Tissue-specific isoform usage and gene expression revealed through RNA-seq and ATAC-seq in developing cattle

Establishing a comprehensive characterization of the regulatory landscapes of cattle tissues facilitates a better understanding of the biological mechanisms responsible for condition-dependent phenotypes that drive tissue-specific gene regulation, developmental processes, and responses to environmental or physiological cues. This can be achieved through the characterization of gene expression, transcript usage and open chromatin accessibility. While much of this work has been done in human and biomedical model species, there is a lack of research in cattle that jointly characterizes chromatin accessibility and transcript usage alongside gene expression to define tissue-specific regulatory landscapes in cattle. Samples of prefrontal cortex (PFC), liver (L), and gracilis skeletal muscle (SM) were collected from four 3-month-old Angus steers and subjected to ATAC-seq and RNA-seq analyses. Differential gene expression (DGE) and transcript usage (DTU) were quantified across the tissues and evaluated in PFC-L, PFC-SM, and L-SM pairwise comparisons. In total, 4,840, 4,151, and 3,663 genes were identified as differentially expressed, while 209, 236, and 154 genes exhibited differential transcript usage in PFC-L, PFC-SM, and L-SM comparisons, respectively. The genes CLTA, SLC25A3 and P2RX5 were highlighted for DTU between tissues, and further comparison of predicted protein sequences identified structural differences between CLTA and P2RX5 isoforms suggesting tissue-specific roles. Differential chromatin accessibility analysis revealed 2,576, 1,820, and 2,960 differential peaks in promoter regions across the same pairwise tissue comparisons. Functional enrichment revealed that PFC regulatory genes were associated with synaptic formation, myelination, and neurodevelopment, L genes with homeostatic regulation and lipid metabolism, and SM genes with muscle differentiation, myonuclear addition, and hypertrophy. These patterns aligned with ATF, HNF, and MEF2 motif enrichment in PFC, L, and SM promoter peaks, respectively. Furthermore, the integration of ATAC-seq and RNA-seq results revealed 62 genes in PFC, 93 genes in L, and 59 genes in SM as potential tissue-specific regulatory genes. These findings provide insight into the complex regulatory mechanisms governing biological processes in the PFC, L, and SM of young Angus steers. This work integrates chromatin accessibility, transcript usage, and gene expression across multiple physiologically important cattle tissues, providing a comprehensive view of tissue-specific regulatory landscapes and generating a resource to support future studies in cattle genomics.