Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation.

Animals Cell Differentiation Chromatin / metabolism Humans Mice Models, Molecular Nucleosomes / metabolism Stem Cells / metabolism
chromatin dynamics chromatin structure mesoscale modeling single molecule tracking

Journal

Cell reports
ISSN: 2211-1247
Titre abrégé: Cell Rep
Pays: United States
ID NLM: 101573691

Informations de publication

Date de publication:
12 01 2021
Historique:
received: 28 02 2020
revised: 29 10 2020
accepted: 16 12 2020
entrez: 13 1 2021
pubmed: 14 1 2021
medline: 5 1 2022
Statut: ppublish

Résumé

Nucleosomes form heterogeneous groups in vivo, named clutches. Clutches are smaller and less dense in mouse embryonic stem cells (ESCs) compared to neural progenitor cells (NPCs). Using coarse-grained modeling of the pluripotency Pou5f1 gene, we show that the genome-wide clutch differences between ESCs and NPCs can be reproduced at a single gene locus. Larger clutch formation in NPCs is associated with changes in the compaction and internucleosome contact probability of the Pou5f1 fiber. Using single-molecule tracking (SMT), we further show that the core histone protein H2B is dynamic, and its local mobility relates to the structural features of the chromatin fiber. H2B is less stable and explores larger areas in ESCs compared to NPCs. The amount of linker histone H1 critically affects local H2B dynamics. Our results have important implications for how nucleosome organization and H2B dynamics contribute to regulate gene activity and cell identity.

Identifiants

DOI: 10.1016/j.celrep.2020.108614 PMID: 33440158 PMC: PMC7842188
pubmed: 33440158
pii: S2211-1247(20)31603-X
doi: 10.1016/j.celrep.2020.108614
pmc: PMC7842188
mid: NIHMS1662661
pii:
doi:

Substances chimiques

Chromatin 0
Nucleosomes 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

108614

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM055164
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM122562
Pays : United States

Informations de copyright

Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of Interests The authors declare no competing interests.

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Auteurs

Pablo Aurelio Gómez-García (PA)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Institute of Photonic Sciences (ICFO), The Barcelona Institute of Science and Technology (BIST), Castelldefels, 08860 Barcelona, Spain.

Stephanie Portillo-Ledesma (S)

Department of Chemistry, 1021 Silver Center, 100 Washington Square East, New York University, New York, NY 10003, USA.

Maria Victoria Neguembor (MV)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.

Martina Pesaresi (M)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.

Walaa Oweis (W)

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.

Talia Rohrlich (T)

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.

Stefan Wieser (S)

Institute of Photonic Sciences (ICFO), The Barcelona Institute of Science and Technology (BIST), Castelldefels, 08860 Barcelona, Spain.

Eran Meshorer (E)

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.

Tamar Schlick (T)

Department of Chemistry, 1021 Silver Center, 100 Washington Square East, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, 251 Mercer Street, New York University, New York, NY 10012, USA; NYU-ECNU Center for Computational Chemistry at New York University Shanghai, 340 Geography Building, 3663 North Zhongshan Road, Shanghai 3663, China.

Maria Pia Cosma (MP)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China. Electronic address: pia.cosma@crg.eu.

Melike Lakadamyali (M)

Perelman School of Medicine, Department of Physiology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Perelman School of Medicine, Department of Cell and Developmental Biology, University of Pennsylvania, Biomedical Research Building, 421 Curie Boulevard, Philadelphia, PA 19104, USA. Electronic address: melikel@pennmedicine.upenn.edu.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Mesoscale Modeling and Single-Nucleosome...
questionsmedicales.fr › Phénomènes physiologiques cellulaires › Différenciation cellulaire › Mesoscale Modeling and Single-Nucleosome...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Mesoscale Modeling and Single-Nucleosome...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Mesoscale Modeling and Single-Nucleosome...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › Mesoscale Modeling and Single-Nucleosome...
questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles moléculaires › Mesoscale Modeling and Single-Nucleosome...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Nucléosomes › Mesoscale Modeling and Single-Nucleosome...
questionsmedicales.fr › Cellules › Cellules souches › Mesoscale Modeling and Single-Nucleosome...