高原低氧环境下藏猪和大白猪的全基因组DNA甲基化图谱
Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia.
作者信息
Zhang Bo, Ban Dongmei, Gou Xiao, Zhang Yawen, Yang Lin, Chamba Yangzom, Zhang Hao
机构信息
1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China.
2College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 China.
出版信息
J Anim Sci Biotechnol. 2019 Feb 5;10:25. doi: 10.1186/s40104-019-0316-y. eCollection 2019.
BACKGROUND
Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude. However, the genetic and epigenetic mechanisms of hypoxic adaptation in animals remain unclear.
METHODS
Whole-genome DNA methylation data were generated for heart tissues of Tibetan pigs grown in the highland (TH, = 4) and lowland (TL, = 4), as well as Yorkshire pigs grown in the highland (YH, = 4) and lowland (YL, = 4), using methylated DNA immunoprecipitation sequencing.
RESULTS
We obtained 480 million reads and detected 280679, 287224, 259066, and 332078 methylation enrichment peaks in TH, YH, TL, and YL, respectively. Pairwise TH vs. YH, TL vs. YL, TH vs. TL, and YH vs. YL comparisons revealed 6829, 11997, 2828, and 1286 differentially methylated regions (DMRs), respectively. These DMRs contained 384, 619, 192, and 92 differentially methylated genes (DMGs), respectively. DMGs that were enriched in the hypoxia-inducible factor 1 signaling pathway and pathways involved in cancer and hypoxia-related processes were considered to be important candidate genes for high-altitude adaptation in Tibetan pigs.
CONCLUSIONS
This study elucidates the molecular and epigenetic mechanisms involved in hypoxic adaptation in pigs and may help further understand human hypoxia-related diseases.
背景
藏猪栖息于青藏高原，表现出与低地猪不同的表型和生理特征，并且已经很好地适应了高海拔的极端条件。然而，动物低氧适应的遗传和表观遗传机制仍不清楚。
方法
利用甲基化DNA免疫沉淀测序技术，对生长在高原（TH，n = 4）和低地（TL，n = 4）的藏猪以及生长在高原（YH，n = 4）和低地（YL，n = 4）的约克夏猪的心脏组织进行全基因组DNA甲基化数据检测。
结果
我们获得了4.8亿条 reads，分别在TH、YH、TL和YL中检测到280679、287224、259066和332078个甲基化富集峰。TH与YH、TL与YL、TH与TL以及YH与YL的两两比较分别揭示了6829、11997、2828和1286个差异甲基化区域（DMR）。这些DMR分别包含384、619、192和92个差异甲基化基因（DMG）。在缺氧诱导因子1信号通路以及与癌症和缺氧相关过程的通路中富集的DMG被认为是藏猪高海拔适应的重要候选基因。
结论
本研究阐明了猪低氧适应所涉及的分子和表观遗传机制，可能有助于进一步了解人类缺氧相关疾病。
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