151
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Gao L, Wu K, Liu Z, Yao X, Yuan S, Tao W, Yi L, Yu G, Hou Z, Fan D, Tian Y, Liu J, Chen ZJ, Liu J. Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. Cell 2018. [PMID: 29526463 DOI: 10.1016/j.cell.2018.02.028] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamics of the chromatin regulatory landscape during human early embryogenesis remains unknown. Using DNase I hypersensitive site (DHS) sequencing, we report that the chromatin accessibility landscape is gradually established during human early embryogenesis. Interestingly, the DHSs with OCT4 binding motifs are enriched at the timing of zygotic genome activation (ZGA) in humans, but not in mice. Consistently, OCT4 contributes to ZGA in humans, but not in mice. We further find that lower CpG promoters usually establish DHSs at later stages. Similarly, younger genes tend to establish promoter DHSs and are expressed at later embryonic stages, while older genes exhibit these features at earlier stages. Moreover, our data show that human active transposons SVA and HERV-K harbor DHSs and are highly expressed in early embryos, but not in differentiated tissues. In summary, our data provide an evolutionary developmental view for understanding the regulation of gene and transposon expression.
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Affiliation(s)
- Lei Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenbo Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xuelong Yao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shenli Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Lizhi Yi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Guanling Yu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Dongdong Fan
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yong Tian
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jianqiao Liu
- Center for Reproductive Medicine, Third Affiliated Hospital, Guangzhou Medical University, 510150 Guangzhou, China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China.
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, 100049 Beijing, China.
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152
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Meng Y, Moore R, Tao W, Smith ER, Tse JD, Caslini C, Xu XX. GATA6 phosphorylation by Erk1/2 propels exit from pluripotency and commitment to primitive endoderm. Dev Biol 2018; 436:55-65. [PMID: 29454706 PMCID: PMC5912698 DOI: 10.1016/j.ydbio.2018.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 02/07/2023]
Abstract
The transcription factor GATA6 and the Fgf/Ras/MAPK signaling pathway are essential for the development of the primitive endoderm (PrE), one of the two lineages derived from the pluripotent inner cell mass (ICM) of mammalian blastocysts. A mutant mouse line in which Gata6-coding exons are replaced with H2BGFP (histone H2B Green Fluorescence Protein fusion protein) was developed to monitor Gata6 promoter activity. In the Gata6-H2BGFP heterozygous blastocysts, the ICM cells that initially had uniform GFP fluorescence signal at E3.5 diverged into two populations by the 64-cell stage, either as the GFP-high PrE or the GFP-low epiblasts (Epi). However in the GATA6-null blastocysts, the originally moderate GFP expression subsided in all ICM cells, indicating that the GATA6 protein is required to maintain its own promoter activity during PrE linage commitment. In embryonic stem cells, expressed GATA6 was shown to bind and activate the Gata6 promoter in PrE differentiation. Mutations of a conserved serine residue (S264) for Erk1/2 phosphorylation in GATA6 protein drastically impacted its ability to activate its own promoter. We conclude that phosphorylation of GATA6 by Erk1/2 compels exit from pluripotent state, and the phosphorylation propels a GATA6 positive feedback regulatory circuit to compel PrE differentiation. Our findings resolve the longstanding question on the dual requirements of GATA6 and Ras/MAPK pathway for PrE commitment of the pluripotent ICM.
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Affiliation(s)
- Yue Meng
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Graduate Program in Molecular Cell and Developmental Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Robert Moore
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Wensi Tao
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Graduate Program in Molecular Cell and Developmental Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Elizabeth R Smith
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jeffrey D Tse
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Graduate Program in Molecular Cell and Developmental Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Corrado Caslini
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xiang-Xi Xu
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Graduate Program in Molecular Cell and Developmental Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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153
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Wang Z, Shen M, Xue P, DiVall SA, Segars J, Wu S. Female Offspring From Chronic Hyperandrogenemic Dams Exhibit Delayed Puberty and Impaired Ovarian Reserve. Endocrinology 2018; 159:1242-1252. [PMID: 29315373 PMCID: PMC5793796 DOI: 10.1210/en.2017-03078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/28/2017] [Indexed: 11/19/2022]
Abstract
Female offspring of many species exposed to high doses of androgens in utero experience endocrine dysfunction during adulthood. The phenotype of offspring from females with prepregnancy hyperandrogenemia and impaired ovulation, however, has not been examined. We developed a mouse model of hyperandrogenemia by implanting a low-dose dihydrotestosterone (DHT) pellet 15 days before conception. Female offspring born to dams with hyperandrogenemia (DHT daughters) had delayed puberty (P < 0.05) with first estrus on postnatal day (PND) 41 compared with daughters from dams with physiological levels of DHT (non-DHT daughters, PND37.5). Serum follicle-stimulating hormone (FSH) levels in the DHT daughters were fourfold higher (P < 0.05) on PND21, and anti-Müllerian hormone levels were higher (P < 0.05) on PND26 than in non-DHT daughters (controls). DHT daughters showed an extended time in metestrus/diestrus and a shorter time in the proestrus/estrus phase compared with non-DHT daughters (P < 0.05). To examine ovarian response to gonadotropins, superovulation was induced and in vitro fertilization (IVF) was performed. Fewer numbers of oocytes were retrieved from the DHT daughters compared with non-DHT daughters (P < 0.05). At IVF, there was no difference in rates of fertilization or cleavage of oocytes from either group. There were fewer (P < 0.01) primordial follicles (6.5 ± 0.8 vs 14.5 ± 2.1 per ovary) in the ovaries of DHT daughters compared with non-DHT daughters. Daughters from hyperandrogenemic females exhibited elevated prepubertal FSH levels, diminished ovarian response to superovulation, impaired estrous cyclicity, delayed onset of puberty, and reduced ovarian reserve, suggesting that fetal androgen exposure had lasting effects on female reproductive function.
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Affiliation(s)
- Zhiqiang Wang
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Mingjie Shen
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
- Department of Gynecology/Obstetrics, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 21203, People’s Republic of China
| | - Ping Xue
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Sara A. DiVall
- Department of Pediatrics, Seattle Children’s Hospital, Seattle, Washington 98105
| | - James Segars
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Sheng Wu
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
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154
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Rahmati M, Pennisi CP, Mobasheri A, Mozafari M. Bioengineered Scaffolds for Stem Cell Applications in Tissue Engineering and Regenerative Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1107:73-89. [DOI: 10.1007/5584_2018_215] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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155
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Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell 2017; 22:50-63.e6. [PMID: 29249463 DOI: 10.1016/j.stem.2017.11.004] [Citation(s) in RCA: 501] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/20/2017] [Accepted: 11/02/2017] [Indexed: 11/25/2022]
Abstract
Trophoblast cells play an essential role in the interactions between the fetus and mother. Mouse trophoblast stem (TS) cells have been derived and used as the best in vitro model for molecular and functional analysis of mouse trophoblast lineages, but attempts to derive human TS cells have so far been unsuccessful. Here we show that activation of Wingless/Integrated (Wnt) and EGF and inhibition of TGF-β, histone deacetylase (HDAC), and Rho-associated protein kinase (ROCK) enable long-term culture of human villous cytotrophoblast (CT) cells. The resulting cell lines have the capacity to give rise to the three major trophoblast lineages, which show transcriptomes similar to those of the corresponding primary trophoblast cells. Importantly, equivalent cell lines can be derived from human blastocysts. Our data strongly suggest that the CT- and blastocyst-derived cell lines are human TS cells, which will provide a powerful tool to study human trophoblast development and function.
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Affiliation(s)
- Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Sato
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Sota Takahashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuka Kabayama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
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156
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Ramos-Ibeas P, Nichols J, Alberio R. States and Origins of Mammalian Embryonic Pluripotency In Vivo and in a Dish. Curr Top Dev Biol 2017; 128:151-179. [PMID: 29477162 DOI: 10.1016/bs.ctdb.2017.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mouse embryonic stem cells (ESC), derived from preimplantation embryos in 1981, defined mammalian pluripotency for many decades. However, after the derivation of human ESC in 1998, comparative studies showed that different types of pluripotency exist in early embryos and that these can be captured in vitro under various culture conditions. Over the past decade much has been learned about the key signaling pathways, growth factor requirements, and transcription factor profiles of pluripotent cells in embryos, allowing improvement of derivation and culture conditions for novel pluripotent stem cell types. More recently, studies using single-cell transcriptomics of embryos from different species provided an unprecedented level of resolution of cellular interactions and cell fate decisions that are informing new ways to understand the emergence of pluripotency in different organisms. These new approaches enhance knowledge of species differences during early embryogenesis and will be instrumental for improving methodologies for generating intra- and interspecies chimeric animals using pluripotent stem cells. Here, we discuss the recent developments in our understanding of early embryogenesis in different mammalian species.
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Affiliation(s)
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom; University of Cambridge, Cambridge, United Kingdom.
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom.
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157
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Rugg-Gunn PJ. Naive pluripotent stem cells as a model for studying human developmental epigenomics: opportunities and limitations. Epigenomics 2017; 9:1485-1488. [DOI: 10.2217/epi-2017-0115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Babraham, Cambridge, CB22 3AT, UK
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158
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Xie L, Torigoe SE, Xiao J, Mai DH, Li L, Davis FP, Dong P, Marie-Nelly H, Grimm J, Lavis L, Darzacq X, Cattoglio C, Liu Z, Tjian R. A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency. Genes Dev 2017; 31:1795-1808. [PMID: 28982762 PMCID: PMC5666677 DOI: 10.1101/gad.303321.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/28/2017] [Indexed: 01/15/2023]
Abstract
Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order of events animating TF assembly at cis-regulatory elements in living cells and the long-range molecular "dialog" between enhancers and promoters. Here, combining genetic, genomic, and imaging approaches, we characterize a complex long-range enhancer cluster governing Krüppel-like factor 4 (Klf4) expression in naïve pluripotency. Genome editing by CRISPR/Cas9 revealed that OCT4 and SOX2 safeguard an accessible chromatin neighborhood to assist the binding of other TFs/cofactors to the enhancer. Single-molecule live-cell imaging uncovered that two naïve pluripotency TFs, STAT3 and ESRRB, interrogate chromatin in a highly dynamic manner, in which SOX2 promotes ESRRB target search and chromatin-binding dynamics through a direct protein-tethering mechanism. Together, our results support a highly dynamic yet intrinsically ordered enhanceosome assembly to maintain the finely balanced transcription program underlying naïve pluripotency.
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Affiliation(s)
- Liangqi Xie
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Sharon E Torigoe
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Jifang Xiao
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
| | - Daniel H Mai
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
| | - Li Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Fred P Davis
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Herve Marie-Nelly
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
| | - Jonathan Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Xavier Darzacq
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | | | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
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159
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Dou D, Zhao H, Li Z, Xu L, Xiong X, Wu X, Sun Y, Zeng S, Ouyang Q, Zhou D, Ma N, Lin G, Hu L. CHD1L Promotes Neuronal Differentiation in Human Embryonic Stem Cells by Upregulating PAX6. Stem Cells Dev 2017; 26:1626-1636. [PMID: 28946814 DOI: 10.1089/scd.2017.0110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromodomain helicase DNA-binding protein 1-like gene (CHD1L) was initially isolated as a candidate oncogene in hepatocellular carcinoma, and it has been associated with many malignancies. Knockdown of Chd1l in zygote-stage mouse embryos resulted in developmental arrest, suggesting that Chd1l is required for mouse early development. However, the exact role of CHD1L in development, especially in humans, has not been reported. In this study, we found that overexpression of CHD1L in human embryonic cells (hESCs) upregulated the expression of ectoderm genes, especially PAX6. Furthermore, ectopic expression of CHD1L promoted hESCs to differentiate into neuroepithelium both in embryoid bodies and in directed neuronal differentiation. Knockdown of CHD1L significantly impaired neuroepithelial differentiation of hESCs. Interestingly, Chd1l colocalized with a PAX6-positive cell population and was highly expressed in the ventricular (germinal) zone of fetal mice. Taken together, these data suggest that CHD1L promotes neuronal differentiation of hESCs and may play an important role in nervous system development.
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Affiliation(s)
- Dandan Dou
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China
| | - Hao Zhao
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China
| | - Zili Li
- 2 National Engineering and Research Center of Human Stem Cells , Changsha, China
| | - Liping Xu
- 3 Department of Histology and Embryology, School of Basic Sciences, Guangzhou Medical University , Guangzhou, China
| | - Xifeng Xiong
- 3 Department of Histology and Embryology, School of Basic Sciences, Guangzhou Medical University , Guangzhou, China
| | - Xingwu Wu
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China
| | - Yi Sun
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China .,2 National Engineering and Research Center of Human Stem Cells , Changsha, China .,4 Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health , Changsha, China .,5 Reproductive and Genetic Hospital of CITIC-Xiangya , Changsha, China
| | - Sicong Zeng
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China .,2 National Engineering and Research Center of Human Stem Cells , Changsha, China .,4 Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health , Changsha, China .,5 Reproductive and Genetic Hospital of CITIC-Xiangya , Changsha, China
| | - Qi Ouyang
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China .,2 National Engineering and Research Center of Human Stem Cells , Changsha, China .,4 Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health , Changsha, China
| | - Di Zhou
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China .,2 National Engineering and Research Center of Human Stem Cells , Changsha, China .,4 Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health , Changsha, China .,5 Reproductive and Genetic Hospital of CITIC-Xiangya , Changsha, China
| | - Ningfang Ma
- 3 Department of Histology and Embryology, School of Basic Sciences, Guangzhou Medical University , Guangzhou, China
| | - Ge Lin
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China .,2 National Engineering and Research Center of Human Stem Cells , Changsha, China .,4 Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health , Changsha, China .,5 Reproductive and Genetic Hospital of CITIC-Xiangya , Changsha, China
| | - Liang Hu
- 1 Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University , Changsha, China .,2 National Engineering and Research Center of Human Stem Cells , Changsha, China .,4 Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health , Changsha, China .,5 Reproductive and Genetic Hospital of CITIC-Xiangya , Changsha, China
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160
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Skeparnias I, Αnastasakis D, Shaukat AN, Grafanaki K, Stathopoulos C. Expanding the repertoire of deadenylases. RNA Biol 2017; 14:1320-1325. [PMID: 28267419 PMCID: PMC5711463 DOI: 10.1080/15476286.2017.1300222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/13/2017] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Deadenylases belong to an expanding family of exoribonucleases involved mainly in mRNA stability and turnover, with the exception of PARN which has additional roles in the biogenesis of several important non-coding RNAs, including miRNAs and piRNAs. Recently, PARN in C. elegans and its homolog PNLDC1 in B. mori were reported as the elusive trimmers mediating piRNA biogenesis. In addition, characterization of mammalian PNLDC1 in comparison to PARN, showed that is specifically expressed in embryonic stem and germ cells, as well as during early embryo development. Moreover, its expression is correlated with epigenetic events mediated by the de novo DNMT3b methyltransferase and knockdown in stem cells upregulates important genes that regulate multipotency. The recent data suggest that at least some new deadenylases may have expanded roles in cell metabolism as regulators of gene expression, through mRNA deadenylation, ncRNAs biogenesis and ncRNA-mediated mRNA targeting, linking essential mechanisms that regulate epigenetic control and transition events during differentiation. The possible roles of mammalian PNLDC1 along those dynamic networks are discussed in the light of new extremely important findings.
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Affiliation(s)
- Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, Greece
| | | | | | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, Greece
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161
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Festuccia N, Owens N, Navarro P. Esrrb, an estrogen-related receptor involved in early development, pluripotency, and reprogramming. FEBS Lett 2017; 592:852-877. [DOI: 10.1002/1873-3468.12826] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/11/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Nick Owens
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Pablo Navarro
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
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162
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Yan P, Luo S, Lu JY, Shen X. Cis- and trans-acting lncRNAs in pluripotency and reprogramming. Curr Opin Genet Dev 2017; 46:170-178. [PMID: 28843809 DOI: 10.1016/j.gde.2017.07.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022]
Abstract
Pervasive transcription in mammalian genomes produces thousands of long noncoding RNA (lncRNA) transcripts. Although they have been implicated in diverse biological processes, the functional relevance of most lncRNAs remains unknown. Recent studies reveal the prevalence of lncRNA-mediated cis regulation on nearby transcription. In this review, we summarize cis- and trans-acting lncRNAs involved in stem cell pluripotency and reprogramming, highlighting the role of regulatory lncRNAs in providing an additional layer of complexity to the regulation of genes that govern cell fate during development.
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Affiliation(s)
- Pixi Yan
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sai Luo
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - J Yuyang Lu
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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163
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Li MA, Amaral PP, Cheung P, Bergmann JH, Kinoshita M, Kalkan T, Ralser M, Robson S, von Meyenn F, Paramor M, Yang F, Chen C, Nichols J, Spector DL, Kouzarides T, He L, Smith A. A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation. eLife 2017; 6:e23468. [PMID: 28820723 PMCID: PMC5562443 DOI: 10.7554/elife.23468] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 07/24/2017] [Indexed: 12/24/2022] Open
Abstract
Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA) linc1281, hereafter Ephemeron (Eprn), that modulates the dynamics of exit from naïve pluripotency. Eprn deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression. In the absence of Eprn, Lin28a expression is reduced which results in persistence of let-7 microRNAs, and the up-regulation of de novo methyltransferases Dnmt3a/b is delayed. Dnmt3a/b deletion retards ES cell transition, correlating with delayed Nanog promoter methylation and phenocopying loss of Eprn or Lin28a. The connection from lncRNA to miRNA and DNA methylation facilitates the acute extinction of naïve pluripotency, a pre-requisite for rapid progression from preimplantation epiblast to gastrulation in rodents. Eprn illustrates how lncRNAs may introduce species-specific network modulations.
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Affiliation(s)
- Meng Amy Li
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Division of Cellular and Developmental Biology, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, United States
| | - Paulo P Amaral
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Priscilla Cheung
- Division of Cellular and Developmental Biology, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, United States
| | - Jan H Bergmann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Masaki Kinoshita
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Tüzer Kalkan
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Meryem Ralser
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sam Robson
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Maike Paramor
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Caifu Chen
- Integrated DNA Technologies, Redwood, United States
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Lin He
- Division of Cellular and Developmental Biology, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, United States
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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164
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Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Epigenetic resetting of human pluripotency. Development 2017; 144:2748-2763. [PMID: 28765214 PMCID: PMC5560041 DOI: 10.1242/dev.146811] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 06/09/2017] [Indexed: 12/12/2022]
Abstract
Much attention has focussed on the conversion of human pluripotent stem cells (PSCs) to a more naïve developmental status. Here we provide a method for resetting via transient histone deacetylase inhibition. The protocol is effective across multiple PSC lines and can proceed without karyotype change. Reset cells can be expanded without feeders with a doubling time of around 24 h. WNT inhibition stabilises the resetting process. The transcriptome of reset cells diverges markedly from that of primed PSCs and shares features with human inner cell mass (ICM). Reset cells activate expression of primate-specific transposable elements. DNA methylation is globally reduced to a level equivalent to that in the ICM and is non-random, with gain of methylation at specific loci. Methylation imprints are mostly lost, however. Reset cells can be re-primed to undergo tri-lineage differentiation and germline specification. In female reset cells, appearance of biallelic X-linked gene transcription indicates reactivation of the silenced X chromosome. On reconversion to primed status, XIST-induced silencing restores monoallelic gene expression. The facile and robust conversion routine with accompanying data resources will enable widespread utilisation, interrogation, and refinement of candidate naïve cells.
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Affiliation(s)
- Ge Guo
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | | | - Maria Rostovskaya
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - James Clarke
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Duncan Baker
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Anna Sahakyan
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Samuel Myers
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Paul Bertone
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Wolf Reik
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Kathrin Plath
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Austin Smith
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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165
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Yang Y, Liu B, Xu J, Wang J, Wu J, Shi C, Xu Y, Dong J, Wang C, Lai W, Zhu J, Xiong L, Zhu D, Li X, Yang W, Yamauchi T, Sugawara A, Li Z, Sun F, Li X, Li C, He A, Du Y, Wang T, Zhao C, Li H, Chi X, Zhang H, Liu Y, Li C, Duo S, Yin M, Shen H, Belmonte JCI, Deng H. Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency. Cell 2017; 169:243-257.e25. [PMID: 28388409 DOI: 10.1016/j.cell.2017.02.005] [Citation(s) in RCA: 321] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/24/2017] [Accepted: 02/01/2017] [Indexed: 10/19/2022]
Abstract
Of all known cultured stem cell types, pluripotent stem cells (PSCs) sit atop the landscape of developmental potency and are characterized by their ability to generate all cell types of an adult organism. However, PSCs show limited contribution to the extraembryonic placental tissues in vivo. Here, we show that a chemical cocktail enables the derivation of stem cells with unique functional and molecular features from mice and humans, designated as extended pluripotent stem (EPS) cells, which are capable of chimerizing both embryonic and extraembryonic tissues. Notably, a single mouse EPS cell shows widespread chimeric contribution to both embryonic and extraembryonic lineages in vivo and permits generating single-EPS-cell-derived mice by tetraploid complementation. Furthermore, human EPS cells exhibit interspecies chimeric competency in mouse conceptuses. Our findings constitute a first step toward capturing pluripotent stem cells with extraembryonic developmental potentials in culture and open new avenues for basic and translational research. VIDEO ABSTRACT.
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Affiliation(s)
- Yang Yang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bei Liu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jun Xu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Jinlin Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Jun Wu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Cheng Shi
- Reproductive Medical Center, Peking University People's Hospital, Peking University, Beijing, 100044, China
| | - Yaxing Xu
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jiebin Dong
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Chengyan Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Weifeng Lai
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jialiang Zhu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Liang Xiong
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, College of Life Sciences, Peking University, Beijing 100871, China
| | - Dicong Zhu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xiang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Weifeng Yang
- Beijing Vitalstar Biotechnology, Beijing 100012, China
| | - Takayoshi Yamauchi
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Atsushi Sugawara
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Zhongwei Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Fangyuan Sun
- College of Animal Science and Technology, Hebei University, Baoding 071002, China
| | - Xiangyun Li
- College of Animal Science and Technology, Hebei University, Baoding 071002, China
| | - Chen Li
- Institute of Molecular Medicine, Peking University, PKU-Tsinghua U Joint Center for Life Sciences, Beijing 100871, China
| | - Aibin He
- Institute of Molecular Medicine, Peking University, PKU-Tsinghua U Joint Center for Life Sciences, Beijing 100871, China
| | - Yaqin Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Ting Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Chaoran Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Haibo Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Xiaochun Chi
- Laboratory of Stem Cells, Development and Reproductive Medicine, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Hongquan Zhang
- Laboratory of Stem Cells, Development and Reproductive Medicine, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yifang Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Cheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China; Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Shuguang Duo
- Institute of Zoology, Chinese Academy Sciences, Beijing 100101, China
| | - Ming Yin
- Beijing Vitalstar Biotechnology, Beijing 100012, China
| | - Huan Shen
- Reproductive Medical Center, Peking University People's Hospital, Peking University, Beijing, 100044, China.
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
| | - Hongkui Deng
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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166
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ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs. Biotechniques 2017; 62:215-222. [DOI: 10.2144/000114545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/20/2017] [Indexed: 11/23/2022] Open
Abstract
Embryonic stem cells (ESCs) can be established as permanent cell lines, and their potential to differentiate into adult tissues has led to widespread use for studying the mechanisms and dynamics of stem cell differentiation and exploring strategies for tissue repair. Imaging live ESCs during development is now feasible due to advances in optical imaging and engineering of genetically encoded fluorescent reporters; however, a major limitation is the low spatio-temporal resolution of long-term 3-D imaging required for generational and neighboring reconstructions. Here, we present the ESC-Track (ESC-T) workflow, which includes an automated cell and nuclear segmentation and tracking tool for 4-D (3-D + time) confocal image data sets as well as a manual editing tool for visual inspection and error correction. ESC-T automatically identifies cell divisions and membrane contacts for lineage tree and neighborhood reconstruction and computes quantitative features from individual cell entities, enabling analysis of fluorescence signal dynamics and tracking of cell morphology and motion. We use ESC-T to examine Myc intensity fluctuations in the context of mouse ESC (mESC) lineage and neighborhood relationships. ESC-T is a powerful tool for evaluation of the genealogical and microenvironmental cues that maintain ESC fitness.
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167
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Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States. Cell Stem Cell 2017; 20:874-890.e7. [PMID: 28343983 PMCID: PMC5459756 DOI: 10.1016/j.stem.2017.02.014] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/25/2017] [Accepted: 02/27/2017] [Indexed: 01/09/2023]
Abstract
Human pluripotent stem cells (PSCs) exist in naive and primed states and provide important models to investigate the earliest stages of human development. Naive cells can be obtained through primed-to-naive resetting, but there are no reliable methods to prospectively isolate unmodified naive cells during this process. Here we report comprehensive profiling of cell surface proteins by flow cytometry in naive and primed human PSCs. Several naive-specific, but not primed-specific, proteins were also expressed by pluripotent cells in the human preimplantation embryo. The upregulation of naive-specific cell surface proteins during primed-to-naive resetting enabled the isolation and characterization of live naive cells and intermediate cell populations. This analysis revealed distinct transcriptional and X chromosome inactivation changes associated with the early and late stages of naive cell formation. Thus, identification of state-specific proteins provides a robust set of molecular markers to define the human PSC state and allows new insights into the molecular events leading to naive cell resetting. Flow cytometry profiles cell surface proteins in naive and primed human PSCs The human PSC state can be defined using robust state-specific protein markers Identified cell surface proteins track the dynamics of naive-primed PSC conversions Analyses of early-stage naive cells reveal transcription events during conversion
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168
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Barry C, Schmitz MT, Jiang P, Schwartz MP, Duffin BM, Swanson S, Bacher R, Bolin JM, Elwell AL, McIntosh BE, Stewart R, Thomson JA. Species-specific developmental timing is maintained by pluripotent stem cells ex utero. Dev Biol 2017; 423:101-110. [PMID: 28179190 DOI: 10.1016/j.ydbio.2017.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/27/2017] [Accepted: 02/04/2017] [Indexed: 12/24/2022]
Abstract
How species-specific developmental timing is controlled is largely unknown. By following human embryonic stem (ES) cell and mouse epiblast stem (EpiS) cell differentiation through detailed RNA-sequencing time courses, here we show that pluripotent stem cells closely retain in vivo species-specific developmental timing in vitro. In identical neural differentiation conditions in vitro, gene expression profiles are accelerated in mouse EpiS cells compared to human ES cells with relative rates of differentiation closely reflecting the rates of progression through the Carnegie stages in utero. Dynamic Time Warping analysis identified 3389 genes that were regulated more quickly in mouse EpiS cells and identified none that were regulated more quickly in human ES cells. Interestingly, we also find that human ES cells differentiated in teratomas maintain the same rate of differentiation observed in vitro in spite of being grown in a mouse host. These results suggest the existence of a cell autonomous, species-specific developmental clock that pluripotent stem cells maintain even out of context of an intact embryo.
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Affiliation(s)
| | | | - Peng Jiang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Michael P Schwartz
- Center for Sustainable Nanotechnology, Department of Chemistry, University of Wisconsin-Madison, WI 53706, USA
| | - Bret M Duffin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Rhonda Bacher
- Department of Statistics, University of Wisconsin-Madison, WI 53706, USA
| | | | | | | | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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