A temporal single cell atlas of dynamic chromatin accessibility during murine lung maturation

Lung maturation involves intricate cellular differentiation and structural remodeling, yet the underlying epigenetic dynamics remain poorly characterized at single-cell resolution. Here we present HTL-ATAC-seq, an ultra-high-throughput, ligation-based single-cell ATAC-seq approach. Applying HTL-ATAC-seq to mouse lung tissue across 15 continuous postnatal time points, we construct a temporal chromatin accessibility atlas of 1,185,619 nuclei, identifying 129 distinct cell subclusters and 713,987 candidate chromatin regulatory elements. Temporal analysis reveals three distinct cellular maturation stages and 12 dynamic chromatin accessibility patterns, capturing the transition from structural morphogenesis to immune maturation. We uncover distinct transcription factor regulatory patterns between alveolar type 1 and 2 cells and identify a putative Sprr1a enhancer specifically active in alveolar type 1 cells. Finally, we identify time- and cell-type-specific cis-regulatory elements associated with lung disease-related gene sets. In this work, we provide a comprehensive resource for understanding the epigenetic mechanisms underlying lung maturation and lung disease-associated regulatory programs. Lung maturation involves dynamic epigenetic remodelling that is not fully understood. Here, the authors develop an ultra-high-throughput single-cell ATAC-seq method and generate a temporal atlas of 1.2 million lung nuclei, revealing regulatory programs that shape postnatal lung development and disease risk.