Proximity Ligation Expands the Toolbox to Assess the Interactome of the Long Non-Coding RNA NEAT1.

Authors:  Victoria Mamontova; Barbara Trifault; Kaspar Burger
Journal:  Int J Mol Sci       Date:  2022-04-17       Impact factor: 6.208

Review 10.  Modulating biomolecular condensates: a novel approach to drug discovery.

Authors:  Diana M Mitrea; Matthäus Mittasch; Beatriz Ferreira Gomes; Isaac A Klein; Mark A Murcko
Journal:  Nat Rev Drug Discov       Date:  2022-08-16       Impact factor: 112.288

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