Fig. 4: Spatial DNA-methylation and RNA-transcription analyses in the P21 mouse brain.
From: Spatial joint profiling of DNA methylome and transcriptome in tissues
a, Bright-field image of the P21 mouse brain section (pixel size, 20 μm; ROI area, 2 × 2 mm2) showing the analysed regions, including the DG, CA1, CA2, CA3 and cortex (n = 1). Scale bar, 500 µm. b, Spatial distribution of clusters identified in DNA-methylation data (left), RNA-transcription data (middle) and integrated DNA and RNA data using WNN analysis (right). c–e, Scatter plot displaying the relationship between CpG and CpA methylation changes (log-transformed fold change) and gene-expression changes (log-transformed fold change; gene exp. (log fold)) for marker genes in DG (c), CA1/2 (d) and CA3 (e). Each dot represents a specific gene, coloured by the log-fold change in gene expression, with red indicating upregulation and blue indicating downregulation. These plots demonstrate how differential methylation at CpG and CpA sites correlates with changes in gene expression, illustrating the complex regulatory landscape across different brain regions. f–h, Spatial mapping of CpG (left) and CpA (middle) methylation and RNA-expression levels (right) for selected genes in different brain regions.
