Fig. 2: Divergent regulatory principles of early and late stages of neuronal development.
a, Schematic of analyses. b, Summary of gene expression clusters from Fig. 1c. c, TF expression specificity within the brain for TFs in different categories of cluster, from expression data from the Allen Brain Atlas (left). Higher values indicate more specific expression. TF expression specificity across 397 mouse cell types from the FANTOM5 project (right). Box and midline: 25th, 50th and 75th percentiles; whiskers: 1.5× interquartile range from box. d, Summary of ATAC peak clusters from Fig. 1d. e, Fraction of open chromatin regions (ATAC-seq peaks) in different categories of clusters that overlap CGIs or annotated promoter regions. f, Fraction of DMRs in ATAC clusters of different categories that are static or dynamic over the time course. g, Fraction of ATAC-seq peaks from different classes of ATAC clusters that overlap DNAse hypersensitivity sites (DHSs) across 35 cell types from the mouse ENCODE project. Adult (8-week) whole-brain and telencephalon samples highlighted in red; embryonic (E14.5 and E18.5) brain samples are highlighted in blue. Also see Extended Data Fig. 5f. Error bars: mean ± s.e.m. h, Open chromatin specificity across ATAC peak clusters (nEarly = 10,488, nLate = 17,570), as the concordance of ATAC peaks with an scATAC-seq panel of 85 mouse primary tissues and cell types17. Box plot as in c. i, Distribution of phyloP sequence conservation across all placental mammals for early developmental and late developmental ATAC clusters. Box plot as in c. j, Density of known TF binding motifs within ATAC clusters of different types. Box plot as in c. k, Average sequence entropy within ATAC clusters of different types. Box plot as in c. l, Summary of characteristics from c and g–j for each of the shared developmental ATAC peak clusters individually. Each arm of the plot represents an individual metric (center = low, edge = high). Also see Extended Data Fig. 5b.
