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Genome-wide nucleosome positioning during embryonic stem cell development

Abstract

We determined genome-wide nucleosome occupancies in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell-type- and protein-specific binding preferences of transcription factors to sites with either low (Myc, Klf4 and Zfx) or high (Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome-depleted regions around transcription start and transcription termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to CpG content or histone methylation marks. Throughout the genome, nucleosome occupancy was correlated with certain histone methylation or acetylation modifications. In addition, the average nucleosome repeat length increased during differentiation by 5–7 base pairs, with local variations for specific regions. Our results reveal regulatory mechanisms of cell differentiation that involve nucleosome repositioning.

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Figure 1: Nucleosome occupancies of exemplary genomic regions in ESCs, NPCs and MEFs.
Figure 2: Nucleosome occupancies at binding sites of developmentally important transcription factors and enzymes.
Figure 3: Genome-wide average nucleosome patterns at CTCF binding sites.
Figure 4: Average nucleosome occupancy patterns around TSSs and TTSs in ESCs, NPCs and MEFs.
Figure 5: Nucleosome occupancy patterns around TSSs in different classes of promoters.
Figure 6: Average nucleosome occupancy patterns around clusters of H3K9me3, H3K9ac and H3K27ac histone modifications.
Figure 7: Nucleosome repeat length in ESCs, NPCs and MEFs.

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Gene Expression Omnibus

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Acknowledgements

We are grateful to A. Valouev and R. Chereji for help with the algorithms for calculations of NRL and average TSS patterns, respectively; to M. Gerstein for advice on data processing; to G. Längst, G. Wedemann and K. Fejes Tóth for discussions; and to the Deutsches Krebsforschungszentrum Sequencing Core Facility for conducting the sequencing. This work was funded within project EpiGenSys by the German Federal Ministry of Education and Research (BMBF) as a partner of the ERASysBio+ initiative in the EU FP7 ERA-NET Plus program through grant 0315712A to K.R. Computational resources and data storage were provided by grants from the BMBF (01IG07015G, Services@MediGRID) and the German Research Foundation (DFG INST 295/27-1). V.B.T. acknowledges the support from the Heidelberg Center for Modeling and Simulation in the Biosciences and a Deutsches Krebsforschungszentrum intramural grant, and Y.V. was supported by BMBF MedSys grant 0315409E to T.H.

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V.B.T. and K.R. designed the research. M.C.-H., J.-P.M. and C.M. performed experiments. V.B.T., Y.V., J.-P.M., T.H. and K.R. analyzed data. V.B.T., T.H. and K.R. wrote the manuscript.

Corresponding authors

Correspondence to Vladimir B Teif or Karsten Rippe.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–4 and Supplementary Note (PDF 5299 kb)

Supplementary Table 5

Genes in cluster I of bivalent ESC promoters. (XLS 40 kb)

Supplementary Table 6

Differential promoter nucleosome occupancy and expression profiles of MEFs versus ESCs. (XLS 22311 kb)

Supplementary Table 7

Differential promoter nucleosome occupancy and expression profiles of NPCs versus ESCs. (XLS 24253 kb)

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Teif, V., Vainshtein, Y., Caudron-Herger, M. et al. Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol 19, 1185–1192 (2012). https://doi.org/10.1038/nsmb.2419

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