Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGP

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RESEARCH ARTICLE

Open Access

Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production Jinwei Xin1,2†, Zhixin Chai3†, Chengfu Zhang1,2†, Qiang Zhang1,2, Yong Zhu1,2, Hanwen Cao1,2, Cidan Yangji1,2, Xiaoying Chen1,2, Hui Jiang1,2, Jincheng Zhong3* and Qiumei Ji1,2*

Abstract Background: Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiological adaptations to high-altitude environment, including strong blood oxygen transportation capabilities and high metabolism. The roles of DNA methylation and gene expression in milk production and high-altitudes adaptation need further exploration. Results: We performed genome-wide DNA methylome and transcriptome analyses of breast, lung, and biceps brachii muscle tissues from yaks of different ages. We identified 432,350 differentially methylated regions (DMRs) across the age groups within each tissue. The post-mature breast tissue had considerably more differentially methylated regions (155,957) than that from the three younger age groups. Hypomethylated genes with high expression levels might regulate milk production by influencing protein processing in the endoplasmic reticulum. According to weighted gene correlation network analysis, the “hub” gene ZGPAT was highly expressed in the postmature breast tissue, indicating that it potentially regulates the transcription of 280 genes that influence protein synthesis, processing, and secretion. The tissue network analysis indicated that high expression of HIF1A regulates energy metabolism in the lung. Conclusions: This study provides a basis for understanding the epigenetic mechanisms underlying milk production in yaks, and the results offer insight to breeding programs aimed at improving milk production. Keywords: Milk production, DNA methylation, Transcription factor, Epigenetic regulation

* Correspondence: [email protected]; [email protected] † Jinwei Xin, Zhixin Chai and Chengfu Zhang contributed equally to this work. 3 Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China 1 State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence,