Genome-Wide DNA Methylation Patterns of Muscle and Tail-Fat in DairyMeade Sheep and Mongolian Sheep

Abstract

This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs had a higher DNA methylation level than CHHs and CHGs, and tail-fat tissues had higher CG methylation levels than muscle tissues. For DNA repeat elements, SINE had the highest methylation level, while Simple had the lowest. When dividing the gene promoter region into small bins (200 bp per bin), the bins near the transcription start site (±200 bp) had the highest CG count per bin but the lowest DNA methylation levels. A series of DMRs were identified in muscle and tail-fat tissues between the two breeds. Among them, the introns of gene CAMK2D (calcium/calmodulin-dependent protein kinase II δ) demonstrated significant DNA methylation level differences between the two breeds in both muscle and tail-fat tissues, and it may play a crucial role in fat metabolism and meat quality traits. This study may provide basic datasets and references for further epigenetic modification studies during sheep genetic improvement.

Keywords: CAMK2D; CpG; fat-tailed sheep; gene promoter region; whole-genome bisulfite sequencing.

Figure 1

Global DNA methylation patterns. (A) Muscle tissue and (B) tail-fat tissue of DairyMeade sheep and Mongolian sheep, distribution of DNA methylation under CG, CHH and CHG contexts, only cytosines covered at least 3 times were considered.

Figure 2

DNA methylation patterns under different cytosine contexts. (A) DNA methylation levels of CHG and CHH contexts in tail-fat tissue and muscle tissue, (B) DNA methylation level of CG context.

Figure 3

DNA methylation dynamics of gene body and flank regions. DNA methylation dynamics of (A) muscle tissue and (B) tail-fat tissue, averaged DNA methylation levels along the gene body and 15 kb upstream of TSS and 15 kb downstream of TES of all annotated RefSeq genes.

Figure 4

DNA methylation dynamics of repeat elements, intergenic regions, and intragenic regions. DNA methylation dynamics of (A) muscle tissue, and (B) tail-fat tissue. (C) Comparison of DNA methylation levels between muscle tissue and tail-fat tissue.

Figure 5

The CG density and distribution of the 20 consecutive bins in promoter regions. (A) Classification of the CG density for all RefSeq gene promoters. The promoters were separated into three classes: (1) HCG, more than 8 CGs per 200 bp; (2) LCG, less than 4 CGs per 200 bp; (3) ICG, 4–8 CGs per 200 bp. (B) Distribution of CG counts at the 20 bins of all RefSeq genes. The number of CGs at bin1 was the highest.

Figure 6

DNA methylation patterns of the promoter region for muscle tissue and tail-fat tissue. (A) Global DNA methylation level of prompter region (left), and DNA methylation of HCG, ICG and LCG-types promoter for muscle tissue (middle) and tail-fat tissue (right). (B) DNA methylation patterns of muscle tissue and (C) tail-fat tissue at the consecutive 20 bins of the promoter region.

Figure 7

DNA methylation level of differentially methylated sites within CAMK2D, all the methylated cytosine were covered more than three times.