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DNMT1 maintains progenitor function in self-renewing somatic tissue

Abstract

Progenitor cells maintain self-renewing tissues throughout life by sustaining their capacity for proliferation while suppressing cell cycle exit and terminal differentiation1,2. DNA methylation3,4,5 provides a potential epigenetic mechanism for the cellular memory needed to preserve the somatic progenitor state through repeated cell divisions. DNA methyltransferase 1 (DNMT1)6,7 maintains DNA methylation patterns after cellular replication. Although dispensable for embryonic stem cell maintenance8, the role for DNMT1 in maintaining the progenitor state in constantly replenished somatic tissues, such as mammalian epidermis, is unclear. Here we show that DNMT1 is essential for epidermal progenitor cell function. DNMT1 protein was found enriched in undifferentiated cells, where it was required to retain proliferative stamina and suppress differentiation. In tissue, DNMT1 depletion led to exit from the progenitor cell compartment, premature differentiation and eventual tissue loss. Genome-wide analysis showed that a significant portion of epidermal differentiation gene promoters were methylated in self-renewing conditions but were subsequently demethylated during differentiation. Furthermore, UHRF1 (refs 9, 10), a component of the DNA methylation machinery that targets DNMT1 to hemi-methylated DNA, is also necessary to suppress premature differentiation and sustain proliferation. In contrast, Gadd45A11,12 and B13, which promote active DNA demethylation, are required for full epidermal differentiation gene induction. These data demonstrate that proteins involved in the dynamic regulation of DNA methylation patterns are required for progenitor maintenance and self-renewal in mammalian somatic tissue.

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Figure 1: DNMT1 is downregulated during epidermal differentiation.
Figure 2: DNMT1 loss triggers differentiation and failure of self-renewal.
Figure 3: DNMT1 is required to repress differentiation and sustain proliferation.
Figure 4: DNA methylation during epidermal differentiation.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

Profiling and MeDIP-chip data have been deposited with the GEO database under accession code GSE18590.

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Acknowledgements

This work was supported by the USVA Office of Research and Development, NIH/NIAMS AR45192, an unrestricted research gift from LVMH Recherche to P.A.K. and an NIH National Research Service Award AR055849 to G.L.S. We thank M. P. Scott, G. R. Crabtree, M. T. Fuller, J. Wysocka, H. Y. Chang, A. E. Oro, T. W. Ridky, B. J. Zarnegar, M. Kretz, D. Webster, R. Flockhart for critical comments and pre-submission review, X. Bao for help with figures, and G. Lai for informatics.

Author Contributions G.L.S. performed and designed the experiments and wrote the manuscript. J.A.R. analysed the bioinformatic data and wrote the manuscript. D.E.W. analysed the bioinformatic data. L.Z. performed experiments. P.A.K. supervised the project, discussed the results and wrote the manuscript.

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Correspondence to Paul A. Khavari.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-11 with Legends. (PDF 1364 kb)

Supplementary Table 1

This table shows differentially expressed genes during epidermal differentiation. (XLS 515 kb)

Supplementary Table 2

This table shows differentially expressed genes with DNMT1 knockdown. (XLS 136 kb)

Supplementary Table 3

This table shows the gene overlap between DNMT1 knockdown and differentiated cells. (XLS 70 kb)

Supplementary Table 4

This table shows methylation peaks in undifferentiated epidermal cells. (XLS 2703 kb)

Supplementary Table 5

This table shows methylation peaks in differentiated epidermal cells. (XLS 3435 kb)

Supplementary Table 6

This table shows methylated differentiation genes. (XLS 32 kb)

Supplementary Table 7

This table shows differentially methylated epidermal differentiation genes. (XLS 64 kb)

Supplementary Table 8

This table shows de novo methylated genes during differentiation. (XLS 36 kb)

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Sen, G., Reuter, J., Webster, D. et al. DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature 463, 563–567 (2010). https://doi.org/10.1038/nature08683

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