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      FUS-dependent liquid–liquid phase separation is important for DNA repair initiation

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          Abstract

          FUS-dependent liquid–liquid phase separation is a critical process in the early activation of the DNA damage response and in the recruitment of key proteins, which facilitates the proper assembly of double-strand break repair complexes.

          Abstract

          RNA-binding proteins (RBPs) are emerging as important effectors of the cellular DNA damage response (DDR). The RBP FUS is implicated in RNA metabolism and DNA repair, and it undergoes reversible liquid–liquid phase separation (LLPS) in vitro. Here, we demonstrate that FUS-dependent LLPS is necessary for the initiation of the DDR. Using laser microirradiation in FUS-knockout cells, we show that FUS is required for the recruitment to DNA damage sites of the DDR factors KU80, NBS1, and 53BP1 and of SFPQ, another RBP implicated in the DDR. The relocation of KU80, NBS1, and SFPQ is similarly impaired by LLPS inhibitors, or LLPS-deficient FUS variants. We also show that LLPS is necessary for efficient γH2AX foci formation. Finally, using superresolution structured illumination microscopy, we demonstrate that the absence of FUS impairs the proper arrangement of γH2AX nanofoci into higher-order clusters. These findings demonstrate the early requirement for FUS-dependent LLPS in the activation of the DDR and the proper assembly of DSB repair complexes.

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          Most cited references86

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          Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

          Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.
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            PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.

            DNA microarrays can be used to identify gene expression changes characteristic of human disease. This is challenging, however, when relevant differences are subtle at the level of individual genes. We introduce an analytical strategy, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes. Using this approach, we identify a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle. Expression of these genes is high at sites of insulin-mediated glucose disposal, activated by PGC-1alpha and correlated with total-body aerobic capacity. Our results associate this gene set with clinically important variation in human metabolism and illustrate the value of pathway relationships in the analysis of genomic profiling experiments.
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              A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.

              Many proteins contain disordered regions of low-sequence complexity, which cause aging-associated diseases because they are prone to aggregate. Here, we study FUS, a prion-like protein containing intrinsically disordered domains associated with the neurodegenerative disease ALS. We show that, in cells, FUS forms liquid compartments at sites of DNA damage and in the cytoplasm upon stress. We confirm this by reconstituting liquid FUS compartments in vitro. Using an in vitro "aging" experiment, we demonstrate that liquid droplets of FUS protein convert with time from a liquid to an aggregated state, and this conversion is accelerated by patient-derived mutations. We conclude that the physiological role of FUS requires forming dynamic liquid-like compartments. We propose that liquid-like compartments carry the trade-off between functionality and risk of aggregation and that aberrant phase transitions within liquid-like compartments lie at the heart of ALS and, presumably, other age-related diseases.
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                Author and article information

                Journal
                J Cell Biol
                J Cell Biol
                jcb
                The Journal of Cell Biology
                Rockefeller University Press
                0021-9525
                1540-8140
                03 May 2021
                11 March 2021
                : 220
                : 5
                : e202008030
                Affiliations
                [1 ]Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
                [2 ]Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
                [3 ]Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
                [4 ]UK Dementia Research Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
                [5 ]Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
                Author notes
                Correspondence to Silvia M.L. Barabino: silvia.barabino@ 123456unimib.it
                [*]

                A. Maiser and A. Rapp contributed equally to this paper.

                F. Conte’s present address is Institute of Molecular Biology, Mainz, Germany.

                Author information
                https://orcid.org/0000-0003-3368-4261
                https://orcid.org/0000-0002-5759-8133
                https://orcid.org/0000-0002-5255-465X
                https://orcid.org/0000-0002-2349-5822
                https://orcid.org/0000-0001-9108-3929
                https://orcid.org/0000-0003-0842-9314
                https://orcid.org/0000-0002-3905-1038
                https://orcid.org/0000-0002-5086-6449
                https://orcid.org/0000-0001-8427-8859
                https://orcid.org/0000-0003-3264-9800
                https://orcid.org/0000-0003-3584-4417
                Article
                jcb.202008030
                10.1083/jcb.202008030
                7953258
                33704371
                74485a9f-6f37-4d41-86c1-08ec79251ae9
                © 2021 Levone et al.

                This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

                History
                : 08 August 2020
                : 17 January 2021
                : 04 February 2021
                Page count
                Pages: 20
                Funding
                Funded by: Swiss National Fond Sinergia;
                Award ID: CRSII3_136222
                Funded by: UK Dementia Research Institute;
                Funded by: NOMIS Foundation;
                Funded by: Deutsche Forschungsgemeinschaft, DOI http://dx.doi.org/10.13039/501100001659;
                Award ID: LE 721/18-1
                Award ID: CA 198/16-1
                Categories
                Article
                DNA biology
                Biochemistry

                Cell biology
                Cell biology

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