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A histone H3 lysine 27 demethylase regulates animal posterior development

Nature volume 449, pages 689–694 (2007)Cite this article

Abstract

The recent discovery of a large number of histone demethylases suggests a central role for these enzymes in regulating histone methylation dynamics. Histone H3K27 trimethylation (H3K27me3) has been linked to polycomb-group-protein-mediated suppression of Hox genes and animal body patterning, X-chromosome inactivation and possibly maintenance of embryonic stem cell (ESC) identity. An imbalance of H3K27 methylation owing to overexpression of the methylase EZH2 has been implicated in metastatic prostate and aggressive breast cancers. Here we show that the JmjC-domain-containing related proteins UTX and JMJD3 catalyse demethylation of H3K27me3/2. UTX is enriched around the transcription start sites of many HOX genes in primary human fibroblasts, in which HOX genes are differentially expressed, but is selectively excluded from the HOX loci in ESCs, in which HOX genes are largely silent. Consistently, RNA interference inhibition of UTX led to increased H3K27me3 levels at some HOX gene promoters. Importantly, morpholino oligonucleotide inhibition of a zebrafish UTX homologue resulted in mis-regulation of hox genes and a striking posterior developmental defect, which was partially rescued by wild-type, but not by catalytically inactive, human UTX. Taken together, these findings identify a small family of H3K27 demethylases with important, evolutionarily conserved roles in H3K27 methylation regulation and in animal anterior–posterior development.

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Figure 1: Histone demethylation mediated by UTX.
Figure 2: UTX regulates H3K27me3 at the HOXD gene locus
Figure 3: UTX binds near HOX gene start sites to facilitate H3K27 demethylation and gene activation.
Figure 4: Inhibition of zebrafish Utx1 results in improper development of the posterior trunk.

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Acknowledgements

HeLa nucleosomes were a gift from X. Shi and O. Gozani. We thank G. Schnitzler for discussion. J.L.R. is a Fellow and H.Y.C. is the Kenneth G. and Elaine A. Langone Scholar of the Damon Runyon Cancer Research Foundation. J.R.W. is a recipient of the Ruth L. Kirschstein National Service Award. This work was supported by grants from the National Science Foundation (to J.K.W.), NIH, Scleroderma Research Foundation and Emerald Foundation (to H.Y.C), and from the NIH to Y.S. This work was also supported in part by a grant from the Novartis Biomedical Research Institute (to Y.S).

ChIP-chip data have GEO accession number GSE8855.

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Author notes

  1. Peter E. Bayliss, John L. Rinn and Johnathan R. Whetstine: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA,

    Fei Lan, Johnathan R. Whetstine, Shuzhen Chen, Shigeki Iwase, Roman Alpatov & Yang Shi

  2. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,

    Peter E. Bayliss & Thomas M. Roberts

  3. Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, 269 Campus Drive, Stanford, California 94305, USA,

    John L. Rinn, Jordon K. Wang & Howard Y. Chang

  4. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel

    Irina Issaeva & Eli Canaani

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Correspondence to Yang Shi.

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Lan, F., Bayliss, P., Rinn, J. et al. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449, 689–694 (2007). https://doi.org/10.1038/nature06192

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