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DNA Res. 2019 Apr 1;26(2):105-117. doi: 10.1093/dnares/dsy042.

Molecular characteristics of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome-wide DNA methylation.

Ma B1, Lee TL2, Hu B3,4, Li J5, Li X1, Zhao X6, Hou C1, Zhang C1, He L1, Huang X3,4, Chen X7, Li J5, Wu J1,8.

Author information

1
Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.
2
Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
3
MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.
4
School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
5
Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
6
Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
7
Department of Laboratory Animal Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
8
Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China.

Abstract

High-throughput stage-specific transcriptomics provides an unbiased approach for understanding the process of cell development. Here, we report transcriptome analysis of primordial germ cell, female germline stem cell (FGSC), germinal vesicle and mature oocyte by performing RNA sequencing of freshly isolated cells in mice. As expected, these stages and gene-expression profiles are consistent with developmental timing. Analysis of genome-wide DNA methylation during female germline development was used for confirmation. By pathway analysis and blocking experiments, we demonstrate PI3K-AKT pathway is critical for FGSC maintenance. We also identify functional modules with hub genes and lncRNAs, which represent candidates for regulating FGSC self-renewal and differentiation. Remarkably, we note alternative splicing patterns change dramatically during female germline development, with the highest occurring in FGSCs. These findings are invaluable resource for dissecting the molecular pathways and processes into oogenesis and will be wider applications for other types of stem cell research.

KEYWORDS:

DNA methylation; RNA sequencing; development; female germ cells; transcriptomics

PMID:
30590473
PMCID:
PMC6476728
DOI:
10.1093/dnares/dsy042
[Indexed for MEDLINE]
Free PMC Article

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