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Sci Rep. 2019 Oct 2;9(1):14212. doi: 10.1038/s41598-019-50572-8.

Generation of Remosomes by the SWI/SNF Chromatin Remodeler Family.

Author information

1
Université de Lyon, Laboratoire de Biologie et Modélisation de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, cedex 07, France. v1mshukl@exseed.ed.ac.uk.
2
Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France. v1mshukl@exseed.ed.ac.uk.
3
Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Swann Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, United Kingdom. v1mshukl@exseed.ed.ac.uk.
4
Université de Lyon, Laboratoire de Biologie et Modélisation de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, cedex 07, France.
5
Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France.
6
Pharmacology Division, CSIR-IIIM, Sanatnagar, Srinagar, 190005, Jammu and Kashmir, India.
7
Laboratoire de Physique, UMR 5672, CNRS, Université de Lyon 1, Ecole Normale Supérieure de Lyon, 69364, Lyon, cedex 07, France.
8
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.
9
Izmir Biomedicine and Genome Center, Izmir, Turkey.
10
Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Parc d'innovation, 1 rue Laurent Fries, 67404, Ilkirch, Cedex, France. hamiche@igbmc.fr.
11
Cellule LBMC, 46 Allée d'Italie, 69007, Lyon, France. hamiche@igbmc.fr.
12
Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France. jan.bednar@univ-grenoble-alpes.fr.
13
Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics and Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague 2, Czech Republic. jan.bednar@univ-grenoble-alpes.fr.

Abstract

Chromatin remodelers are complexes able to both alter histone-DNA interactions and to mobilize nucleosomes. The mechanism of their action and the conformation of remodeled nucleosomes remain a matter of debates. In this work we compared the type and structure of the products of nucleosome remodeling by SWI/SNF and ACF complexes using high-resolution microscopy combined with novel biochemical approaches. We find that SWI/SNF generates a multitude of nucleosome-like metastable particles termed "remosomes". Restriction enzyme accessibility assay, DNase I footprinting and AFM experiments reveal perturbed histone-DNA interactions within these particles. Electron cryo-microscopy shows that remosomes adopt a variety of different structures with variable irregular DNA path, similar to those described upon RSC remodeling. Remosome DNA accessibility to restriction enzymes is also markedly increased. We suggest that the generation of remosomes is a common feature of the SWI/SNF family remodelers. In contrast, the ACF remodeler, belonging to ISWI family, only produces repositioned nucleosomes and no evidence for particles associated with extra DNA, or perturbed DNA paths was found. The remosome generation by the SWI/SNF type of remodelers may represent a novel mechanism involved in processes where nucleosomal DNA accessibility is required, such as DNA repair or transcription regulation.

PMID:
31578361
DOI:
10.1038/s41598-019-50572-8
Free PMC Article

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