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Diverse epigenetic strategies interact to control epidermal differentiation

Nature Cell Biology volume 14, pages 753–763 (2012)Cite this article

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Abstract

It is becoming clear that interconnected functional gene networks, rather than individual genes, govern stem cell self-renewal and differentiation. To identify epigenetic factors that impact on human epidermal stem cells we performed siRNA-based genetic screens for 332 chromatin modifiers. We developed a Bayesian mixture model to predict putative functional interactions between epigenetic modifiers that regulate differentiation. We discovered a network of genetic interactions involving EZH2, UHRF1 (both known to regulate epidermal self-renewal), ING5 (a MORF complex component), BPTF and SMARCA5 (NURF complex components). Genome-wide localization and global mRNA expression analysis revealed that these factors impact two distinct but functionally related gene sets, including integrin extracellular matrix receptors that mediate anchorage of epidermal stem cells to their niche. Using a competitive epidermal reconstitution assay we confirmed that ING5, BPTF, SMARCA5, EZH2 and UHRF1 control differentiation under physiological conditions. Thus, regulation of distinct gene expression programs through the interplay between diverse epigenetic strategies protects epidermal stem cells from differentiation.

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Figure 1: Chromatin-wide siRNA-based screen.
Figure 2: siRNA screen reveals known and previously unknown players controlling epidermal differentiation.
Figure 3: A Bayesian statistical model predicts functional/genetic interactions.
Figure 4: Genome-wide identification of subnetwork target genes.
Figure 5: Subnetwork components target distinct gene sets.
Figure 6: Targeted gene sets encode proteins with overlapping functions.
Figure 7: Genes regulated by distinct arms of the self-renewal subnetwork exhibit genetic interactions themselves.
Figure 8: Epidermal reconstitution assays verify physiological relevance of self-renewal subnetwork components.

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Acknowledgements

We thank A. Brenkman, J. Carroll, N. Rosenfeld, M. Narita, D. Odom and Watt laboratory members for critical discussion and comments. This work was supported by Cancer Research UK (CRUK), Hutchinson Wampoa, University of Cambridge (F.M.W.) and a Marie Curie Fellowship (PIEF-GA-2008-220642) to K.W.M. We are indebted to the core facilities of the CRUK Cambridge Research Institute for excellent technical assistance.

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Authors and Affiliations

  1. Epithelial Cell Biology Group, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK

    Klaas W. Mulder, Carles Escriu, Giacomo Donati & Fiona M. Watt

  2. Computational Biology Research Group, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK

    Xin Wang, Roland F. Schwarz & Florian Markowetz

  3. Genomic Imprinting Group, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK

    Yoko Ito, Santiago Uribe-Lewis & Adele Murrell

  4. Centre for High-throughput Biology, 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada

    Jesse Gillis & Paul Pavlidis

  5. The Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK

    Gábor Sirokmány & Fiona M. Watt

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  1. Klaas W. Mulder
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Contributions

K.W.M. conceived the study, designed, performed and analysed experiments and performed bioinformatic analysis. X.W. developed the Bayesian mixture model and network analysis. C.E. and G.S. contributed to the skin reconstitution assays. Y.I. performed bisulphite sequencing analysis. R.F.S. performed bioinformatic analysis. J.G. performed mRNA co-expression analysis. G.D. analysed data and contributed to experimental design. S.U-L. performed 5hmeDNA dot-blot analysis. P.P. performed mRNA co-expression analysis. A.M. oversaw the work of Y.I. and S.U-L. F.M. analysed data, performed bioinformatic analysis and contributed computational tools. F.M.W. designed experiments, analysed the data and oversaw the study. K.W.M and F.M.W. wrote the manuscript with input from all authors.

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Correspondence to Klaas W. Mulder or Fiona M. Watt.

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Mulder, K., Wang, X., Escriu, C. et al. Diverse epigenetic strategies interact to control epidermal differentiation. Nat Cell Biol 14, 753–763 (2012). https://doi.org/10.1038/ncb2520

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