Integrated Single‐Nucleus Multi‐Omics Atlases Reveal Lineage Plasticity and Regulatory Networks of Luminal Epithelial Cells During Mammary Gland Lactation and Involution

Dynamic changes in mammary cells are essential for sustaining lactation and maintaining epithelial homeostasis. However, the phenotypic transition process of mammary cells during lactation remains unclear. Here, single-nucleus RNA sequencing (snRNA-seq) of 64 199 cells and single-nucleus chromatin accessibility sequencing (snATAC-seq) of 78 984 cells were generated from the goat mammary gland of dry and lactation stages. A total of 18 cell types were annotated, and spatial transcriptomic analysis confirmed the localization of lactation-related cell types within the mammary tissue. Enrichment analysis of SNP within cell type-specific chromatin accessibility regions revealed strong associations between mammary epithelial cells (MECs) with milk production traits. To further explore the MECs functional diversification during lactation and their differences from the dry stage, four differentiation trajectories from luminal progenitor to luminal mature cells were reconstructed. Lineage-specific gene regulatory networks (GRNs) were constructed by integrating snRNA-seq and snATAC-seq data, and stage-specific signals were identified through cell-cell communications. Finally, to explore the evolutionary conservation and divergence of MECs, cross-species comparative analyses were conducted and revealed MEC differential evolutionary rates, conserved milk-producing subtypes, and lineage-specific populations driving species-specific differences in milk composition. Overall, these findings uncover the coordinated transcriptional and chromatin dynamics that drive mammary epithelial differentiation and functional maintenance during lactation.