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A chromatin-modifying function of JNK during stem cell differentiation

Nature Genetics volume 44, pages 94–100 (2012)Cite this article

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Abstract

Signaling mediates cellular responses to extracellular stimuli. The c-Jun NH2-terminal kinase (JNK) pathway exemplifies one subgroup of the mitogen-activated protein (MAP) kinases, which, besides having established functions in stress response, also contribute to development by an unknown mechanism1,2,3,4. We show by genome-wide location analysis that JNK binds to a large set of active promoters during the differentiation of stem cells into neurons. JNK-bound promoters are enriched with binding motifs for the transcription factor NF-Y but not for AP-1. NF-Y occupies these predicted sites, and overexpression of dominant-negative NF-YA reduces the JNK presence on chromatin. We find that histone H3 Ser10 (H3S10) is a substrate for JNK, and JNK-bound promoters are enriched for H3S10 phosphorylation. Inhibition of JNK signaling in post-mitotic neurons reduces phosphorylation at H3S10 and the expression of target genes. These results establish MAP kinase binding and function on chromatin at a novel class of target genes during stem cell differentiation.

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Figure 1: JNK is upregulated during stem cell differentiation and directly binds promoters.
Figure 2: JNK target promoters are active and show increased JNK binding during terminal differentiation.
Figure 3: NF-Y mediates JNK recruitment to chromatin.
Figure 4: Inhibition of JNK signaling blocks differentiation and reduces H3S10 phosphorylation.
Figure 5: Blocking JNK kinase activity downregulates target gene expression.

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Acknowledgements

We thank L. Hoerner, M. Seimiya and I. Nissen for technical assistance, N. Tiwari for help with reagents and critical suggestions, G. Christofori, M. Bentires-Alj and members of the Schübeler laboratory for comments to the manuscript, R. Davis (University of Massachusetts Medical School, Worcester, Massachusetts, USA) for providing wild-type NIH3T3 cells and those lacking JNK1 and JNK2, and R. Mantovani (University of Milan, Milan, Italy) for the wild-type and dominant-negative NF-Y constructs. We thank the facilities at the Friedrich Miescher Institute, especially T. Roloff. Illumina sequencing was carried out at the Quantitative Genomics Facility of the Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich. V.K.T. is supported by a Marie Curie International Incoming fellowship and an EMBO long-term postdoctoral fellowship. Research in the laboratory of R.P. is supported by the Deutsche Forschungsgemeinschaft (DFG), the European Union Epigenome Network of Excellence (EU-NoE) Epigenesys, Novartis and the ETH Zürich. Research in the laboratory of D.S. is supported by the Novartis Research Foundation, the European Union ((EU-NoE) Epigenesys, Blueprint)), the European Research Council (ERC-204264) and SystemsX.ch (Cell Plasticity).

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Authors and Affiliations

  1. Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

    Vijay K Tiwari, Michael B Stadler, Christiane Wirbelauer & Dirk Schübeler

  2. Swiss Institute of Bioinformatics, Basel, Switzerland

    Michael B Stadler

  3. Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel, Switzerland

    Renato Paro & Christian Beisel

  4. Faculty of Science, University of Basel, Basel, Switzerland

    Renato Paro & Dirk Schübeler

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  1. Vijay K Tiwari
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Contributions

V.K.T. initiated and designed the study, performed experiments, analyzed data and wrote the manuscript. M.B.S. designed and performed the computational analysis and wrote the manuscript. C.W. performed experiments and analyzed data. R.P. provided input during the study and comments on the manuscript. C.B. initiated the study, performed experiments, analyzed data and wrote the manuscript. D.S. designed the study, analyzed data and wrote the manuscript.

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Correspondence to Michael B Stadler or Dirk Schübeler.

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Tiwari, V., Stadler, M., Wirbelauer, C. et al. A chromatin-modifying function of JNK during stem cell differentiation. Nat Genet 44, 94–100 (2012). https://doi.org/10.1038/ng.1036

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