Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells

Zhang, Xiao-Li; Wu, Jun; Wang, Jian; Shen, Tingting; Li, Hua; Lu, Jun; Gu, Yunzhao; Kang, Yani; Wong, Chee-Hong; Ngan, Chew Yee; Shao, Zhifeng; Wu, Ji; Zhao, Xiaodong

doi:10.1186/s13059-016-1023-z

Title: Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells

Journal Article · Wed Jul 27 00:00:00 EDT 2016 · Genome Biology (Online)

DOI:https://doi.org/10.1186/s13059-016-1023-z· OSTI ID:1626936

Zhang, Xiao-Li ^[1]; Wu, Jun ^[1]; Wang, Jian ^[2]; Shen, Tingting ^[1]; Li, Hua ^[1]; Lu, Jun ^[1]; Gu, Yunzhao ^[1]; Kang, Yani ^[1]; Wong, Chee-Hong ^[3]; Ngan, Chew Yee ^[3]; Shao, Zhifeng ^[1]; Wu, Ji ^[4]; Zhao, Xiaodong ^[1]

Shanghai Jiao Tong Univ. (China). Shanghai Center for Systems Biomedicine. School of Biomedical Engineering. Bio-ID Center
Shanghai Jiao Tong Univ. (China). Bio-X Inst.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Shanghai Jiao Tong Univ. (China). Bio-X Inst.; Ningxia Medical Univ., Yinchuan (China). Key Lab. of Fertility Preservation and Maintenance of Ministry of Education

Background: Germline stem cells play an essential role in establishing the fertility of an organism. Although extensively characterized, the regulatory mechanisms that govern the fundamental properties of mammalian female germline stem cells remain poorly understood. Results: We generate genome-wide profiles of the histone modifications H3K4me1, H3K27ac, H3K4me3, and H3K27me3, DNA methylation, and RNA polymerase II occupancy and perform transcriptome analysis in mouse female germline stem cells. Comparison of enhancer regions between embryonic stem cells and female germline stem cells identifies the lineage-specific enhancers involved in germline stem cell features. Additionally, our results indicate that DNA methylation primarily contributes to female germline stem cell unipotency by suppressing the somatic program and is potentially involved in maintenance of sexual identity when compared with male germline stem cells. Moreover, we demonstrate down-regulation of Prmt5 triggers differentiation and thus uncover a role for Prmt5 in maintaining the undifferentiated status of female germline stem cells. Conclusions: The genome-wide epigenetic signatures and the transcription regulators identified here provide an invaluable resource for understanding the fundamental features of mouse female germline stem cells.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Development Program for Basic Research of China; Longhua Hospital; National Natural Science Foundation of China (NSFC)

Grant/Contract Number:: AC02-05CH11231; 2013CB967402; LYTD-21; JDZX2012123; 91229123; 91019004

OSTI ID:: 1626936

Journal Information:: Genome Biology (Online), Vol. 17, Issue 1; ISSN 1474-760X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biotechnology & Applied Microbiology
Genetics & Heredity
Female germline stem cell
Epigenome
ChIP-Seq

Additional file 4: Table S4. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d1.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 5: Table S5. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/M9.FIGSHARE.C.3623297_D4 The current record is supplemented by this dataset	dataset	January 2016
Additional file 2: Table S2. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/M9.FIGSHARE.C.3623297_D5 The current record is supplemented by this dataset	dataset	January 2016
Additional file 6: Table S6. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/M9.FIGSHARE.C.3623297_D6 The current record is supplemented by this dataset	dataset	January 2016
Additional file 4: Table S4. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/M9.FIGSHARE.C.3623297_D1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 5: Table S5. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d4.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 2: Table S2. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d5.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 3: Table S3. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d3.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 1: of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d2 The current record is supplemented by this text	text	January 2016
Additional file 3: Table S3. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d3 The current record is supplemented by this dataset	dataset	January 2016
Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297 The current record is supplemented by this collection	collection	January 2016
Additional file 6: Table S6. of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d6.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 1: of Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297_d2.v1 The current record is supplemented by this text	text	January 2016
Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells Zhang, Xiao-Li; Wu, Jun; Wang, Jian https://doi.org/10.6084/m9.figshare.c.3623297.v1 The current record is supplemented by this collection	collection	January 2016