The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation

Abstract

Gene transcription is critically influenced by chromatin structure and the modification status of histone tails1. Methylation of lysine residues in histone tails is dynamically regulated by the opposing activities of histone methyltransferases and histone demethylases2. Here we show that JARID1C/SMCX, a JmjC-domain-containing protein implicated in X-linked mental retardation and epilepsy3,4, possesses H3K4 tri-demethylase activity and functions as a transcriptional repressor. An SMCX complex isolated from HeLa cells contains additional chromatin modifiers (the histone deacetylases HDAC1 and HDAC2, and the histone H3K9 methyltransferase G9a) and the transcriptional repressor REST5, suggesting a direct role for SMCX in chromatin dynamics and REST-mediated repression. Chromatin immunoprecipitation reveals that SMCX and REST co-occupy the neuron-restrictive silencing elements in the promoters of a subset of REST target genes. RNA-interference-mediated depletion of SMCX derepresses several of these targets and simultaneously increases H3K4 trimethylation at the sodium channel type 2A (SCN2A) and synapsin I (SYN1) promoters. We propose that loss of SMCX activity impairs REST-mediated neuronal gene regulation, thereby contributing to SMCX-associated X-linked mental retardation.

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Figure 1: The SMCX complex contains an H3K4 tri-demethylase activity.
Figure 2: Recombinant SMCX purified from insect Sf9 cells demethylates H3K4me2 and H3K4me3 in vitro.
Figure 3: SMCX demethylates di- and trimethyl H3K4 in cells.
Figure 4: SMCX regulates promoter H3K4me2/H3K4me3 levels and expression of several REST target genes.

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Acknowledgements

We thank Y. Shi and F. Lan for the gift of the His-JMJD2C protein. We also thank G. Mandel, T. Westbrook and P. Mulligan for sharing the anti-REST antibody and Y. Nakatani for the anti-RING2 antibody. This work was supported by NIH grants to Y.S. and by NIH and Harvard Stem Cell Institute (HSCI) grants to A.R. Y.S. is a PEW scholar. M.T. is supported by the HSCI and is a pre-doctoral fellow of the Ryan Foundation.

Author Contributions M.T. and P.M. contributed equally to this work.

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Correspondence to Yujiang Shi.

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Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S8 with Legends and Supplementary Table 1. Supplementary Figure S1 shows that GST-SMCX pulls down REST in vitro. Supplementary Figures S2-S5 contain additional data on the enzymatic activity of SMCX. Supplementary Figure S6 demonstrates that SMCX is a transcriptional co-repressor. Supplementary Figure S7 and S8 provide additional data on the effect of SMCX knockdown on histone methylation and acetylation both globally and at several REST target genes. Supplementary Table 1 summarises the effect of SMCX knockdown on the expression of genes in the RT-PCR array. (PDF 2562 kb)

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Tahiliani, M., Mei, P., Fang, R. et al. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature 447, 601–605 (2007). https://doi.org/10.1038/nature05823

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