ATAC-seq and RNA-seq reveal key genes and pathways regulating lactation in the mammary gland of Yili horses

Mammary gland development and lactation are dynamic biological processes governed by coordinated changes in chromatin accessibility and gene expression. We performed paired ATAC-seq and RNA-seq profiling to characterize stage-associated chromatin accessibility and transcriptional programs in the Yili horse mammary gland. Using a conservative overlap-based integration, we prioritized candidate genes showing concordant changes across both layers as hypothesis-generating signals for future functional studies. We sequenced mammary gland tissues from early lactation (S1) and peak lactation (S2) stages. We identified 32,187 S1-specific peaks and 46,661 S2-specific peaks. Upregulated genes were enriched in biological processes related to cell differentiation, tissue development, and signaling pathways, including PI3K-Akt, JAK-STAT, and Rap1 signaling, which may be involved in lactation regulation. In addition, motif enrichment analysis suggested several key transcription factors, including STAT5, SMAD4, and KLF3. Integration of ATAC-seq and RNA-seq data highlighted 22 differentially expressed genes (DEGs) with altered chromatin accessibility, including PTGES, NFATC4, RET, RGS2, and EQMHCB2, which are involved in the oxytocin signaling pathway, glutathione metabolism, and Wnt signaling. This study presents a stage-resolved atlas of chromatin accessibility and gene expression in the Yili horse mammary gland, suggesting candidate pathways and genes for further validation.