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

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 methyl...

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Published inDNA research Vol. 22; no. 5; pp. 343 - 355
Main Authors Choi, Minkyeung, Lee, Jongin, Le, Min Thong, Nguyen, Dinh Truong, Park, Suhyun, Soundrarajan, Nagasundarapandian, Schachtschneider, Kyle M, Kim, Jaebum, Park, Jin-Ki, Kim, Jin-Hoi, Park, Chankyu
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.10.2015
Subjects
Animals
CpG Islands
DNA Methylation
Epigenesis, Genetic
Genome
Humans
Liver - metabolism
Muscles - metabolism
Neocortex - metabolism
Olfactory Mucosa - metabolism
Organ Specificity
RRBS
Sequence Analysis, DNA
Spleen - metabolism
Sulfites - chemistry
Sus scrofa - genetics
DNA methylation
methylome
epigenetics
RRBS
pig
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Summary: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.
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Present address: School of Biotechnology, Tan Tao University, Duc Hoa, Vietnam.
These authors contributed equally to this work.
Edited by Prof. Takashi Ito
ISSN:1340-2838
1756-1663
DOI:10.1093/dnares/dsv017