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Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

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Science  11 Aug 2017:
Vol. 357, Issue 6351, pp. 600-604
DOI: 10.1126/science.aan3351
  • Fig. 1 High-throughput single-nucleus methylome sequencing (snmC-seq) of mouse and human frontal cortex (FC) neurons.

    (A) Workflow of snmC-seq. (B and C) Number of single-neuron methylomes (B) and distribution of genomic coverage per data set (C).

  • Fig. 2 Non-CG methylation (mCH) signatures identify distinct neuron populations in mouse and human FC.

    (A and B) Hierarchical clustering of neuron types according to gene body mCH level. (C and D) Two-dimensional visualization of single neuron clusters (tSNE) (9). Mouse and human homologous clusters are labeled with similar colors. (E and F) Gene body mCH at Rorb for each single neuron (top) and the distribution for each cluster (bottom); hyper- and hypomethylated clusters are highlighted in red and blue, respectively. (G) Comparison of human neuron clusters defined by mCH with clusters from single-nucleus RNA sequencing (4, 9). (H) Fraction of cells in each human cluster assigned to each mouse cluster based on mCH correlation at orthologous genes (9). Mutual best matches are highlighted with black rectangles.

  • Fig. 3 Conserved and divergent neuron type–specific gene regulatory elements.

    (A) Heat map showing differentially methylated regions (CG-DMRs) hypomethylated in one or two neuron clusters; categories of DMRs containing >1000 regions are shown. (B) TF binding motif enrichment in CG-DMRs of homologous mouse and human clusters (false discovery rate < 10−10). (C) Mouse- or human-specific enrichment and depletion of TF binding motifs. Asterisks indicate TF binding motifs that are significantly enriched in one species but depleted in the other.

  • Fig. 4 Gene body mCH and CG-DMRs conserved between mouse and human.

    (A) Global mCH and mCG levels are strongly conserved within homologous cell types between mouse and human. (B) Cross-species correlation of gene body mCH at orthologous genes shows cell type–specific conservation. Black boxes denote homologous neuron clusters. (C) The median correlation of gene body mCH for homologous clusters is higher than the within-species correlation for distinct clusters. (D) Cross-species correlation of mCG at neuron type–specific CG-DMRs. (E) Sequence conservation at neuron type–specific DMRs.

Supplementary Materials

  • Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

    Chongyuan Luo, Christopher L. Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R. Nery, Justin P. Sandoval, Brian Bui, Terrence J. Sejnowski, Timothy T. Harkins, Eran A. Mukamel, M. Margarita Behrens, Joseph R. Ecker

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Supplementary Text
    • Figs. S1 to S17
    • Captions for tables S1 to S8
    • Table S9
    • References
    Table S1
    Metadata of mouse single neuron methylomes (separate file)
    Table S2
    Metadata of human single neuron methylomes (separate file)
    Table S3
    Marker genes for human and mouse clusters (separate file)
    Table S4
    Genes showing layer-specific mCH in inhibitory neuron populations (separate file)
    Table S5
    List of mouse CG-DMRs (separate file)
    Table S6
    List of human CG-DMRs (separate file)
    Table S7
    List of mouse large CG-DMRs (separate file)
    Table S8
    List of human large CG-DMRs (separate file)

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