Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle

Abstract Intramuscular fat content is one of the most important factors affecting beef quality. However, the role of alternate polyadenylation (APA) in intramuscular fat deposition remains unclear. We compared APA events in muscle samples from high and low intramuscular fat (IMF) cattle, based on RNA-seq data. A total of 363 significant APAs were identified. Notably, the number of shortened 3′UTR events exceeded the number of lengthened 3′UTR events, and genes associated with shortened 3′UTR events were enriched in fatty acid metabolism-related pathways. Most APA events had alternative 3′UTR (aUTR) lengths of 200-300 bp. As the 3′UTR lengthened, the aUTR also lengthened (R2 = 0.79). These findings indicate that genes with longer 3′UTRs are more likely to be regulated by APA in the muscle of cattle with high IMF. To determine whether the identified APA events drove alterations in the expression of fat deposition-related genes, we analyzed the relationship between APA events and differentially expressed genes and identified several genes critical for fat deposition (e.g., PFKL and SLC1A5). Since miRNAs usually bind to the 3'UTR region of protein-coding genes and affect gene expression, we constructed an miRNA-APA network to detect several key miRNAs that may regulate fat deposition. We identified 10 important miRNAs that affect changes in IMF content, which may be gained (gained miRNA-binding sites) or lost (lost miRNA-binding sites) owing to 187 differential APA events. Our study characterized the APA profiles of cattle with high and low intramuscular fat content and provided further insights into the relationship between APA, miRNA, and fat deposition.