Fig. 3

Previously analyzed PMC-specific cis-regulatory modules. Previously analyzed cis-regulatory modules (CRMs) (orange and yellow rectangles) that control the spatio-temporal expression of four PMC DE genes are represented in both ATAC-seq (light green trace: isolated PMCs; dark green trace: other cells) and DNase-seq (violet trace: control whole embryos, purple trace: U0126-treated embryos) datasets. a Sp-alx1 cis-regulatory modules are not represented as differential peaks in the ATAC-seq or DNase-seq datasets. b The Sp-sm50 enhancer (orange rectangle) and the minimal element (yellow rectangle) required for correct spatio-temporal expression of Sp-sm50 are encompassed within a differential peak identified in the DNase-seq dataset (violet rectangle), but not identified as differential in the ATAC-seq dataset. c The Sp-sm30a enhancer overlaps a differential peak identified in the ATAC- seq dataset (light green), but is not identified as differential in the DNase-seq dataset. d Two of four previously studied Sp-tbr cis-regulatory modules overlap 2 differential peaks in the ATAC-seq (light green) dataset and 1 differential peak in the DNase-seq (violet) dataset