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Asian-Australas J Anim Sci. 2018 Jan;31(1):3-12. doi: 10.5713/ajas.16.0793. Epub 2017 May 14.

Characterization and functional inferences of a genome-wide DNA methylation profile in the loin (longissimus dorsi) muscle of swine.

Author information

1
Department of Animal Biosystem Sciences, Chungnam National University, Daejeon 34134, Korea.
2
Department of Animal Science & Technology, College of Life Science and Natural Resources, Suncheon National University, Suncheon 57922, Korea.

Abstract

OBJECTIVE:

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 (longissimus dorsi) muscle (LDM) of swine.

METHODS:

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.

RESULTS:

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.

CONCLUSION:

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.

KEYWORDS:

DNA Methylation; DNA Methylome; Longissimus dorsi Muscle; Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq); Pig

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