Kim Woonsu, Park Hyesun, Seo Kang-Seok, Seo Seongwon
Department of Animal Biosystem Sciences, Chungnam National University, Daejeon 34134, Korea.
Department of Animal Science & Technology, College of Life Science and Natural Resources, Suncheon National University, Suncheon 57922, Korea.
Asian-Australas J Anim Sci. 2018 Jan;31(1):3-12. doi: 10.5713/ajas.16.0793. Epub 2017 May 14.
DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin () muscle (LDM) of swine.
A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates). The reference pig genome was annotated with 78.5% of the raw reads. A total of 33,506 putative methylated regions (PMR) were identified from methylated regions that overlapped at least two samples.
Of these, only 3.1% were commonly observed in all eight samples. DNA methylation patterns between two littermates were as diverse as between unrelated individuals (p = 0.47), indicating that maternal genetic effects have little influence on the variation in DNA methylation of porcine LDM. The highest density of PMR was observed on chromosome 10. A major proportion (47.7%) of PMR was present in the repeat regions, followed by introns (21.5%). The highest conservation of PMR was found in CpG islands (12.1%). These results show an important role for DNA methylation in species- and tissue-specific regulation of gene expression. PMR were also significantly related to muscular cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism.
This study indicated the biased distribution and functional role of DNA methylation in gene expression of porcine LDM. DNA methylation was related to cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism (e.g., insulin signaling pathways). Nutritional and environmental management may have a significant impact on the variation in DNA methylation of porcine LDM.
DNA甲基化在调节家畜与经济性状（如体重增加）相关基因的表达中起主要作用。本研究对猪里脊肉（LDM）的全基因组DNA甲基化组进行了表征和功能推断研究。
从八头杜洛克猪（四对同窝仔猪）的LDM样本中获得了总共8.99 Gb的甲基化DNA免疫沉淀序列数据。参考猪基因组用78.5%的原始读数进行注释。从至少两个样本重叠的甲基化区域中鉴定出总共33506个推定甲基化区域（PMR）。
其中，只有3.1%在所有八个样本中都普遍观察到。两个同窝仔猪之间的DNA甲基化模式与不相关个体之间的模式一样多样（p = 0.47），这表明母体遗传效应对猪LDM的DNA甲基化变异影响很小。在10号染色体上观察到PMR的最高密度。大部分（47.7%）的PMR存在于重复区域，其次是内含子（21.5%）。在CpG岛中发现PMR的保守性最高（12.1%）。这些结果表明DNA甲基化在基因表达的物种和组织特异性调节中起重要作用。PMR也与肌肉细胞发育、细胞间通讯、细胞完整性和运输以及营养代谢显著相关。
本研究表明DNA甲基化在猪LDM基因表达中的偏向分布和功能作用。DNA甲基化与细胞发育、细胞间通讯、细胞完整性和运输以及营养代谢（如胰岛素信号通路）有关。营养和环境管理可能对猪LDM的DNA甲基化变异有重大影响。
