Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #412166
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

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

Author
item LI, CHENGLONG - Ningxia University
item XU, JUNJIE - Ningxia University
item ZHANG, YANFENG - Ningxia University
item DING, YANLING - Ningxia University
item ZHOU, XIAONAN - Ningxia University
item SU, ZONGHUA - Ningxia University
item QU, CHANG - Ningxia University
item LIANG, JIAHAO - Ningxia University
item HAN, YURUN - Ningxia University
item WANG, DINGXIANG - Ningxia University
item SHI, YUANGANG - Ningxia University
item Li, Congjun
item Liu, Ge
item KANG, XIAOLONG - Ningxia University

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2024
Publication Date: 11/20/2024
Citation: Li, C., Xu, J., Zhang, Y., Ding, Y., Zhou, X., Su, Z., Qu, C., Liang, J., Han, Y., Wang, D., Shi, Y., Li, C., Liu, G., Kang, X. 2024. Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle. Journal of Animal Science. https://doi.org/10.1093/jas/skae357.
DOI: https://doi.org/10.1093/jas/skae357

Interpretive Summary: Intramuscular fat content is one of the most important factors affecting beef quality. We analyzed alternate polyadenylation events between high and low bovine intramuscular fat groups based on RNA-seq data. These results fill our knowledge gaps and provide the foundation for incorporating new molecular signals into the future animal breeding program. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Intramuscular fat content is one of the most important factors affecting beef quality. However, the role of post-transcriptional modifications, especially alternate polyadenylation (APA), in the process of intramuscular fat deposition is unclear. We analyzed APA events between high and low bovine intramuscular fat groups based on RNA-seq data. In total, we identified 363 significant APA events. Notably, the number of shortened 3'UTR events exceeded the number of lengthened 3'UTR events, and the genes associated with shortened 3'UTR events were enriched in fatty acid metabolism-related pathways. Most of APA events had alternative 3'UTR (aUTR) lengths of 200-300 bp. In addition, 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 during bovine intramuscular fat deposition. 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 a number of genes that are critical for fat deposition function (e.g., PFKL, SLC1A5). Since miRNAs usually bind to the 3UTR region of protein-coding genes, they affect gene expression. Therefore, we constructed a miRNA-APA network to detect several key miRNAs that may regulate fat deposition. We identified 10 miRNAs important in intramuscular fat deposition that may be gained (gained miRNA binding sites) or lost (lost miRNA binding sites) due to 187 differential APA events. Our study characterized the APA profiles during bovine intramuscular fat deposition and provides further insights into understanding the relationship between APA, miRNA, and fat deposition.