Chromatin accessibility landscapes define stromal cell identities across tissues.

Chromatin accessibility is crucial in regulating gene expression and maintaining cellular identity. While single-cell RNA sequencing has revolutionized transcriptomic profiling, the understanding of chromatin dynamics across diverse tissues remains limited. Here, we use single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) to explore chromatin accessibility landscapes across murine tissues. We profile chromatin accessibility in 51,248 cells from nine mouse tissues, identifying 28 major cell types with distinct accessibility signatures. Our data reveal both conserved and tissue-specific cis-regulatory elements, highlighting the dynamic interplay between transcription factors and chromatin states in cell differentiation and tissue function. Motif enrichment analyses uncover transcription factor motifs driving these regulatory landscapes. Notably, we demonstrate that chromatin accessibility profiles enable tracing stromal cells, including endothelial cells, fibroblasts, and macrophages back to their tissue of origin. Using a metacell approach, we identify specific chromatin modules reflecting tissue-specific epigenomic landscapes, underscoring the role of chromatin accessibility in defining stromal cell identities. Our study provides a comprehensive atlas of chromatin accessibility across murine tissues, offering insights into the regulatory architecture that governs tissue and cell-type specificity. The ability to trace stromal cells to their tissue of origin through chromatin signatures holds important implications for diagnostics and therapeutic interventions in disease contexts.