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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Figure 1: Characterization of genomic long-range interactions during the circadian cycle.
Figure 2: Genomic locations of Dbp long-range contacts that follow a BMAL1-dependent circadian pattern of interaction.
Figure 3: FISH validation of 4C data.
Figure 4: Circadian gene expression profiles in DEX-synchronized MEFs.
Figure 5: Circadian expression of Dbp and genes located in spatial proximity.
Figure 6: A schematic model of the cyclic events in chromosomal organization along the circadian cycle.

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Acknowledgements

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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Contributions

L.A.-A., O.H., G.L.H. and P.S.-C. conceived and designed the research. L.A.-A. and O.H. performed 4C experiments. L.A.-A. performed FISH and gene expression experimental work. L.A.-A., O.H., V.R.P. and P.B. performed bioinformatical analyses. V.R.P. performed promoter analyses using MotifMap. L.A.-A. and O.H. analyzed and interpreted the data. L.A.-A. and P.S.-C. wrote the manuscript.

Corresponding authors

Correspondence to Pierre Baldi or Paolo Sassone-Corsi.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 6704 kb)

Supplementary Table 1

4C genomic regions that interact in trans with Dbp (XLSX 35 kb)

Supplementary Table 2

Gene content of Dbp contacts detected in wild type MEFs (XLSX 240 kb)

Supplementary Table 3

Dbp circadian interactome (XLSX 30 kb)

Supplementary Table 4

Motif Map analyses on 4C contact regions (XLSX 4286 kb)

Supplementary Table 5

p scores at the region analyzed by FISH (XLSX 20 kb)

Supplementary Table 6

Circadian gene expression in wild type MEFs (XLSX 6515 kb)

Supplementary Table 7

Ontological analyses (XLSX 32 kb)

Supplementary Table 8

Lists of circadian genes (XLSX 120 kb)

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Aguilar-Arnal, L., Hakim, O., Patel, V. et al. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat Struct Mol Biol 20, 1206–1213 (2013). https://doi.org/10.1038/nsmb.2667

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