Extended Data Fig. 14: Differential accessibility peaks associated with the Cux2 gene in different cell types or different developmental ages.

(a) Heatmap representation of accessibility of differentially accessible peaks located in Cux2 gene body and 50 kb upstream. Each row corresponds to a peak, ordered by peak module, and each column corresponds to a cell category defined by subclass and age group. The Cux2 gene expression level is shown in purple at the top. The heatmap color represents the average peak accessibility (height) in each subclass-by-age group, normalized with 1 indicating the maximum value for each peak and 0 indicating no accessibility. The peak module and maximum peak height are shown for each peak to the right. Specific peaks are numbered and labeled. (b) The accessibility tracks per subclass surrounding the Cux2 gene, along with the genomic locations of labeled peaks in (a). TSS, transcription start site. (c) UMAP representation of Multiome nuclei, colored by Cux2 expression and accessibility of a subset of peaks labeled in (a). TF gene Cux2 exhibits markedly distinct temporal patterns across different cell types. We extracted all the accessibility peaks located within the Cux2 gene body (193 kb) and 50 kb upstream of Cux2’s main TSS. We observed strikingly complex accessibility patterns of different peaks in different subclasses and ages (a). There are distinct peak modules specific to IP (module 2), IP IT and IMN IT (module 3), IMN IT and upper layer IT cells (module 5), Car3 cells (module 6), shared by L2/3 IT, L4/5 IT and Car3 cells (module 7), specific to early L2/3 (module 9), shared by OPC and MGE (module 14), shared by IP and MGE (module 1), or specific to MGE (modules 10,11,13). We labeled specific peaks with distinct patterns in both the heatmap and the cell-type genomic tracks (a and b). Most of the peaks present in early-stage RG and IP populations disappear in adulthood, except those that are present near the promoter or widely accessible. The accessibility of peaks in the promoter area overall shows strong consistency with RNA expression across all the cell types under study, while the peaks in more distal areas show accessibility in a highly cell-type and temporally specific manner. To study the subtler temporal progression, we examined the expression of Cux2 gene and accessibility of specific peaks at the single cell level (c). Peak 1 is specific to IP, Peak 10 to IMN IT and L2-4, Peak 8 to MGE (decreasing over time), Peak 5 to L2-4 (increasing over time), and Peak 15 specific to Car3 and surprisingly in microglia (although expression of Cux2 gene in microglia was not observed).