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

Pablo Aurelio Gómez-García; Stephanie Portillo-Ledesma; Maria Victoria Neguembor; Martina Pesaresi; Walaa Oweis; Talia Rohrlich; Stefan Wieser; Eran Meshorer; Tamar Schlick; Maria Pia Cosma; Melike Lakadamyali

doi:10.1016/j.celrep.2020.108614

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

Pablo Aurelio Gómez-García, Stephanie Portillo-Ledesma, Maria Victoria Neguembor, Martina Pesaresi, Walaa Oweis, Talia Rohrlich, Stefan Wieser, Eran Meshorer, Tamar Schlick, Maria Pia Cosma^*, Melike Lakadamyali^*

^*Corresponding author for this work

Department of Genetics

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

Gómez-García et al. show that the Pou5f1 gene folds into nucleosome clutches, with larger clutches in differentiated cells than in stem cells. These clutch changes are accompanied by enhanced hierarchical looping in differentiated cells. H2B dynamics is cell-type specific, correlates with clutch patterns, and is regulated by linker histone H1.

Original language	American English
Article number	108614
Journal	Cell Reports
Volume	34
Issue number	2
DOIs	https://doi.org/10.1016/j.celrep.2020.108614
State	Published - 12 Jan 2021

Bibliographical note

Funding Information:
This work was supported by a University of Pennsylvania Epigenetics Pilot Award (M.L.); an NSF Center for Engineering and Mechanobiology (CEMB) Pilot Award (M.L.); a Linda Pechenik Montague Investigator Award (M.L.); the European Union’s Horizon 2020 Research and Innovation Programme (CellViewer grant 686637 to M.L., M.P.C., and E.M.); Ministerio de Ciencia, Innovación y Universidades ( BFU2017-86760-P [AEI/FEDER, UE]) and Secretaria d’Universitats i Recerca del Departament d’Empresa i Coneixement de la Generalitat de Catalunya (AGAUR grant 2017 SGR 689 to M.P.C.); National NSFC grant 319711771003712 (M.P.C.); National Institutes of Health , National Institute of General Medical Sciences awards R01-GM055264 and R35-GM122562 ; Phillip-Morris USA and Phillip-Morris International (T.S.); People Program (Marie Curie Actions) FP7/2007–2013 under REA grant 608959 (M.V.N.); and Juan de la Cierva-Incorporación 2017 (M.V.N.).

Funding Information:
This work was supported by a University of Pennsylvania Epigenetics Pilot Award (M.L.); an NSF Center for Engineering and Mechanobiology (CEMB) Pilot Award (M.L.); a Linda Pechenik Montague Investigator Award (M.L.); the European Union's Horizon 2020 Research and Innovation Programme (CellViewer grant 686637 to M.L. M.P.C. and E.M.); Ministerio de Ciencia, Innovaci?n y Universidades (BFU2017-86760-P [AEI/FEDER, UE]) and Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya (AGAUR grant 2017 SGR 689 to M.P.C.); National NSFC grant 319711771003712 (M.P.C.); National Institutes of Health, National Institute of General Medical Sciences awards R01-GM055264 and R35-GM122562; Phillip-Morris USA and Phillip-Morris International (T.S.); People Program (Marie Curie Actions) FP7/2007?2013 under REA grant 608959 (M.V.N.); and Juan de la Cierva-Incorporaci?n 2017 (M.V.N.). Conceptualization, M.L. and M.P.C.; Methodology, P.A.G.-G. S.P.-L. T.S. and M.L.; Modeling, S.P.L. and T.S.; Software, P.A.G.-G. S.P.-L.; Experiments, P.A.G.-G. M.V.N, M.P, W.O. and T.R.; Reagents, cell lines and other resources: M.V.N. M.P. W.O. T.R. E.M. and S.W.; Analysis, P.A.G.-G. and S.P.-L. Writing ? Original Draft: M.L. M.P.C. P.A.G.-G. and T.S.; Supervision, M.L. M.P.C. and T.S. Funding Acquisition, M.L. M.P.C. T.S. and E.M. All authors read and provided comments on the manuscript. The authors declare no competing interests.

Publisher Copyright:
© 2020 The Author(s)

Keywords

chromatin dynamics
chromatin structure
mesoscale modeling
single molecule tracking

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10.1016/j.celrep.2020.108614

Cite this

Gómez-García, P. A., Portillo-Ledesma, S., Neguembor, M. V., Pesaresi, M., Oweis, W., Rohrlich, T., Wieser, S., Meshorer, E., Schlick, T., Cosma, M. P., & Lakadamyali, M. (2021). Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation. Cell Reports, 34(2), Article 108614. https://doi.org/10.1016/j.celrep.2020.108614

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title = "Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation",

abstract = "G{\'o}mez-Garc{\'i}a et al. show that the Pou5f1 gene folds into nucleosome clutches, with larger clutches in differentiated cells than in stem cells. These clutch changes are accompanied by enhanced hierarchical looping in differentiated cells. H2B dynamics is cell-type specific, correlates with clutch patterns, and is regulated by linker histone H1.",

keywords = "chromatin dynamics, chromatin structure, mesoscale modeling, single molecule tracking",

author = "G{\'o}mez-Garc{\'i}a, {Pablo Aurelio} and Stephanie Portillo-Ledesma and Neguembor, {Maria Victoria} and Martina Pesaresi and Walaa Oweis and Talia Rohrlich and Stefan Wieser and Eran Meshorer and Tamar Schlick and Cosma, {Maria Pia} and Melike Lakadamyali",

note = "Funding Information: This work was supported by a University of Pennsylvania Epigenetics Pilot Award (M.L.); an NSF Center for Engineering and Mechanobiology (CEMB) Pilot Award (M.L.); a Linda Pechenik Montague Investigator Award (M.L.); the European Union{\textquoteright}s Horizon 2020 Research and Innovation Programme (CellViewer grant 686637 to M.L., M.P.C., and E.M.); Ministerio de Ciencia, Innovaci{\'o}n y Universidades ( BFU2017-86760-P [AEI/FEDER, UE]) and Secretaria d{\textquoteright}Universitats i Recerca del Departament d{\textquoteright}Empresa i Coneixement de la Generalitat de Catalunya (AGAUR grant 2017 SGR 689 to M.P.C.); National NSFC grant 319711771003712 (M.P.C.); National Institutes of Health , National Institute of General Medical Sciences awards R01-GM055264 and R35-GM122562 ; Phillip-Morris USA and Phillip-Morris International (T.S.); People Program (Marie Curie Actions) FP7/2007–2013 under REA grant 608959 (M.V.N.); and Juan de la Cierva-Incorporaci{\'o}n 2017 (M.V.N.). Funding Information: This work was supported by a University of Pennsylvania Epigenetics Pilot Award (M.L.); an NSF Center for Engineering and Mechanobiology (CEMB) Pilot Award (M.L.); a Linda Pechenik Montague Investigator Award (M.L.); the European Union's Horizon 2020 Research and Innovation Programme (CellViewer grant 686637 to M.L. M.P.C. and E.M.); Ministerio de Ciencia, Innovaci?n y Universidades (BFU2017-86760-P [AEI/FEDER, UE]) and Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya (AGAUR grant 2017 SGR 689 to M.P.C.); National NSFC grant 319711771003712 (M.P.C.); National Institutes of Health, National Institute of General Medical Sciences awards R01-GM055264 and R35-GM122562; Phillip-Morris USA and Phillip-Morris International (T.S.); People Program (Marie Curie Actions) FP7/2007?2013 under REA grant 608959 (M.V.N.); and Juan de la Cierva-Incorporaci?n 2017 (M.V.N.). Conceptualization, M.L. and M.P.C.; Methodology, P.A.G.-G. S.P.-L. T.S. and M.L.; Modeling, S.P.L. and T.S.; Software, P.A.G.-G. S.P.-L.; Experiments, P.A.G.-G. M.V.N, M.P, W.O. and T.R.; Reagents, cell lines and other resources: M.V.N. M.P. W.O. T.R. E.M. and S.W.; Analysis, P.A.G.-G. and S.P.-L. Writing ? Original Draft: M.L. M.P.C. P.A.G.-G. and T.S.; Supervision, M.L. M.P.C. and T.S. Funding Acquisition, M.L. M.P.C. T.S. and E.M. All authors read and provided comments on the manuscript. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2020 The Author(s)",

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doi = "10.1016/j.celrep.2020.108614",

language = "American English",

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Gómez-García, PA, Portillo-Ledesma, S, Neguembor, MV, Pesaresi, M, Oweis, W, Rohrlich, T, Wieser, S, Meshorer, E, Schlick, T, Cosma, MP & Lakadamyali, M 2021, 'Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation', Cell Reports, vol. 34, no. 2, 108614. https://doi.org/10.1016/j.celrep.2020.108614

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T1 - Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation

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AU - Portillo-Ledesma, Stephanie

AU - Neguembor, Maria Victoria

AU - Pesaresi, Martina

AU - Oweis, Walaa

AU - Rohrlich, Talia

AU - Wieser, Stefan

AU - Meshorer, Eran

AU - Schlick, Tamar

AU - Cosma, Maria Pia

AU - Lakadamyali, Melike

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N2 - Gómez-García et al. show that the Pou5f1 gene folds into nucleosome clutches, with larger clutches in differentiated cells than in stem cells. These clutch changes are accompanied by enhanced hierarchical looping in differentiated cells. H2B dynamics is cell-type specific, correlates with clutch patterns, and is regulated by linker histone H1.

AB - Gómez-García et al. show that the Pou5f1 gene folds into nucleosome clutches, with larger clutches in differentiated cells than in stem cells. These clutch changes are accompanied by enhanced hierarchical looping in differentiated cells. H2B dynamics is cell-type specific, correlates with clutch patterns, and is regulated by linker histone H1.

KW - chromatin dynamics

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

Abstract

Bibliographical note

Keywords

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