Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing

Minkyeung Choi, Jongin Lee, Min Thong Le, Dinh Truong Nguyen, Suhyun Park, Nagasundarapandian Soundrarajan, K.M. Schachtschneider, Jaebum Kim, Jin Ki Park, Jin Hoi Kim, Chankyu Park*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

32 Citations (Scopus)

Abstract

DNA methylation plays a major role in the epigenetic regulation of gene expression. Although a few DNA methylation profiling studies of porcine genome which is one of the important biomedical models for human diseases have been reported, the available data are still limited. We tried to study methylation patterns of diverse pig tissues as a study of the International Swine Methylome Consortium to generate the swine reference methylome map to extensively evaluate the methylation profile of the pig genome at a single base resolution. We generated and analysed the DNA methylome profiles of five different tissues and a cell line originated from pig. On average, 39.85 and 62.1% of cytosine and guanine dinucleotides (CpGs) of CpG islands and 2 kb upstream of transcription start sites were covered, respectively. We detected a low rate (an average of 1.67%) of non-CpG methylation in the six samples except for the neocortex (2.3%). The observed global CpG methylation patterns of pigs indicated high similarity to other mammals including humans. The percentage of CpG methylation associated with gene features was similar among the tissues but not for a 3D4/2 cell line. Our results provide essential information for future studies of the porcine epigenome.

Original languageEnglish
Pages (from-to)343-355
JournalDNA research
Volume22
Issue number5
DOIs
Publication statusPublished - 2015

Keywords

  • RRBS

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    Choi, M., Lee, J., Le, M. T., Nguyen, D. T., Park, S., Soundrarajan, N., Schachtschneider, K. M., Kim, J., Park, J. K., Kim, J. H., & Park, C. (2015). Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing. DNA research, 22(5), 343-355. https://doi.org/10.1093/dnares/dsv017