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Chd1 regulates open chromatin and pluripotency of embryonic stem cells


An open chromatin largely devoid of heterochromatin is a hallmark of stem cells. It remains unknown whether an open chromatin is necessary for the differentiation potential of stem cells, and which molecules are needed to maintain open chromatin. Here we show that the chromatin remodelling factor Chd1 is required to maintain the open chromatin of pluripotent mouse embryonic stem cells. Chd1 is a euchromatin protein that associates with the promoters of active genes, and downregulation of Chd1 leads to accumulation of heterochromatin. Chd1-deficient embryonic stem cells are no longer pluripotent, because they are incapable of giving rise to primitive endoderm and have a high propensity for neural differentiation. Furthermore, Chd1 is required for efficient reprogramming of fibroblasts to the pluripotent stem cell state. Our results indicate that Chd1 is essential for open chromatin and pluripotency of embryonic stem cells, and for somatic cell reprogramming to the pluripotent state.

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Figure 1: Chd1 RNAi ES cells have decreased self-renewal but maintain expression of markers of the undifferentiated state.
Figure 2: Chd1 is required for ES cell pluripotency.
Figure 3: Chd1 associates with euchromatic promoter regions in ES cells.
Figure 4: Chd1 is required to maintain open chromatin in ES cells.
Figure 5: Chd1 is required for efficient induction of pluripotency.

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Gene Expression Omnibus

Data deposits

Expression and ChIP-chip microarray data are deposited in the Gene Expression Omnibus (GEO) under accession number GSE16462.


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The authors wish to thank A. Smith for Oct4-GiP ES cells, M. S. Parmacek for Gata6-/- ES cells, R. P. Perry and D. G. Stokes for the Chd1 antibody, M. Bigos and V. Stepps at the Flow Cytometry Core Facility and L. Ta and C. Barker at the Genomics Core Facility of the Gladstone Institutes for expert assistance, C. Chiu for technical assistance, members of the Santos laboratory, in particular M. Grskovic for advice, and A. Kriegstein, D. Melton, A. Alvarez-Buylla, D. Stainier, R. Blelloch, B. Panning, J. Reiter and M. Grskovic for discussions and critical reading of the manuscript. A.G.-M. was the recipient of a predoctoral fellowship from the Foundation for Science and Technology (POCI2010/FSE), Portugal. R.S. was the recipient of a CIRM postdoctoral training grant. This work was supported by grants from the Sandler Family to M.T.M., CIRM Young Investigator Award and NIH Director’s New Innovator Award to K.P., Israel Science Foundation (ISF 215/07), European Union (IRG-206872) and Alon Fellowship to E.M., and NIH Director’s New Innovator Award, California Institute for Regenerative Medicine and Juvenile Diabetes Research Foundation to M.R.-S.

Author Contributions A.G.-M., J.R.-S., M.T.M., K.P., E.M. and M.R.-S. planned the project; A.G.-M., A.A., F.P., R.S., M.J.M. and A.H. performed the experiments; A.G.-M., A.A., F.P., R.S., M.J.M., K.P., E.M. and M.R.-S. analysed the data; and A.G.-M., K.P., E.M. and M.R.-S. wrote the manuscript.

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Correspondence to Miguel Ramalho-Santos.

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Supplementary Figures

This file contains Supplementary Figures 1-14 plus Legends. (PDF 6338 kb)

Supplementary Data

This file contains Supplementary Data 1: Normalized expression microarray data of control and Chd1 RNAi ES cells. (XLS 10540 kb)

Supplementary Data

This file contains Supplementary Data 2: Chd1 target genes in ES cells as determined by ChIP-chip. (XLS 432 kb)

Supplementary Table

This file contains Supplementary Table 1: Sequences of the short-hairpin RNAs used in the RNAi screen. (XLS 19 kb)

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Gaspar-Maia, A., Alajem, A., Polesso, F. et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 460, 863–868 (2009).

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