The Profiling of DNA Methylation and Its Regulation on Divergent Tenderness in Angus Beef Cattle

Abstract

Beef is an essential food source in the world. Beef quality, especially tenderness, has a significant impact on consumer satisfaction and industry profit. Many types of research to date have focused on the exploration of physiological and developmental mechanisms of beef tenderness. Still, the role and impact of DNA methylation status on beef tenderness have yet to be elucidated. In this study, we exhaustively analyzed the DNA methylation status in divergent tenderness observed in Angus beef. We characterized the methylation profiles related to beef tenderness and explored methylation distributions on the whole genome. As a result, differentially methylated regions (DMRs) associated with tenderness and toughness of beef were identified. Importantly, we annotated these DMRs on the bovine genome and explored bio-pathways of underlying genes and methylation biomarkers in beef quality. Specifically, we observed that the ATP binding cassette subfamily and myosin-related genes were highly methylated gene sets, and generation of neurons, regulation of GTPase activity, ion transport and anion transport, etc. , were the significant pathways related with beef tenderness. Moreover, we explored the relationship between DNA methylation and gene expression in DMRs. Some methylated genes were identified as candidate biomarkers for beef tenderness. These results provide not only novel epigenetic information associated with beef quality but offer more significant insights into meat science, which will further help us explore the mechanism of muscle biology.

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

“…Meanwhile, a number of DMRs on genes associated with important biological processes such as lipid translocation and lipid transport were identified in latissimus dorsi muscle from different breeds of beef cattle with diverse meat quality traits ( Fang et al, 2017 ). For instance, DNA methylation profiling in relation to beef tenderness in Angus cattle revealed 7,215 DMRs between tender and tough beef ( Zhao et al, 2020 ). The DMRs were significantly enriched in ATP binding cassette subfamily and myosin-related genes, including ABCA1 , ABCA7 , and ABCG1 , with roles in beef tenderness and fatty acid metabolism ( Zhao et al, 2020 ).…”

“…For instance, DNA methylation profiling in relation to beef tenderness in Angus cattle revealed 7,215 DMRs between tender and tough beef ( Zhao et al, 2020 ). The DMRs were significantly enriched in ATP binding cassette subfamily and myosin-related genes, including ABCA1 , ABCA7 , and ABCG1 , with roles in beef tenderness and fatty acid metabolism ( Zhao et al, 2020 ). Besides, demethylation of a DMR in the SIRT4 promoter promoted its transcriptional activity through CMYB mediation or inhibited its transcriptional activity through NRF1 mediation, thereby shedding light on the role of an epigenetic process in the transcriptional regulation of the expression of SIRT4 during bovine adipocyte differentiation ( Hong et al, 2019 ).…”

Examining the extent of environmental contributions toward DNA methylation and phenotypic variation

“…There are a wide range of phenotypes that producers must consider to maximize the health and production of their livestock, and DNA methylation has been shown to influence many of those phenotypes. DNA methylation has been associated with mastitis in dairy cattle ( Ju et al, 2020 ; Wang et al, 2020 ), the rate of egg laying in chickens ( Omer et al, 2020 ), beef tenderness in cattle ( Zhao et al, 2020 ), wool fiber production in goats ( Xiao et al, 2020 ), fat deposition in swine ( Zhang et al, 2016 ), and milk production in dairy cattle ( Liu et al, 2017 ) ( Figure 3 ). The diversity of traits associated with DNA methylation patterns in a variety of species highlights the significance of methylation in determining phenotype.…”

“…Beef tenderness has been of interest to producers and consumers, but previous research has predominantly focused on physiological mechanisms of tenderness. A new study delved into the DNA methylation differences of Angus beef with divergent tenderness, based on measurements of Warner–Bratzler shear force, crude fat, fatty acid contents, and cooking loss ( Zhao et al, 2020 ). Methylated DNA-binding domain sequencing was used to measure DNA methylation in tender beef and tough beef, and 7, 215 DMRs were identified between groups of divergent tenderness.…”

“…Identified DMRs were found in pathways related to beef tenderness, including regulation of guanosine triphosphatases activity, ion transport, and anion transport. Gene expression was then measured using 4 × 44K Bovine Gene Expression Microarrays and compared with DNA methylation to identify candidate genes for beef tenderness biomarkers: myosin heavy chain 8 ( MYH8 ), N -acetylated alpha-linked acidic dipeptidase 2 ( NAALAD2 ), phospholipase A2 group IVA ( PLA2G4A ), and ubiquitin-like with PHD and ring finger domains 1 ( UHRF1 ) ( Zhao et al, 2020 ). This study demonstrated, for the first time, the impact of DNA methylation on beef tenderness.…”