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. 2023 Jun 14:10:1186040.
doi: 10.3389/fvets.2023.1186040. eCollection 2023.

Whole-genome DNA methylation profiling reveals epigenetic signatures in developing muscle in Tan and Hu sheep and their offspring

Caijuan Yue  1   2 , Jiakang Wang  3 , Yifei Shen  4 , Junli Zhang  2 , Jian Liu  2 , Aiping Xiao  5 , Yisha Liu  1 , Hehua Eer  2 , Qiao-E Zhang  1
Affiliations

Whole-genome DNA methylation profiling reveals epigenetic signatures in developing muscle in Tan and Hu sheep and their offspring

Caijuan Yue et al. Front Vet Sci. .

Abstract

Introduction: The Tan sheep is a popular local breed in China because of its tenderness and flavor. The Hu sheep breed is also famous for its high litter size, and its muscle growth rate is faster than that of Tan sheep. However, the epigenetic mechanism behind these muscle-related phenotypes is unknown.

Methods: In this study, the longissimus dorsi tissue from 18 6 month-old Tan sheep, Hu sheep, and Tan-Hu F2 generation (6 sheep per population) were collected. After genomic DNA extraction, whole-genome bisulfite sequencing (WGBS) and bioinformatics analysis were performed to construct genome-wide DNA methylome maps for the Tan sheep, Hu sheep and their Tan-Hu F2 generation.

Results: Distinct genome-wide DNA methylation patterns were observed between Tan sheep and Hu sheep. Moreover, DNA methylated regions were significantly increased in the skeletal muscle from Tan sheep vs. the F2 generation compared to the Hu sheep vs. F2 generation and the Tan sheep vs. Hu sheep. Compared with Hu sheep, the methylation levels of actin alpha 1 (ACTA1), myosin heavy chain 11 (MYH11), Wiskott-Aldrich syndrome protein (WAS), vav guanine nucleotide exchange factor 1 (VAV1), fibronectin 1 (FN1) and Rho-associated protein kinase 2 (ROCK2) genes were markedly distinct in the Tan sheep. Furthermore, Gene Ontology analysis indicated that these genes were involved in myotube differentiation, myotube cell development, smooth muscle cell differentiation and striated muscle cell differentiation.

Conclusion: The findings from this study, in addition to data from previous research, demonstrated that the ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 genes may exert regulatory effects on muscle development.

Keywords: DNA methylation; epigenetics; muscle development; sheep; whole-genome bisulfite sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Methylation patterns in the different sheep breeds. DNA methylation levels in the gene body regions and their 2 kb upstream and downstream regions in the genome (A,C,E) and DNA methylation levels in the transposable element body regions and their upstream and downstream regions in the genome (B,D,F). Each dot represents the mean methylation level per bin and the corresponding lines indicate the 5-bin moving average. H is defined as A, T, or C. TE: transposable element.
Figure 2
Figure 2
Methylation levels in the different repeat regions. LTR, long-terminal repeat; LINE, long interspersed nuclear element; SINE, short interspersed nuclear element; DNA, DNA repeat.
Figure 3
Figure 3
Differences in DNA methylation patterns among Tan sheep, Hu sheep and their offspring. (A) Density plot of different 5 mC peaks in each sequence context (CG, CHG, or CHH) among the three comparisons undertaken. H denotes A, T, or C; TE represents transposable element; the outermost rim indicates the chromosome number and scale. (B) Total number of DMRs among the three comparisons. (C) Unique or shared DMGs among the three comparisons.
Figure 4
Figure 4
Q-values of different GO terms enriched in DMGs.
Figure 5
Figure 5
Gene numbers and q-values of different KEGG pathways enriched among the three comparisons. Rich factor is the ratio of DMGs in the pathway and the total number of genes in the pathway. The smaller the value of rich factor, the lower the degree of KEGG enrichment.
Figure 6
Figure 6
Interactive network of DMGs involved in the developing skeletal muscle.
See this image and copyright information in PMC

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