An atlas of DNA methylomes in porcine adipose and muscle tissues

Abstract

It is evident that epigenetic factors, especially DnA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DnA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DnA immunoprecipitation libraries, and provide a genome-wide DnA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth.

Genome-wide association study of the backfat thickness trait in two pig populations

“…The tenth rib backfat thickness trait is not only controlled by multiple genes but can also be affected to varying degrees by other environmental factors. For quantitative traits, it is difficult to confirm QTL or genes that have common effects and the effects, such as fatness and pork quality, could be verified in different pig populations [12]. Furthermore, the separation of two populations in clustering analysis (Fig.…”

“…GH1 deficiency in mammals has been found to be associated with stunted somatic growth and increased adipose tissue [15]. Also, GH1 gene was found to be related to fat deposition in pigs [12].…”

Developmental methylation pattern regulates porcine GPR120 expression

“…Measurement of porcine adipocyte volume was performed as previously described (Li et al, 2012). All SATs were fixed in 10% neutral buffered formalin solution after sacrifice, embedded in paraffin using a TP1020 semi-enclosed tissue processor (Leica), sliced at a thickness of 6 µm by using the RM2135 rotary microtome (Leica), and stained with hematoxylin and eosin.…”

Promoter and first exon methylation regulate porcine FASN gene expression

“…After being stained with hematoxylin and eosin, digital images were captured with a TE2000 fluorescence microscope (Nikon, Japan). Approximately 100 adipocytes per sample were randomly selected using the Image Pro-Plus 6.0 software (Media-Cybernetics, USA) to measure adipocyte cell volume, as described previously (Li et al, 2012).…”

“…We then performed quantitative methylation analysis on the treated DNA using the Sequenom MassAR-RAY platform (CapitalBio, Beijing, China), as described previously (Li et al, 2012). This platform uses matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, in combination with RNA base-specific cleavage.…”