Fig. 2: DNMT1 regulates the expression of hub genes of cIN development in migrating E14.5 SST⁺ interneurons.

Differential gene expression and methylation analysis of FAC-sorted Sst-Cre/tdTomato control (Ctrl) and Sst-Cre/tdTomato/Dnmt1 loxP² (knockout; KO) cells isolated from the E14.5 basal telencephalon based on total RNA and enzymatic methyl-sequencing. For RNA- and methyl-sequencing, we separately processed two samples per genotype, each consisting of cells pooled from multiple embryos (RNA sequencing: Ctrl N = 23 embryos; KO N = 14 embryos; methyl-sequencing: Ctrl N = 15 embryos; KO N = 11 embryos). a Volcano plot depicting the differentially expressed genes (DEGs) between control and KO samples. Genes annotated as significantly changed (adjusted p value < 0.05) are colored blue and red, with red depicting increased expression in KO. Two-sided Wald test with Benjamini–Hochberg adjustment (DESeq2). b Heatmap of selected genes (coding for transcription factors and guidance cues governing cIN development, as well as epigenetic modifiers), color-coding differential gene expression (DGE) and differential methylated regions (DMRs). c Venn diagram illustrating the overlap between up- or downregulated genes and genes associated with or containing a differentially methylated region (DMR). The intersection of upregulated and differentially methylated genes after knockout was tested for enrichment of the DNMT1 binding motif identified by DNMT1-ChIP-sequencing, shown in d. d DNA motif enriched in DNMT1-interacting chromatin, detected by ChIP-sequencing (N = 2 biological replicates). e DEGs identified in Dnmt1 KO samples were compared to DEGs determined in embryonic stem cell-derived murine neurons overexpressing DNMT1. f Selection of brain development-related gene ontology (GO) terms enriched in genes that were both upregulated and differentially methylated in E14.5 Sst-Cre/tdTomato/Dnmt1 KO cells (ShinyGO 0.82). g Position of differentially methylated regions relative to the transcription start sites of genes related to cIN development. Horizontal bars indicate the region’s size, and the color code represents the mean methylation change for the respective region. h RNA sequencing tracks combined with the methylation profile of the Arx gene locus obtained from Ctrl and KO samples. Further information: Supplementary Tables 1–8. Raw data are available via the hyperlinks listed in the Data Availability Statement.