Fig. 3: Regulatory landscape of neurula cell types.
a Heatmap representing the enrichment of specific TF binding motifs (columns) in the regulatory regions of genes in each cell type of the amphioxus neurula (rows). Names from selected motifs are indicated next to the heatmap (in bold those that also appear in panel b). The amphioxus motif library was obtained by merging experimentally determined vertebrate motifs from CIS-BP with de novo inferred motifs for each amphioxus cell type, and removing redundancy (see Methods). Therefore, motif names do not represent specific amphioxus TFs, but rather sequence similarity with motifs of vertebrate homologs. The regulatory regions associated with each gene were obtained from a bulk ATAC-seq experiment. b Examples of cell type-specific amphioxus TFs whose expression levels (vertical axis, as log2(FC)) match the enrichment of associated motifs (horizontal axis; shown below as information content logos). Circle size is proportional to the BH-adjusted −log10(p) binomial test of motif enrichment comparing motif occurrence near cell type-specific and unspecific genes (see Methods; exact p-values of these tests are shown for significant enrichment at p < 0.01, see Source Data for a complete list). Di/mesenceph. prim= Di/mesencephalon primordium.
