Chromatin signatures of pluripotent cell lines

Abstract

Epigenetic genome modifications are thought to be important for specifying the lineage and developmental stage of cells within a multicellular organism. Here, we show that the epigenetic profile of pluripotent embryonic stem cells (ES) is distinct from that of embryonic carcinoma cells, haematopoietic stem cells (HSC) and their differentiated progeny. Silent, lineage-specific genes replicated earlier in pluripotent cells than in tissue-specific stem cells or differentiated cells and had unexpectedly high levels of acetylated H3K9 and methylated H3K4. Unusually, in ES cells these markers of open chromatin were also combined with H3K27 trimethylation at some non-expressed genes. Thus, pluripotency of ES cells is characterized by a specific epigenetic profile where lineage-specific genes may be accessible but, if so, carry repressive H3K27 trimethylation modifications. H3K27 methylation is functionally important for preventing expression of these genes in ES cells as premature expression occurs in embryonic ectoderm development (Eed)-deficient ES cells. Our data suggest that lineage-specific genes are primed for expression in ES cells but are held in check by opposing chromatin modifications.

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Figure 1: Pluripotent ES cells, multipotent HSC and unipotent T lymphocytes have distinct replication timing profiles.
Figure 2: Replication timing profiles of ES and embryonic carcinoma (EC) cells reflect their distinct lineage potential.
Figure 3: Markers of active and repressed chromatin are simultaneously present at silent tissue-specific genes in undifferentiated ES cells.
Figure 4: Eed is required for repressing neural-specific gene expression in undifferentiated ES cells.
Figure 5: Replication timing is not significantly altered in Eed-deficient ES cells despite gene derepression.

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Acknowledgements

We thank A. Smith for ES cell lines, M. Dexter for the FDCP-mix A4 clone, M. Busslinger for Pax5-deficient pro-B cells, R. Lovell-Badge for the F9-EC line and V. Episkopou for the embryonic carcinoma cell lines F9 and P19. E. O'Connor, R. Brough, G. Reed and R. Newton are thanked for help and advice and A. Allen, M. Harrison, T. Reed and Z. Szarka (at Oxford Gene Technology, Oxford, UK). J. Santos and S. Giadrossi for communicating unpublished information. S. Giadrossi, N. Brockdorff and M. Raff are acknowledged for advice and critical reading of the manuscript. This work was supported by the Medical Research Council (MRC) and by a MRC Collaborative Career Development Fellowship in Stem Cell Research funded by the Parkinson's disease Society (V.A.).

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Correspondence to Véronique Azuara or Amanda G. Fisher.

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Supplementary Figures S1, S2, S3, S4 and Supplementary Methods (PDF 375 kb)

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