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Basu S, Shukron O, Hall D, Parutto P, Ponjavic A, Shah D, Boucher W, Lando D, Zhang W, Reynolds N, Sober LH, Jartseva A, Ragheb R, Ma X, Cramard J, Floyd R, Balmer J, Drury TA, Carr AR, Needham LM, Aubert A, Communie G, Gor K, Steindel M, Morey L, Blanco E, Bartke T, Di Croce L, Berger I, Schaffitzel C, Lee SF, Stevens TJ, Klenerman D, Hendrich BD, Holcman D, Laue ED. Publisher Correction: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD. Nat Struct Mol Biol 2024; 31:390. [PMID: 38102414 PMCID: PMC10873192 DOI: 10.1038/s41594-023-01179-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Affiliation(s)
- S Basu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - O Shukron
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - D Hall
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - P Parutto
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - A Ponjavic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Physics and Astronomy, University of Leeds, Leeds, UK
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - D Shah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Boucher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - D Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Zhang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - N Reynolds
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - L H Sober
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A Jartseva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - R Ragheb
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - X Ma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J Cramard
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - R Floyd
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - J Balmer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T A Drury
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A R Carr
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - L-M Needham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - A Aubert
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - G Communie
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - K Gor
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - L Morey
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, USA
| | - E Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - T Bartke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Functional Epigenetics, Neuherberg, Germany
| | - L Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - I Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - C Schaffitzel
- School of Biochemistry, University of Bristol, Bristol, UK
| | - S F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - T J Stevens
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - D Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - B D Hendrich
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| | - D Holcman
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France.
| | - E D Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
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Basu S, Shukron O, Hall D, Parutto P, Ponjavic A, Shah D, Boucher W, Lando D, Zhang W, Reynolds N, Sober LH, Jartseva A, Ragheb R, Ma X, Cramard J, Floyd R, Balmer J, Drury TA, Carr AR, Needham LM, Aubert A, Communie G, Gor K, Steindel M, Morey L, Blanco E, Bartke T, Di Croce L, Berger I, Schaffitzel C, Lee SF, Stevens TJ, Klenerman D, Hendrich BD, Holcman D, Laue ED. Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD. Nat Struct Mol Biol 2023; 30:1628-1639. [PMID: 37770717 PMCID: PMC10643137 DOI: 10.1038/s41594-023-01095-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/14/2023] [Indexed: 09/30/2023]
Abstract
To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer-promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds to chromatin for minutes, decompacts chromatin structure and increases enhancer dynamics. We also uncovered a rare fast-diffusing state of enhancers and found that NuRD restricts the time spent in this state. Hi-C and Cut&Run experiments revealed that NuRD modulates enhancer-promoter interactions in active chromatin, allowing them to contact each other over longer distances. Furthermore, NuRD leads to a marked redistribution of CTCF and, in particular, cohesin. We propose that NuRD promotes a decondensed chromatin environment, where enhancers and promoters can contact each other over longer distances, and where the resetting of enhancer-promoter interactions brought about by the fast decondensed chromatin motions is reduced, leading to more stable, long-lived enhancer-promoter relationships.
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Affiliation(s)
- S Basu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - O Shukron
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - D Hall
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - P Parutto
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - A Ponjavic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Physics and Astronomy, University of Leeds, Leeds, UK
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - D Shah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Boucher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - D Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Zhang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - N Reynolds
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - L H Sober
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A Jartseva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - R Ragheb
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - X Ma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J Cramard
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - R Floyd
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - J Balmer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T A Drury
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A R Carr
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - L-M Needham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - A Aubert
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - G Communie
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - K Gor
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - L Morey
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, USA
| | - E Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - T Bartke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Functional Epigenetics, Neuherberg, Germany
| | - L Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - I Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - C Schaffitzel
- School of Biochemistry, University of Bristol, Bristol, UK
| | - S F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - T J Stevens
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - D Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - B D Hendrich
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| | - D Holcman
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France.
| | - E D Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
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