Extended Data Fig. 6: Genes that are repeatedly tuned between neuron types have characteristics that predispose them to regulation by the MeCP2 pathway.

a, Number of intragenic cCREs (left) and gene length (right) for genes that are repeatedly tuned between closely related neuron types. Genes are plotted by the number of times they are detected as differential between two closely related neuron types. n = 23822 cells used in single-cell RNA-seq¹ to identify these genes. ****p < 0.0001 two-sided Wilcoxon rank-sum test. b, Aggregate profiles of mCA/CA in the cerebral cortex for genes found to be differentially expressed between closely related neuron types more than three times or non-type-specific genes. Aggregate plots generated as in Fig. 2d. c, Odds ratio of overlap between repeatedly tuned genes and core MeCP2-repressed genes or MeCP2-repressed genes identified in L5, PV, or SST neurons. Analysis was performed on type-specific gene lists described in Tasic et al.¹ in combination with DNA methylation from Luo et al.⁸. Differential gene lists from Fig. 1 were used in c. Boxplots represent data as described in Fig. 2.