Fig. 4: Differential chromatin accessibility at craniofacial in vivo enhancers correlates with expression of nearby genes.

a Unbiased clustering (UMAP) of open chromatin regions from snATAC-seq of the developing mouse face for stages e10.5–15.5 for ~41,000 cells. The cell types are assigned based on label transfer (Seurat) from cell type annotations of the ScanFaceX data. b Correlation between normalized gene expression (x axis) from ScanFaceX and normalized accessibility (y axis) from snATAC-seq for select genes (Epcam, Dsp, Cthrc1, Cldn5) and their transcription start sites with the highest correlation evident in relevant cell types. c Genomic context and evolutionary conservation (in placentals) for corresponding regulatory regions in the vicinity of the Isl2/Scaper locus, and an intronic distal enhancer within Lrrk1. Tracks for individual snATAC-seq clusters from developing mouse face tissue (e10.5 to e15.5), with cluster-specific open chromatin signatures for relevant annotated cell types are shown for the same genomic regions. Colors in b and the individual snATAC-seq tracks in c correspond to the color code used in a. UMAP of ScanFaceX data shows expression of Isl2 and Aldh1a3 (gene adjacent to Lrrk1) in expected cell types. Images for a representative mouse embryo at e11.5 for both loci show validated in vivo lac-Z-reporter activity of the respective regions; black arrowheads point towards stained regions. n, reproducibility of each pattern across embryos resulting from independent transgenic integration events. Source data for 4b are provided as a Source Data file.