Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs [RNA-seq]

To explore the exceptional mechanisms of gene expression and DNA methylation that are induced by low altitude environments in Tibetan pigs, we performed a comparative transcriptomic analysis of skeletal muscle in indigenous Tibetan pigs that reside in high altitude regions (～4,000 m) and their counterparts that migrated to the geographically neighboring low-altitude regions (～500 m) for nearly ten generations. We identified protein coding genes that related to hypoxia response (EGLN3 and FLT1), oxygen transport and energy metabolism (TFB2M), and two long non-coding RNAs (TCONS_00039686 and TCONS_00084992) that associated with the regulation of transcription and various nucleolus and organelle lumen, were differentially expressed between Tibetan pigs and their counterparts in low-altitude regions, thus might be the potential candidate regulators in skeletal muscle of low-altitude acclimation in Tibetan pigs. We also found genes embedded in differentially methylated regions between Tibetan pigs and their counterparts in low-altitude regions were mainly involved in ‘Starch and sucrose metabolism’, ‘glucuronosyltransferase activity’ processes, hypoxia and energy metabolism. We envision that this study will serve as a valuable resource for mammal acclimatization research and agricultural food industry. A total of six healthy female Tibetan pigs were used in this study: three free-ranging individuals in Tibetan highland with the average altitude of 4,000 m (high-altitude); three counterparts under experimental conditions with normal daily feeding in geographically neighboring low-altitude regions (Chengdu plain) with average altitude of 500 m (low-altitude), these pigs were descendants of Tibetan pigs that have been raised in lowland for nearly ten generations.