Fig. 3: Spatiotemporal dynamics of DNA methylation and RNA transcription during embryogenesis.
From: Spatial joint profiling of DNA methylome and transcriptome in tissues
a, Spatial mapping of oligodendrocyte progenitors (left) and premature oligodendrocytes (middle) identified by label transfer from mouse embryo scRNA-seq data17 to spatial-DMT, with pseudotemporal reconstruction of the oligodendrogenesis plotted in space (right). b, Pseudotime heat maps of VMRs that become demethylated (left) and expression changes of nearby genes from oligodendrocyte progenitors to premature oligodendrocytes (right). Each row represents a specific genomic locus (left) and nearby genes (right), with columns representing tissue pixels ordered by pseudotime. The colour scale indicates the z scores of DNA methylation and gene expression. c,d, UMAP visualization (c) and spatial distribution (d) of integrated E11 and E13 WNN analysis. Spatial tissue pixels from different developmental stages conform well and match with the tissue types. e,f, Comparative analysis of RNA-expression levels (log-normalized expression) with two-sided Wilcoxon rank-sum test, unadjusted P = 8.47 × 10−36, P = 7.62 × 10−54, P = 4.00 × 10−37 from top to bottom (e) and DNA methylation (methylation percentage) with two-sided Wilcoxon rank-sum test, unadjusted P = 2.07 × 10–82, P = 5.45 × 10−82, P = 8.55 × 10−80 from top to bottom (f) for upregulated genes in E13 brain and spinal cord. g, GO enrichment analysis from one-sided hypergeometric test of biological processes related to demethylated and upregulated genes in the brain and spinal cord from E11 to E13 stages. h, Spatial mapping of the expression levels (log-normalized expression) of DNA-methylation-related enzymes in the brain and spinal cord regions across E11 and E13 stages.
