Project description:To investigate the upstream regulatory networks in myogenesis that lead to the establishment of the myogenic lineage and subsequent differentiation, we proformed scATAC-seq of pig somite and myotome cells from Tibetan pigs (ZZ) and Duroc×Tibetan pigs (DZ) at several embryonic stages (E18, E21, and E28).
Project description:To investigate the upstream regulatory networks in myogenesis that lead to the establishment of the myogenic lineage and subsequent differentiation, we proformed scRNA-seq of pig somite and myotome cells from Tibetan pigs (ZZ) and Duroc×Tibetan pigs (DZ) at several embryonic stages (E16, E18, E21, and E28).
Project description:To elucidate further molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes in Tibetan pigs, we used transcriptome microarrays from lung tissues of Tibetan pigs and Duroc pigs both at high and low altitude analyzed differentially expressed genes (DEGs), biological pathway and constructed co-expression regulation network. A total of 3,068 DEGs were identified which involved metabolic process, cellular process, immune biological process and angiogenesis pathway. The regulatory (RIF) and phenotypic (PIF) impact factors analysis identified several known and potentially regulators of hypoxia adaption, including IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2).
Project description: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.
Project description: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.
Project description:We investigated the heart tissue whole-genome DNA methylation data of Tibetan and Yorkshire pigs raised at high and low altitudes using MeDIP-seq (methylated DNA immunoprecipitation sequencing) technologies, in order to comparatively analyze epigenetic regulation in the two breeds under normoxic and hypoxic conditions. In addition, we aimed to identify the key genes and molecular mechanisms that are involved in adaptation to high altitude in the Tibetan pig. The results of bisulphite sequencing and RT-qPCR indicated that the differentially methylated genes identified in MeDIP-seq were credible. Our results provide new insights into the molecular mechanisms and the epigenetic mechanism involved in hypoxic adaptation in pigs, and a greater understanding of human hypoxic diseases.
Project description:In this study, miRNA-seq technique was used to identify differentially expressed miRNAs (DE miRNAs) in cardiac muscle of the Tibetan pig (TP) and Yorkshire pig (YP), which were both raised in highland environments. We obtained 108 M clean reads and 372 unique miRNAs that included 210 known pre-miRNAs and 162 novel pre-miRNAs. In addition, 20 DE miRNAs, including 10 upregulated and 10 downregulated miRNAs, were identified by comparing TP and YP. Based on the expression abundance and differentiation between the two populations, we predicted their targets, and KEGG pathway analyses suggested that DE miRNAs between the Tibetan pigs and Yorkshire pigs are involved in hypoxia-related pathways, such as the MAPK, mTOR, and VEGF signaling pathways, cancer-related signaling pathways, etc. Five DE miRNAs were randomly selected to validate the veracity of miRNA-seq using real-time PCR. The results showed that the expression corresponds to the trend in miRNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related miRNAs in pig and indicated that the expression patterns of hypoxia-related miRNAs are significantly altered in the Tibetan pig. DE miRNAs may play important roles in hypoxic adaptation after migration to hypoxic environments. mRNA profiles of 6-month old Tibetan pig (TP) and Yorkshire pig (YP) were generated by deep sequencing, in duplicate, using Hiseq 2000.
