Fig. 2: Spatial ATAC uncovers spatiotemporal patterns of regulatory element accessibility underlying gene expression.

a, Visium gene expression signature scores for differentially accessible genes in spatial ATAC (sATAC) clusters. Visium clusters (left) on an E12.5 section for reference. CNS, central nervous system; Men./PNS, meninges/peripheral nervous system; and Mesen., mesenchyme. b, Pou3f2 expression (top, cyan), gene activity and accessibility of a co-accessible distal regulatory element (magenta). c, Genomic track and co-accessibility scores for peaks around the Pou3f2 locus. The distal element shown in b is highlighted in gray and tracks are colored according to spatial ATAC clusters. d, Inset of a SOX2-immunostained E15.5 spatial ATAC section (n = 2) with highlighted SOX2+ (progenitor, pink) and SOX2− (neuronal, purple) regions. e, Top 500 differentially accessible peaks by fold change in SOX2+ and SOX2− regions. Avg. acc., average accessibility. f, Motif enrichment analysis of peaks from e. Selected motifs for transcription factors expressed in the region are highlighted. P values by a one-sided hypergeometric test. g, Accessibility (Acc.) (spatial ATAC; magenta) and expression (expr.) of the nearest gene (Visium; cyan) for loci enriched in progenitor (Sox1) or neuronal (Fyn) regions. h, Gene signature score in lower and upper cortical regions for differentially accessible genes in SOX2+ and SOX2− regions. i, UMAP of integrated single-cell RNA-seq and spatial ATAC from the E15.5 developing cortex colored by pseudotime and split by technology. P values by Wilcoxon test (***<0.001). j, Pseudotime scores projected onto their spatial locations in a spatial ATAC E15.5 section. k, Hematoxylin and eosin image of a breast cancer section processed using Visium (n = 1) with overlaid pathologist annotations. Expression of ERBB2 (HER2) and myeloid cell marker C1QB in the boxed inset. l, Annotated hematoxylin and eosin image of an adjacent (200 µm) section processed using spatial ATAC (n = 3). On the right, accessibility of the ERBB2 locus, C1QB locus and two associated regulatory regions in the boxed inset (right). m, Spatial interaction between tumor cell and myeloid cell clusters at the tumor interface. Pathology is denoted as follows: red, invasive cancer; blue, tumor infiltrating lymphocytes; green, intravascular cancer and yellow, normal gland. Scale bars, 500 µm.