Oncotarget

Research Papers:

Reduced representation bisulfite sequencing (RRBS) of dairy goat mammary glands reveals DNA methylation profiles of integrated genome-wide and critical milk-related genes

Xiaoyan Zhang, Sihuan Zhang, Lin Ma, Enhui Jiang, Han Xu, Rui Chen, Qing Yang, Hong Chen, Zhuanjian Li and Xianyong Lan _

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Oncotarget. 2017; 8:115326-115344. https://doi.org/10.18632/oncotarget.23260

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Abstract

Xiaoyan Zhang1,*, Sihuan Zhang1,*, Lin Ma1, Enhui Jiang1, Han Xu1, Rui Chen1, Qing Yang1, Hong Chen1, Zhuanjian Li2 and Xianyong Lan1

1College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China

2College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China

*These authors have contributed equally to this work

Correspondence to:

Xianyong Lan, email: lanxianyong79@nwsuaf.edu.cn

Zhuanjian Li, email: lizhuanjian@163.com

Keywords: dairy goat; mammary gland; DNA methylation; reduced representation bisulfite sequencing (RRBS); milk-related genes

Received: April 26, 2017    Accepted: December 05, 2017    Published: December 15, 2017

ABSTRACT

DNA methylation (DNAm), a major element of epigenetics, plays critical roles in individual development. Reduced representation bisulfite sequencing (RRBS) is an effective and economical method for analyzing the DNA methylation of a single base. The aims of this study were to determine the DNAm profiles of the methylation contexts (CGs and non-CGs) of lactation and dry periods of goat mammary glands using the RRBS, and to identify potential milk-related genes. The proportion of CG was the highest among all the sequence contexts. The highest CG levels (72.44% to 75.24%) occurred in the 3′ UTR region, followed by the gene body region (61.14% to 65.45%). The non-CG levels were low compared to the CG levels. Bioinformatic analysis demonstrated that the CGs were mainly enriched at high methylation levels (>90%), while non-CGs were enriched at low methylation levels. Methylation levels of 95 and 54 genes in the lactation period were up- or downregulated, respectively, relative to the dry period, such as PPARα, RXRα and NPY genes. The bisulfite sequencing PCR results showed that the methylation level of goat PPARα gene during the lactation period was significant lower than in the dry period, while the methylation level of the RXRα gene was lower in the dry period than in the lactation period. Meanwhile, the methylation levels of human PPARα and NPY genes were significantly higher in MCF-7 than in MCF-10A cells. These findings provide essential information for DNA methylation profiles of goat mammary gland and detect some potential milk-related genes in dairy goats.


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