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Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome

Nature Medicine volume 23, pages 1203–1214 (2017)Cite this article

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Abstract

Mutations in MECP2 cause Rett syndrome (RTT), an X-linked neurological disorder characterized by regressive loss of neurodevelopmental milestones and acquired psychomotor deficits. However, the cellular heterogeneity of the brain impedes an understanding of how MECP2 mutations contribute to RTT. Here we developed a Cre-inducible method for cell-type-specific biotin tagging of MeCP2 in mice. Combining this approach with an allelic series of knock-in mice carrying frequent RTT-associated mutations (encoding T158M and R106W) enabled the selective profiling of RTT-associated nuclear transcriptomes in excitatory and inhibitory cortical neurons. We found that most gene-expression changes were largely specific to each RTT-associated mutation and cell type. Lowly expressed cell-type-enriched genes were preferentially disrupted by MeCP2 mutations, with upregulated and downregulated genes reflecting distinct functional categories. Subcellular RNA analysis in MeCP2-mutant neurons further revealed reductions in the nascent transcription of long genes and uncovered widespread post-transcriptional compensation at the cellular level. Finally, we overcame X-linked cellular mosaicism in female RTT models and identified distinct gene-expression changes between neighboring wild-type and mutant neurons, providing contextual insights into RTT etiology that support personalized therapeutic interventions.

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Figure 1: Utilization and characterization of Mecp2Tavi mice and associated RTT variants.
Figure 2: Cell-type-specific transcriptional profiling of neuronal nuclei.
Figure 3: Analysis of T158M and R106W DEGs.
Figure 4: Genome-wide length-dependent transcriptional changes in mutant mice.
Figure 5: T158M and R106W DEGs in mosaic female mice.

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Acknowledgements

We would like to thank the IDDRC Mouse Gene Manipulation Core at Children's Hospital Boston (U54HD090255, M. Thompson), the Gene Targeting Core (P01DK049210, K. Kaestner) and the Transgenic and Chimeric Mouse Facility (J. Richa) at University of Pennsylvania for help in generating transgenic mice, the Flow Cytometry and Cell Sorting Resource Laboratory (H. Pletcher, W. DeMuth), and the Next Generation Sequencing Core (J. Schug) for technical assistance. B.S.J. is supported by a Cell and Molecular Biology Training Grant (TG32GM072290) and the UNCF/Merck Graduate Research Dissertation Fellowship. This work is supported by NIH grants K22AI112570 (G.V.), R21AI107067 and R01CA140485 (T.H.K.), R01MH091850 and R01NS081054 (Z.Z.), and a basic research grant from Rettsyndrome.org (Z.Z.). Z.Z. is a Pew Scholar in the Biomedical Sciences.

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  1. Brian S Johnson, Ying-Tao Zhao and Maria Fasolino: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA

    Brian S Johnson, Ying-Tao Zhao, Maria Fasolino, Janine M Lamonica, George Georgakilas, Kathleen H Wood, Daniel Bu, Yue Cui, Darren Goffin, Golnaz Vahedi & Zhaolan Zhou

  2. Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, USA

    Yoon Jung Kim & Tae Hoon Kim

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Contributions

Conceptualization, B.S.J. and Z.Z.; methodology, B.S.J., J.M.L., D.G. and Z.Z.; investigation, B.S.J., Y.-T.Z., M.F., J.M.L., K.H.W., Y.J.K. and D.B.; formal analyses, B.S.J., Y.-T.Z., G.G. and T.H.K.; validation, B.S.J., M.F., J.M.L. and G.V.; resources, B.S.J., Y.-T.Z. and Y.C.; data curation, Y.-T.Z.; writing manuscript, B.S.J.; review and editing, B.S.J., Y.-T.Z., M.F. and Z.Z.; visualization, B.S.J.; project administration and funding acquisition, Z.Z.

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Correspondence to Zhaolan Zhou.

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Supplementary information

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Supplementary Figures 1–13 (PDF 29209 kb)

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Supplementary Table 1

Summary of RNA-seq experimental conditions used in this study (XLSX 14 kb)

Supplementary Table 2

RT-PCR primers used in this study (XLSX 65 kb)

Supplementary Table 3

List of HITS-CLIP data sets used for RBP analysis (XLSX 55 kb)

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Johnson, B., Zhao, YT., Fasolino, M. et al. Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome. Nat Med 23, 1203–1214 (2017). https://doi.org/10.1038/nm.4406

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