Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq

Despite recent advances in single -cell genomics, the lack of maps for single -cell candidate cis -regulatory elements (cCREs) in non -mammal species has limited our exploration of conserved regulatory programs across vertebrates and invertebrates. Here, we developed a combinatorial -hybridization -based method for single -cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) named CH-ATACseq, enabling the construction of single -cell accessible chromatin landscapes for zebrafish, Drosophila , and earthworms ( Eisenia andrei ). By integrating scATAC censuses of humans, monkeys, and mice, we systematically identified 152 distinct main cell types and around 0.8 million cell -type -specific cCREs. Our analysis provided insights into the conservation of neural, muscle, and immune lineages across species, while epithelial cells exhibited a higher organ -origin heterogeneity. Additionally, a large-scale gene regulatory network (GRN) was constructed in four vertebrates by integrating scRNA-seq censuses. Overall, our study provides a valuable resource for comparative epigenomics, identifying the evolutionary conservation and divergence of gene regulation across different species.