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Siersbæk R, Madsen JGS, Javierre BM, Nielsen R, Bagge EK, Cairns J, Wingett SW, Traynor S, Spivakov M, Fraser P, Mandrup S. Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation. Mol Cell 2017; 66:420-435.e5. [PMID: 28475875 DOI: 10.1016/j.molcel.2017.04.010] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [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: 12/13/2016] [Revised: 03/06/2017] [Accepted: 04/11/2017] [Indexed: 01/08/2023]
Abstract
Interactions between transcriptional promoters and their distal regulatory elements play an important role in transcriptional regulation; however, the extent to which these interactions are subject to rapid modulations in response to signals is unknown. Here, we use promoter capture Hi-C to demonstrate a rapid reorganization of promoter-anchored chromatin loops within 4 hr after inducing differentiation of 3T3-L1 preadipocytes. The establishment of new promoter-enhancer loops is tightly coupled to activation of poised (histone H3 lysine 4 mono- and dimethylated) enhancers, as evidenced by the acquisition of histone H3 lysine 27 acetylation and the binding of MED1, SMC1, and P300 proteins to these regions, as well as to activation of target genes. Intriguingly, formation of loops connecting activated enhancers and promoters is also associated with extensive recruitment of corepressors such as NCoR and HDACs, indicating that this class of coregulators may play a previously unrecognized role during enhancer activation.
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Affiliation(s)
- Rasmus Siersbæk
- University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | | | | | - Ronni Nielsen
- University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | | | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Steven William Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Sofie Traynor
- University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
| | - Susanne Mandrup
- University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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Chandra T, Ewels PA, Schoenfelder S, Furlan-Magaril M, Wingett SW, Kirschner K, Thuret JY, Andrews S, Fraser P, Reik W. Global reorganization of the nuclear landscape in senescent cells. Cell Rep 2015; 10:471-83. [PMID: 25640177 PMCID: PMC4542308 DOI: 10.1016/j.celrep.2014.12.055] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/13/2014] [Accepted: 12/22/2014] [Indexed: 02/03/2023] Open
Abstract
Cellular senescence has been implicated in tumor suppression, development, and aging and is accompanied by large-scale chromatin rearrangements, forming senescence-associated heterochromatic foci (SAHF). However, how the chromatin is reorganized during SAHF formation is poorly understood. Furthermore, heterochromatin formation in senescence appears to contrast with loss of heterochromatin in Hutchinson-Gilford progeria. We mapped architectural changes in genome organization in cellular senescence using Hi-C. Unexpectedly, we find a dramatic sequence- and lamin-dependent loss of local interactions in heterochromatin. This change in local connectivity resolves the paradox of opposing chromatin changes in senescence and progeria. In addition, we observe a senescence-specific spatial clustering of heterochromatic regions, suggesting a unique second step required for SAHF formation. Comparison of embryonic stem cells (ESCs), somatic cells, and senescent cells shows a unidirectional loss in local chromatin connectivity, suggesting that senescence is an endpoint of the continuous nuclear remodelling process during differentiation.
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Affiliation(s)
- Tamir Chandra
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
| | | | | | | | | | - Kristina Kirschner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Jean-Yves Thuret
- CEA, iBiTec-S, SBIGeM/CNRS FRE3377 I2BC/Université Paris-Sud, Gif-sur-Yvette 91191, France
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
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