title: Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing.
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.
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Minkyeung
authors.initials: M
authors.lastname: Choi
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Jongin
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Min Thong
authors.initials: MT
authors.lastname: Le
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Dinh Truong
authors.initials: DT
authors.lastname: Nguyen
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Suhyun
authors.initials: S
authors.lastname: Park
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Nagasundarapandian
authors.initials: N
authors.lastname: Soundrarajan
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL, USA Animal Breeding and Genomics Center, Wageningen University, Wageningen, The Netherlands.
authors.forename: Kyle M
authors.initials: KM
authors.lastname: Schachtschneider
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Jaebum
authors.initials: J
authors.lastname: Kim
authors.affiliation: Animal Biotechnology Division, National Institute of Animal Science, Suwon, Korea.
authors.forename: Jin-Ki
authors.initials: JK
authors.lastname: Park
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.
authors.forename: Jin-Hoi
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea chankyu@konkuk.ac.kr.
authors.forename: Chankyu
authors.initials: C
authors.lastname: Park
mesh_terms: D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D016678:Genome; D006801:Humans; D008099:Liver / Q000378:metabolism; D009132:Muscles / Q000378:metabolism; D019579:Neocortex / Q000378:metabolism; D009831:Olfactory Mucosa / Q000378:metabolism; D009928:Organ Specificity; D017422:Sequence Analysis, DNA; D013154:Spleen / Q000378:metabolism; D013447:Sulfites / Q000737:chemistry; D034421:Sus scrofa / Q000235:genetics*
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite
keywords: DNA methylation; RRBS; epigenetics; methylome; pig