DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation

Yanghua He; Qisheng Zuo; John Edwards; Keji Zhao; Jinzhi Lei; Wentao Cai; Qing Nie; Bichun Li; Jiuzhou Song

doi:10.1016/j.stemcr.2018.03.018

DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation

Stem Cell Reports. 2018 Jun 5;10(6):1793-1806. doi: 10.1016/j.stemcr.2018.03.018. Epub 2018 Apr 19.

Authors

Yanghua He¹, Qisheng Zuo², John Edwards³, Keji Zhao⁴, Jinzhi Lei⁵, Wentao Cai⁶, Qing Nie⁷, Bichun Li⁸, Jiuzhou Song⁹

Affiliations

¹ Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA.
² College of Animal Science and Technology, Yangzhou University, Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, Yangzhou 225009, People's Republic of China.
³ Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8220, St. Louis, MO 63110, USA.
⁴ Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
⁵ Zhou Peiyuan Center for Applied Mathematics, Tsinghua University, Beijing, 100084, People's Republic of China.
⁶ Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA; Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
⁷ Department of Mathematics, University of California, Irvine, CA 92697-3875, USA.
⁸ College of Animal Science and Technology, Yangzhou University, Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, Yangzhou 225009, People's Republic of China. Electronic address: yubcli@yzu.edu.cn.
⁹ Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA. Electronic address: songj88@umd.edu.

Abstract

The production of germ cells in vitro would open important new avenues for stem biology and human medicine, but the mechanisms of germ cell differentiation are not well understood. The chicken, as a great model for embryology and development, was used in this study to help us explore its regulatory mechanisms. In this study, we reported a comprehensive genome-wide DNA methylation landscape in chicken germ cells, and transcriptomic dynamics was also presented. By uncovering DNA methylation patterns on individual genes, some genes accurately modulated by DNA methylation were found to be associated with cancers and virus infection, e.g., AKT1 and CTNNB1. Chicken-unique markers were also discovered for identifying male germ cells. Importantly, integrated epigenetic mechanisms were explored during male germ cell differentiation, which provides deep insight into the epigenetic processes associated with male germ cell differentiation and possibly improves treatment options to male infertility in animals and humans.

Keywords: DNA methylation; ESCs; PGCs; SSCs; chicken; epigenetics; gene expression; germline stem cell differentiation; non-coding RNAs; transcription factor motifs.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Binding Sites
Biomarkers
Bone Morphogenetic Proteins / metabolism
Cell Differentiation / genetics*
Chickens
DNA Methylation*
Epigenesis, Genetic
Epigenomics / methods
Gene Expression Regulation, Developmental
Germ Cells / cytology*
Germ Cells / metabolism*
Models, Biological
Nucleotide Motifs
Protein Binding
RNA, Long Noncoding
Regulatory Sequences, Nucleic Acid*
Signal Transduction
Transforming Growth Factor beta / metabolism

Substances

Biomarkers
Bone Morphogenetic Proteins
RNA, Long Noncoding
Transforming Growth Factor beta

Grants and funding

R01 GM108811/GM/NIGMS NIH HHS/United States