中国滩羊不同生长阶段基因组甲基化图谱的动态变化
Dynamic changes of genomic methylation profiles at different growth stages in Chinese Tan sheep.
作者信息
Liu Yufang, Xu Qiao, Kang Xiaolong, Wang Kejun, Wang Jve, Feng Dengzhen, Bai Ying, Fang Meiying
机构信息
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056021, People's Republic of China.
出版信息
J Anim Sci Biotechnol. 2021 Nov 2;12(1):118. doi: 10.1186/s40104-021-00632-9.
BACKGROUND
Tan sheep, an important local sheep breed in China, is famous for their fur quality. One-month-old Tan sheep have white, curly hair with beautiful flower spikes, commonly known as "nine bends", which has high economic value. However, the "nine bends" characteristic gradually disappears with age; consequently, the economic value of the Tan sheep decreases. Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression. Until now, no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages. In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing, and compared the DNA methylation levels at three different growth stages: 1, 24, and 48 months old (mon1, mon24, and mon48, respectively).
RESULTS
In this study, 11 skin samples from three growth stages (four for mon1, four for mon24, and three for mon48) were used for DNA methylation analysis and gene expression profiling. There were 52, 288 and 236 differentially methylated genes (DMGs) identified between mon1 and mon24, mon1 and mon48, and mon24 and mon48, respectively. Of the differentially methylated regions, 1.11%, 7.61%, and 7.65% were in the promoter in mon1 vs. mon24, mon24 vs. mon48, and mon1 vs. mon48, respectively. DMGs were enriched in the MAPK and WNT signaling pathways, which are related to age growth and hair follicle morphogenesis processes. There were 51 DMGs associated with age growth and curly fleece formation. Four DMGs between mon1 and mon48 (KRT71, CD44, ROR2 and ZDHHC13) were further validated by bisulfite sequencing.
CONCLUSIONS
This study revealed dynamic changes in the genomic methylation profiles of mon1, mon24, and mon48 sheep, and the percentages of methylated cytosines were 3.38%, 2.85% and 4.17%, respectively. Of the DMGs, KRT71 and CD44 were highly methylated in mon1, and ROR2 and ZDHHC13 were highly methylated in mon48. These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.
背景
滩羊是中国重要的地方绵羊品种，以其毛皮品质而闻名。1月龄的滩羊有白色卷曲的毛发，带有美丽的花穗，俗称“九道弯”，具有很高的经济价值。然而，“九道弯”特征会随着年龄增长逐渐消失，因此滩羊的经济价值会降低。据报道，DNA甲基化与年龄相关的变化有关，可能是导致基因表达随年龄变化的原因。到目前为止，尚未进行全基因组调查来确定参与绵羊不同生长阶段的潜在DNA甲基化位点。在本研究中，我们使用皮肤DNA和全基因组亚硫酸氢盐测序，研究了滩羊全基因组DNA甲基化图谱的动态变化，并比较了三个不同生长阶段（分别为1、24和48月龄，即mon1、mon24和mon48）的DNA甲基化水平。
结果
在本研究中，来自三个生长阶段的11个皮肤样本（mon1有4个，mon24有4个，mon48有3个）用于DNA甲基化分析和基因表达谱分析。在mon1和mon24、mon1和mon48、mon24和mon48之间分别鉴定出52个、288个和236个差异甲基化基因（DMG）。在差异甲基化区域中，mon1与mon24、mon24与mon48、mon1与mon48相比，分别有1.11%、7.61%和7.65%位于启动子区域。DMG在与年龄增长和毛囊形态发生过程相关的MAPK和WNT信号通路中富集。有51个DMG与年龄增长和卷曲羊毛形成有关。通过亚硫酸氢盐测序进一步验证了mon1和mon48之间的4个DMG（KRT71、CD44、ROR2和ZDHHC13）。
结论
本研究揭示了mon1、mon24和mon48绵羊基因组甲基化图谱的动态变化，甲基化胞嘧啶的百分比分别为3.38%、2.85%和4.17%。在DMG中，KRT71和CD44在mon1中高度甲基化，ROR2和ZDHHC13在mon48中高度甲基化。这些发现提供了基础信息，可用于制定潜在保留羔羊毛皮从而提高滩羊经济价值的策略。
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