Cycles in spatial and temporal chromosomal organization driven by the circadian clock

Lorena Aguilar-Arnal; Ofir Hakim; Vishal R. Patel; Pierre Baldi; Gordon L. Hager; Paolo Sassone-Corsi

doi:10.1038/nsmb.2667

Cycles in spatial and temporal chromosomal organization driven by the circadian clock

Lorena Aguilar-Arnal, Ofir Hakim, Vishal R. Patel, Pierre Baldi, Gordon L. Hager, Paolo Sassone-Corsi

The Mina and Everard Goodman Faculty of Life Sciences

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

99 Scopus citations

Abstract

Dynamic transitions in the epigenome have been associated with regulated patterns of nuclear organization. The accumulating evidence that chromatin remodeling is implicated in circadian function prompted us to explore whether the clock may control nuclear architecture. We applied the chromosome conformation capture on chip technology in mouse embryonic fibroblasts (MEFs) to demonstrate the presence of circadian long-range interactions using the clock-controlled Dbp gene as bait. The circadian genomic interactions with Dbp were highly specific and were absent in MEFs whose clock was disrupted by ablation of the Bmal1 gene (also called Arntl). We establish that the Dbp circadian interactome contains a wide variety of genes and clock-related DNA elements. These findings reveal a previously unappreciated circadian and clock-dependent shaping of the nuclear landscape.

Original language	English
Pages (from-to)	1206-1215
Number of pages	10
Journal	Nature Structural and Molecular Biology
Volume	20
Issue number	10
DOIs	https://doi.org/10.1038/nsmb.2667
State	Published - Oct 2013

Bibliographical note

Funding Information:
We thank R.L. Schiltz and T.A. Johnson (NCI, NIH) for assisting with cell culture; R. Orozco-Solis, K. Eckel-Mahan, S. Sahar (Center for Epigenetics and Metabolism, University of California Irvine) and M. Groudine (Fred Hutchinson Cancer Research Center) for critical reading of the manuscript; S. Dilag (Center for Epigenetics and Metabolism, University of California Irvine) for technical support; X. Kong (Department of Biological Chemistry, University of California Irvine) for sharing FISH expertise and reagents; and all the members of the P.S.-C., G.L.H. and P.B. laboratories for discussions. This work was supported in part by the following grants: European Molecular Biology Organization (EMBO) long-term fellowship ALTF 411-2009 (to L.A.-A.), NIH grants R01-GM081634, AG041504 and AG033888 (to P.S.-C.) and Sirtris Pharmaceuticals grant SP-48984 (to P.S.-C.). The work of V.R.P. and P.B. is supported by the following grants: National Science Foundation grant IIS-0513376 and NIH grants LM010235-01A1 and 5T15LM007743 (to P.B.).

Funding

We thank R.L. Schiltz and T.A. Johnson (NCI, NIH) for assisting with cell culture; R. Orozco-Solis, K. Eckel-Mahan, S. Sahar (Center for Epigenetics and Metabolism, University of California Irvine) and M. Groudine (Fred Hutchinson Cancer Research Center) for critical reading of the manuscript; S. Dilag (Center for Epigenetics and Metabolism, University of California Irvine) for technical support; X. Kong (Department of Biological Chemistry, University of California Irvine) for sharing FISH expertise and reagents; and all the members of the P.S.-C., G.L.H. and P.B. laboratories for discussions. This work was supported in part by the following grants: European Molecular Biology Organization (EMBO) long-term fellowship ALTF 411-2009 (to L.A.-A.), NIH grants R01-GM081634, AG041504 and AG033888 (to P.S.-C.) and Sirtris Pharmaceuticals grant SP-48984 (to P.S.-C.). The work of V.R.P. and P.B. is supported by the following grants: National Science Foundation grant IIS-0513376 and NIH grants LM010235-01A1 and 5T15LM007743 (to P.B.).

Funders	Funder number
National Science Foundation	IIS-0513376
National Institutes of Health	5T15LM007743, LM010235-01A1
National Cancer Institute	P30CA062203
European Molecular Biology Organization	ALTF 411-2009

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title = "Cycles in spatial and temporal chromosomal organization driven by the circadian clock",

abstract = "Dynamic transitions in the epigenome have been associated with regulated patterns of nuclear organization. The accumulating evidence that chromatin remodeling is implicated in circadian function prompted us to explore whether the clock may control nuclear architecture. We applied the chromosome conformation capture on chip technology in mouse embryonic fibroblasts (MEFs) to demonstrate the presence of circadian long-range interactions using the clock-controlled Dbp gene as bait. The circadian genomic interactions with Dbp were highly specific and were absent in MEFs whose clock was disrupted by ablation of the Bmal1 gene (also called Arntl). We establish that the Dbp circadian interactome contains a wide variety of genes and clock-related DNA elements. These findings reveal a previously unappreciated circadian and clock-dependent shaping of the nuclear landscape.",

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note = "Funding Information: We thank R.L. Schiltz and T.A. Johnson (NCI, NIH) for assisting with cell culture; R. Orozco-Solis, K. Eckel-Mahan, S. Sahar (Center for Epigenetics and Metabolism, University of California Irvine) and M. Groudine (Fred Hutchinson Cancer Research Center) for critical reading of the manuscript; S. Dilag (Center for Epigenetics and Metabolism, University of California Irvine) for technical support; X. Kong (Department of Biological Chemistry, University of California Irvine) for sharing FISH expertise and reagents; and all the members of the P.S.-C., G.L.H. and P.B. laboratories for discussions. This work was supported in part by the following grants: European Molecular Biology Organization (EMBO) long-term fellowship ALTF 411-2009 (to L.A.-A.), NIH grants R01-GM081634, AG041504 and AG033888 (to P.S.-C.) and Sirtris Pharmaceuticals grant SP-48984 (to P.S.-C.). The work of V.R.P. and P.B. is supported by the following grants: National Science Foundation grant IIS-0513376 and NIH grants LM010235-01A1 and 5T15LM007743 (to P.B.).",

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Cycles in spatial and temporal chromosomal organization driven by the circadian clock

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