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Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

Abstract

Development, differentiation and response to environmental stimuli are characterized by sequential changes in cellular state initiated by the de novo binding of regulated transcriptional factors to their cognate genomic sites1,2,3. The mechanism whereby a given regulatory factor selects a limited number of in vivo targets from a myriad of potential genomic binding sites is undetermined. Here we show that up to 95% of de novo genomic binding by the glucocorticoid receptor4, a paradigmatic ligand-activated transcription factor, is targeted to preexisting foci of accessible chromatin. Factor binding invariably potentiates chromatin accessibility. Cell-selective glucocorticoid receptor occupancy patterns appear to be comprehensively predetermined by cell-specific differences in baseline chromatin accessibility patterns, with secondary contributions from local sequence features. The results define a framework for understanding regulatory factor–genome interactions and provide a molecular basis for the tissue selectivity of steroid pharmaceuticals and other agents that intersect the living genome.

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Figure 1: Dominant effect of chromatin accessibility on glucocorticoid receptor occupancy patterns.
Figure 2: The quantitative effect of chromatin context on glucocorticoid receptor occupancy of GRBEs.
Figure 3: Cell-specific chromatin landscapes determine cell-selective glucocorticoid receptor occupancy.
Figure 4: Regulatory motifs in glucocorticoid receptor–occupied regions differ substantially between cell types.

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Acknowledgements

We would like to thank T. Miranda, S. Morris, K. Nalley and L. Grontved for critical reading of the manuscript. We also thank M. Weaver, K. Lee, F. Neri, D. Bates and M. Diegel for technical assistance with the DNase I library preparation and sequencing. This research was supported in part by the Intramural Research Program of the US NIH, National Cancer Institute, Center for Cancer Research and funding from US NIH grant 1RC2HG005654 to J.A.S.

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Authors and Affiliations

Authors

Contributions

S.J., P.J.S., G.L.H. and J.A.S. designed the experiments. S.J., P.J.S., S.C.B. and T.A.J. conducted the DNase-seq, ChIP-seq and expression array experiments. S.J., P.J.S., R.E.T., M.-H.S. and J.A.S. analyzed the data. S.J., P.J.S., R.E.T., M.-H.S., G.L.H. and J.A.S. wrote the manuscript.

Corresponding authors

Correspondence to Gordon L Hager or John A Stamatoyannopoulos.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–10 (PDF 6921 kb)

Supplementary Table 1

DNaseI sensitive regions in the baseline (pre-hormone) state in the murine mammary adenocarcinoma cell line, 3134; DNase I sensitive regions in post dexamethasone-treated 3134 cells (XLS 3781 kb)

Supplementary Table 2

DNaseI hypersensitive sites (DHSs) in the baseline (pre-hormone) state in the murine mammary adenocarcinoma cell line, 3134 (XLS 3781 kb)

Supplementary Table 3

DNaseI hypersensitive sites (DHSs) in post dexamethasone-treated 3134 cells (XLS 3781 kb)

Supplementary Table 4

GR occupancy sites in the murine mammary adenocarcinoma cell line, 3134 (FDR 0%) (XLS 489 kb)

Supplementary Table 5

Expression analysis of mammary (3134) and pituitary (AtT-20) cells (XLS 132 kb)

Supplementary Table 6

GRBE sequence classes with greater than 50 instances in the genome. Chromatin Context Coefficient (CCC) classes in the murine genome (XLS 302 kb)

Supplementary Table 7

DNaseI sensitive regions in the baseline (pre-hormone) state in the murine pituitary cell line, AtT-20; DNase I sensitive regions in the post-hormone state in the murine pituitary cell line, AtT-20 (XLS 3781 kb)

Supplementary Table 8

DNaseI hypersensitive sites (DHSs) in the baseline (pre-hormone) state in the murine pituitary cell line, AtT-20 (XLS 3781 kb)

Supplementary Table 9

DNaseI hypersensitive sites (DHSs) post-hormone in AtT-20 cells (XLS 3781 kb)

Supplementary Table 10

GR occupancy sites in the murine pituitary cell line, AtT-20 (FDR 0%) (XLS 202 kb)

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John, S., Sabo, P., Thurman, R. et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43, 264–268 (2011). https://doi.org/10.1038/ng.759

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