Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
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. We generate genome-wide profiles of the hist...
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| Veröffentlicht in: | Genome Biology 2016-07, Vol.17 (1), p.162-162, Article 162 |
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| creator | 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 |
| description | 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.
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.
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. |
| doi_str_mv | 10.1186/s13059-016-1023-z |
| format | Article |
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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.
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.</description><identifier>ISSN: 1474-760X</identifier><identifier>ISSN: 1474-7596</identifier><identifier>EISSN: 1474-760X</identifier><identifier>DOI: 10.1186/s13059-016-1023-z</identifier><identifier>PMID: 27465593</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Adult Germline Stem Cells - metabolism ; Animals ; BASIC BIOLOGICAL SCIENCES ; Biotechnology & Applied Microbiology ; Cell Lineage - genetics ; ChIP-Seq ; Chromatin - genetics ; Chromatin - metabolism ; Deoxyribonucleic acid ; DNA ; DNA methylation ; DNA Methylation - genetics ; DNA-directed RNA polymerase ; Embryo cells ; Embryonic stem cells ; Enhancers ; Epigenetic inheritance ; Epigenetics ; Epigenome ; Epigenomics ; Female ; Female germline stem cell ; females ; Fertility ; Fertility - genetics ; Gene expression ; Genetic aspects ; Genetics & Heredity ; Genome ; Genomes ; Genomics ; germ cells ; histones ; Histones - genetics ; Histones - metabolism ; Male ; males ; Mice ; Mouse Embryonic Stem Cells ; Oogonial Stem Cells - metabolism ; Physiological aspects ; RNA polymerase ; Stem cell transplantation ; Stem cells ; Transcription ; transcription factors ; Transcriptome - genetics ; transcriptomics</subject><ispartof>Genome Biology, 2016-07, Vol.17 (1), p.162-162, Article 162</ispartof><rights>COPYRIGHT 2016 BioMed Central Ltd.</rights><rights>2016. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s). 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c622t-3ea7679027a2bd071115b44545d12463be88554339e9bff618868c402e732d833</citedby><cites>FETCH-LOGICAL-c622t-3ea7679027a2bd071115b44545d12463be88554339e9bff618868c402e732d833</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4963954/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4963954/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27465593$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1626936$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Xiao-Li</creatorcontrib><creatorcontrib>Wu, Jun</creatorcontrib><creatorcontrib>Wang, Jian</creatorcontrib><creatorcontrib>Shen, Tingting</creatorcontrib><creatorcontrib>Li, Hua</creatorcontrib><creatorcontrib>Lu, Jun</creatorcontrib><creatorcontrib>Gu, Yunzhao</creatorcontrib><creatorcontrib>Kang, Yani</creatorcontrib><creatorcontrib>Wong, Chee-Hong</creatorcontrib><creatorcontrib>Ngan, Chew Yee</creatorcontrib><creatorcontrib>Shao, Zhifeng</creatorcontrib><creatorcontrib>Wu, Ji</creatorcontrib><creatorcontrib>Zhao, Xiaodong</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><title>Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells</title><title>Genome Biology</title><addtitle>Genome Biol</addtitle><description>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.
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.
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.</description><subject>Adult Germline Stem Cells - metabolism</subject><subject>Animals</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Biotechnology & Applied Microbiology</subject><subject>Cell Lineage - genetics</subject><subject>ChIP-Seq</subject><subject>Chromatin - genetics</subject><subject>Chromatin - metabolism</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA methylation</subject><subject>DNA Methylation - genetics</subject><subject>DNA-directed RNA polymerase</subject><subject>Embryo cells</subject><subject>Embryonic stem cells</subject><subject>Enhancers</subject><subject>Epigenetic inheritance</subject><subject>Epigenetics</subject><subject>Epigenome</subject><subject>Epigenomics</subject><subject>Female</subject><subject>Female germline stem cell</subject><subject>females</subject><subject>Fertility</subject><subject>Fertility - genetics</subject><subject>Gene expression</subject><subject>Genetic aspects</subject><subject>Genetics & Heredity</subject><subject>Genome</subject><subject>Genomes</subject><subject>Genomics</subject><subject>germ cells</subject><subject>histones</subject><subject>Histones - genetics</subject><subject>Histones - metabolism</subject><subject>Male</subject><subject>males</subject><subject>Mice</subject><subject>Mouse Embryonic Stem Cells</subject><subject>Oogonial Stem Cells - metabolism</subject><subject>Physiological aspects</subject><subject>RNA polymerase</subject><subject>Stem cell transplantation</subject><subject>Stem cells</subject><subject>Transcription</subject><subject>transcription factors</subject><subject>Transcriptome - genetics</subject><subject>transcriptomics</subject><issn>1474-760X</issn><issn>1474-7596</issn><issn>1474-760X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>KPI</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkktv1DAUhSMEomXgB7BBFmxgkeJXbGdTqap4jKgEC5DYWR7nJnWV2IPtjJhu-Os4mrZq2SAvbNnfPdY991TVS4JPCFHifSIMN22NiagJpqy-flQdEy55LQX--fje-ah6ltIVxqTlVDytjqjkomladlz9WfsMQzTZ7QDB1g3gw-QsMt6M--QSirADMyY0e_drvkUgFyS5wZs8R0jI-V0Yd9CVwwJuQwZv9yj0aApzAtTDZEZAA8RpdB5QyjAhC-OYnldP-iIPL272VfXj44fv55_ri6-f1udnF7UVlOaagZFCtphKQzcdloSQZsN5w5uOUC7YBpRqGs5YC-2m7wVRSijLMQXJaKcYW1WnB93tvJmgs-BzNKPeRjeZuNfBOP3wxbtLPYSd5q1gbVFeVa8PAiFlp5N1GeylDd6DzZoIKlomCvT25pcYilsp68mlpU_joRihKcaY4TIV9V-UKCyVLHNa0Df_oFdhjmVARZBiRVkj2NLhyYEaitXa-T6UPmxZHZSBBg-9K_dnRVC1RJKl4N2DgsJk-J0HM6ekv3xbP2TJgbUxpBShv3OOYL1kUR-yqEsW9ZJFfV1qXt23_K7iNnzsL2lT2rs</recordid><startdate>20160727</startdate><enddate>20160727</enddate><creator>Zhang, Xiao-Li</creator><creator>Wu, Jun</creator><creator>Wang, Jian</creator><creator>Shen, Tingting</creator><creator>Li, Hua</creator><creator>Lu, Jun</creator><creator>Gu, Yunzhao</creator><creator>Kang, Yani</creator><creator>Wong, Chee-Hong</creator><creator>Ngan, Chew Yee</creator><creator>Shao, Zhifeng</creator><creator>Wu, Ji</creator><creator>Zhao, Xiaodong</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>KPI</scope><scope>IAO</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>OIOZB</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20160727</creationdate><title>Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells</title><author>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</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c622t-3ea7679027a2bd071115b44545d12463be88554339e9bff618868c402e732d833</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Adult Germline Stem Cells - metabolism</topic><topic>Animals</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Biotechnology & Applied Microbiology</topic><topic>Cell Lineage - genetics</topic><topic>ChIP-Seq</topic><topic>Chromatin - genetics</topic><topic>Chromatin - metabolism</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA methylation</topic><topic>DNA Methylation - genetics</topic><topic>DNA-directed RNA polymerase</topic><topic>Embryo cells</topic><topic>Embryonic stem cells</topic><topic>Enhancers</topic><topic>Epigenetic inheritance</topic><topic>Epigenetics</topic><topic>Epigenome</topic><topic>Epigenomics</topic><topic>Female</topic><topic>Female germline stem cell</topic><topic>females</topic><topic>Fertility</topic><topic>Fertility - genetics</topic><topic>Gene expression</topic><topic>Genetic aspects</topic><topic>Genetics & Heredity</topic><topic>Genome</topic><topic>Genomes</topic><topic>Genomics</topic><topic>germ cells</topic><topic>histones</topic><topic>Histones - genetics</topic><topic>Histones - metabolism</topic><topic>Male</topic><topic>males</topic><topic>Mice</topic><topic>Mouse Embryonic Stem Cells</topic><topic>Oogonial Stem Cells - metabolism</topic><topic>Physiological aspects</topic><topic>RNA polymerase</topic><topic>Stem cell transplantation</topic><topic>Stem cells</topic><topic>Transcription</topic><topic>transcription factors</topic><topic>Transcriptome - genetics</topic><topic>transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Xiao-Li</creatorcontrib><creatorcontrib>Wu, Jun</creatorcontrib><creatorcontrib>Wang, Jian</creatorcontrib><creatorcontrib>Shen, Tingting</creatorcontrib><creatorcontrib>Li, Hua</creatorcontrib><creatorcontrib>Lu, Jun</creatorcontrib><creatorcontrib>Gu, Yunzhao</creatorcontrib><creatorcontrib>Kang, Yani</creatorcontrib><creatorcontrib>Wong, Chee-Hong</creatorcontrib><creatorcontrib>Ngan, Chew Yee</creatorcontrib><creatorcontrib>Shao, Zhifeng</creatorcontrib><creatorcontrib>Wu, Ji</creatorcontrib><creatorcontrib>Zhao, Xiaodong</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Global Issues</collection><collection>Gale Academic OneFile</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome Biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Xiao-Li</au><au>Wu, Jun</au><au>Wang, Jian</au><au>Shen, Tingting</au><au>Li, Hua</au><au>Lu, Jun</au><au>Gu, Yunzhao</au><au>Kang, Yani</au><au>Wong, Chee-Hong</au><au>Ngan, Chew Yee</au><au>Shao, Zhifeng</au><au>Wu, Ji</au><au>Zhao, Xiaodong</au><aucorp>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells</atitle><jtitle>Genome Biology</jtitle><addtitle>Genome Biol</addtitle><date>2016-07-27</date><risdate>2016</risdate><volume>17</volume><issue>1</issue><spage>162</spage><epage>162</epage><pages>162-162</pages><artnum>162</artnum><issn>1474-760X</issn><issn>1474-7596</issn><eissn>1474-760X</eissn><abstract>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.
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.
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.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>27465593</pmid><doi>10.1186/s13059-016-1023-z</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Springer Nature - Complete Springer Journals; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Springer Nature OA Free Journals |
| subjects | Adult Germline Stem Cells - metabolism Animals BASIC BIOLOGICAL SCIENCES Biotechnology & Applied Microbiology Cell Lineage - genetics ChIP-Seq Chromatin - genetics Chromatin - metabolism Deoxyribonucleic acid DNA DNA methylation DNA Methylation - genetics DNA-directed RNA polymerase Embryo cells Embryonic stem cells Enhancers Epigenetic inheritance Epigenetics Epigenome Epigenomics Female Female germline stem cell females Fertility Fertility - genetics Gene expression Genetic aspects Genetics & Heredity Genome Genomes Genomics germ cells histones Histones - genetics Histones - metabolism Male males Mice Mouse Embryonic Stem Cells Oogonial Stem Cells - metabolism Physiological aspects RNA polymerase Stem cell transplantation Stem cells Transcription transcription factors Transcriptome - genetics transcriptomics |
| title | Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells |
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