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Polycomb complexes repress developmental regulators in murine embryonic stem cells

Abstract

The mechanisms by which embryonic stem (ES) cells self-renew while maintaining the ability to differentiate into virtually all adult cell types are not well understood. Polycomb group (PcG) proteins are transcriptional repressors that help to maintain cellular identity during metazoan development by epigenetic modification of chromatin structure1. PcG proteins have essential roles in early embryonic development2,3,4,5,6 and have been implicated in ES cell pluripotency2, but few of their target genes are known in mammals. Here we show that PcG proteins directly repress a large cohort of developmental regulators in murine ES cells, the expression of which would otherwise promote differentiation. Using genome-wide location analysis in murine ES cells, we found that the Polycomb repressive complexes PRC1 and PRC2 co-occupied 512 genes, many of which encode transcription factors with important roles in development. All of the co-occupied genes contained modified nucleosomes (trimethylated Lys 27 on histone H3). Consistent with a causal role in gene silencing in ES cells, PcG target genes were de-repressed in cells deficient for the PRC2 component Eed, and were preferentially activated on induction of differentiation. Our results indicate that dynamic repression of developmental pathways by Polycomb complexes may be required for maintaining ES cell pluripotency and plasticity during embryonic development.

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Figure 1: PRC1 and PRC2 colocalize at genes encoding developmental regulators.
Figure 2: De-repression of PcG target genes and loss of PRC1 binding in the absence of the PRC2 component Eed.
Figure 3: PcG target genes are preferentially upregulated during ES cell differentiation.

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Acknowledgements

We thank Biology and Research Computing (BaRC), especially B. Yuan, T. Dicesare and T. Volkert, at the Whitehead Institute's Center for Microarray Technology, as well as E. Herbolsheimer, for computational and technical support. We also thank members of the Gifford, Young and Jaenisch laboratories for discussions and critical review of the manuscript. We are grateful to T. Magnuson for the Eed mutant (17Rn5-3354SB) ES cell lines. L.A.B. was supported in part by an NIH NRSA fellowship. K.P. is a special fellow of the Leukemia and Lymphoma Society. M.W. is supported by a Human Frontiers Science Program Organization Fellowship. M.V. is supported by a grant from the Spanish Ministry of Science and Education. This work was supported in part by grants from the NIHGRI and NIGMS to R.A.Y. and from the NIH and NCI to R.J.

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Correspondence to Rudolf Jaenisch.

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T.I.L., D.K.G. and R.A.Y. consult for Agilent Technologies.

Supplementary information

Supplementary Notes

This file contains the Supplementary Methods and Supplementary Discussion; Supplementary Notes; Supplementary Figure Legends 1–9; Supplementary Figures 1–9. (PDF 9721 kb)

Supplementary Table 1

This file contains chromosomal coordinates for genomic regions bound by Suz12. (XLS 102 kb)

Supplementary Table 2

This file contains chromosomal coordinates for genomic regions bound by Eed. (XLS 69 kb)

Supplementary Table 3

This file contains chromosomal coordinates for genomic regions bound by Rnf2. (XLS 91 kb)

Supplementary Table 4

This file contains chromosomal coordinates for genomic regions bound by Phc1. (XLS 69 kb)

Supplementary Table 5

This file contains the assignment of bound genomic regions to annotated transcripts. (XLS 4189 kb)

Supplementary Table 6

This file contains data from the independent site specific validation used to estimate error rates in location analysis data. (XLS 53 kb)

Supplementary Table 7.

This file contains chromosomal coordinates for genomic regions bound by H3K27me3. (XLS 175 kb)

Supplementary Table 8

This file contains all enriched gene ontology classifications for bound genes. (XLS 103 kb)

Supplementary Table 9

This file contains the complete list of transcription factor genes bound by PcG proteins. (DOC 36 kb)

Supplementary Table 10

This file contains all oligo sequences and RT-PCR results in wild-type and eed mutant ES cells used to generate Figure 2 in the main text. (XLS 39 kb)

Supplementary Table 11

This file contains the microarray expression data used to analyse the expression of PcG bound genes in ES cells and during ES cell differentiation as displayed in Figure 3 in the main text. (XLS 6725 kb)

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Boyer, L., Plath, K., Zeitlinger, J. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006). https://doi.org/10.1038/nature04733

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