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Interaction of methyl-CpG-binding protein 2 (MeCP2) with distinct enhancers in the mouse cortex

Nature Neuroscience volume 28, pages 62–71 (2025)Cite this article

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Abstract

Mutations in methyl-CpG-binding protein 2 (MeCP2) cause Rett syndrome. MeCP2 is thought to regulate gene transcription by binding to methylated DNA broadly across the genome. Here, using cleavage under target and release under nuclease (CUT&RUN) assays in the adult mouse cortex, we show that MeCP2 strongly binds to specific gene enhancers that we call MeCP2-binding hotspots (MBHs). Unexpectedly, we find that MeCP2 binding to MBHs occurs in a DNA methylation-independent manner at MBHs. Multiple MBH sites surrounding genes mediate the transcriptional repression of genes enriched for neuronal functions. We show that MBHs regulate genes irrespective of genic methylation levels, suggesting that MeCP2 controls transcription via an intragenic methylation-independent mechanism. Hence, disruption of intragenic methylation-independent gene regulation by MeCP2 may in part underlie Rett syndrome.

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Fig. 1: CUT&RUN uncovers MBHs across the neural genome.
Fig. 2: MeCP2 binding to MBH sites is largely methylation-independent at MBHs.
Fig. 3: MECP2 modulates enhancer activity at MBH sites.
Fig. 4: MeCP2 preferentially represses genes harboring multiple MBH sites.
Fig. 5: MBHs are correlated with gene repression independently of intragenic mCA.

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Data availability

The sequencing data have been deposited in the GEO under accession no. GSE266300. Publicly available datasets include GSE150538, GSE67293, GSE139509, GSE213752 and GSE103214.

Code availability

The core next-generation sequencing analysis was performed using publicly available open-source software, as described in the Methods. The custom R scripts used in the analysis are available upon request.

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Acknowledgements

We thank members of the Stroud laboratory and G. Konopka for discussions. This work was supported by the UT Southwestern Endowed Scholars Program, the Simons Foundation Autism Research Initiative, the International Rett Syndrome Foundation, the Klingenstein-Simons Fellowship, the Whitehall Foundation and the Brain and Behavior Research Foundation to H.S., and the O’Donnell Brain Institute Sprouts Grant to M.E. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

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  1. Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA

    Gyan Prakash Mishra, Eric X. Sun, Tiffany Chin, Mandy Eckhardt & Hume Stroud

  2. Department of Neurobiology, Harvard Medical School, Boston, MA, USA

    Michael E. Greenberg

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Contributions

G.P.M. performed all the data analyses. E.X.S., T.C., M.E. and H.S. performed the experiments. M.E.G. provided key reagents. H.S. conceived the study. H.S. and G.P.M. wrote the manuscript, with edits from E.X.S., T.C. and M.E.

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Correspondence to Hume Stroud.

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Mishra, G.P., Sun, E.X., Chin, T. et al. Interaction of methyl-CpG-binding protein 2 (MeCP2) with distinct enhancers in the mouse cortex. Nat Neurosci 28, 62–71 (2025). https://doi.org/10.1038/s41593-024-01808-y

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