title: Swine liver methylomes of Berkshire, Duroc and Landrace breeds by MeDIPS.
abstract: Using a methyl-DNA immunoprecipitation technique in combination with next-generation deep sequencing, we conducted comprehensive DNA methylation profiling of liver genomes from three pig breeds: Berkshire, Duroc and Landrace. The profiles revealed that the distribution patterns of methylation signals along the genome are conserved among the three pig breeds. Specifically, many signals in coding genes were found in introns, and most signals in the repetitive elements were identified in non-long terminal repeat (LTR) retrotransposons such as long and short interspersed repetitive elements, implying a significant association with alternative splicing and expression of retrotransposable elements respectively. Differentially methylated regions among the three pig breeds were identified in the non-LTR retrotransposons, suggesting that they may lead to differential retrotransposable element activity. Altogether, this study provides advanced swine methylome data and valuable resources for understanding the function of DNA methylation in the evolutionary divergence of different pig breeds.
authors: Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, Korea.
authors: Woo Young
authors: WY
authors: Bang
authors: Sam Woong
authors: SW
authors: Kim
authors: Seul Gi
authors: SG
authors: Kwon
authors: Jung Hye
authors: JH
authors: Hwang
authors: Tae Wan
authors: TW
authors: Kim
authors: Moon-Suck
authors: MS
authors: Ko
authors: In-Cheol
authors: IC
authors: Cho
authors: Young Kuk
authors: YK
authors: Joo
authors: Kwang Keun
authors: KK
authors: Cho
authors: Jin Young
authors: JY
authors: Jeong
authors: Chul Wook
authors: CW
authors: Kim
mesh_terms: D000818:Animals; D001947:Breeding; D004247:DNA / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary; D047468:Immunoprecipitation / Q000662:veterinary; D007438:Introns / Q000235:genetics; D008099:Liver; D008297:Male; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000662:veterinary; D013552:Swine / Q000145:classification / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D018626:Retroelements; D004247:DNA
keywords: DNA methylation; methyl-DNA immunoprecipitation; retrotransposon; swine methylome