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DNA Res. 2015 Oct;22(5):343-55. doi: 10.1093/dnares/dsv017. Epub 2015 Sep 10.

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

Author information

1
Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
2
Department of Animal Sciences, University of Illinois, Urbana, IL, USA Animal Breeding and Genomics Center, Wageningen University, Wageningen, The Netherlands.
3
Animal Biotechnology Division, National Institute of Animal Science, Suwon, Korea.
4
Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea chankyu@konkuk.ac.kr.

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.

KEYWORDS:

DNA methylation; RRBS; epigenetics; methylome; pig

PMID:
26358297
PMCID:
PMC4596400
DOI:
10.1093/dnares/dsv017
[Indexed for MEDLINE]
Free PMC Article

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