Fig. 1: Single-cell triple-omics of the adult NSC lineage.
From: DNA methylation controls stemness of astrocytes in health and ischaemia
a, Schematic depiction of the adult NSC lineage of the vSVZ. NSCs represent a specialized subset of astrocytes. OB, olfactory bulb. b, Schematic of the workflow to obtain scNMT-seq data from three brain regions. c, UMAP visualization of each molecular layer, colour coded as in a. Single-cell transcriptomes (540 cells from 5 replicates) were integrated with the larger dataset from ref. 18, which comprises cells from the vSVZ (light grey) and striatum, RMS and olfactory bulb (dark grey). Bottom left, tissue of origin for each cell. d, UMAP and pseudotime ranks (excluding oligodendrocytes) based on data from all three molecular layers. e, Average methylation and chromatin accessibility levels around TSSs and CTCF-binding sites of one individual neuroblast. f, Correlation of VMR methylation and VAR accessibility with expression of the nearest gene. Negative correlations (blue) indicate a repressive effect of methylation or accessibility; positive correlations (orange) indicate activation. n is the number of nominally significant correlations (Pearson’s two-sided correlation test) after Benjamini–Hochberg adjustment. The y axis shows unadjusted P values. g, Top, distance histogram of all significant correlations (blue, negative; orange, positive) between gene expression and all VMRs and VARs within 2 Mb of the TSS. Bottom, magnified view of the indicated region. h, Genes binned according to methylation change downstream of their TSS. Bar colour denotes the proportion of genes upregulated or downregulated, according to their transcript expression in the NSC lineage; parenthesized numbers denote gene number per bin. NS, not significant. i,j, Overlap of significantly correlating VMRs and VARs with gene features (i) and candidate cis-regulatory elements (j). UTR, untranslated region.
