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Dirks RAM, van Mierlo G, Kerstens HHD, Bernardo AS, Kobolák J, Bock I, Maruotti J, Pedersen RA, Dinnyés A, Huynen MA, Jouneau A, Marks H. Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states. Epigenetics Chromatin 2019; 12:14. [PMID: 30767785 PMCID: PMC6376749 DOI: 10.1186/s13072-019-0259-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we apply allele-specific RNA-seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic tissues between E3.5 and E7.25 and in pluripotent cell lines to evaluate maintenance of imprinted gene expression. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos and from embryos obtained after nuclear transfer (NT) or parthenogenetic activation (PGA). RESULTS As homozygous genomic regions of PGA-derived cells are not compatible with allele-specific RNA-seq, we developed an RNA-seq-based genotyping strategy allowing identification of informative heterozygous regions. Global analysis shows that proper imprinted gene expression as observed in embryonic tissues is largely lost in the ESC lines included in this study, which mainly consisted of female ESCs. Differentiation of ESC lines to embryoid bodies or NPCs does not restore monoallelic expression of imprinted genes, neither did reprogramming of the serum-cultured ESCs to the pluripotent ground state by the use of 2 kinase inhibitors. Fertilized EpiSC and EpiSC-NT lines largely maintain imprinted gene expression, as did EpiSC-PGA lines that show known paternally expressed genes being silent and known maternally expressed genes consistently showing doubled expression. Notably, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. With respect to female EpiSC, most of the lines displayed completely skewed X inactivation suggesting a (near) clonal origin. CONCLUSIONS Altogether, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands
| | - Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Hindrik H D Kerstens
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands
| | - Andreia S Bernardo
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust- Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK.,Mill Hill Laboratory, The Ridgeway, The Francis Crick Institute, London, NW7 1AA, UK
| | | | | | - Julien Maruotti
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France.,Phenocell SAS, Evry, France
| | - Roger A Pedersen
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust- Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - András Dinnyés
- BioTalentum Ltd., Gödöllő, Hungary.,Molecular Animal Biotechnology Laboratory, Szent István University, Gödöllő, Hungary
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Alice Jouneau
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands.
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2
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Li T, Zheng Y, Li Y, Ye D. Comparison of in vitro Neuronal Differentiation Capacity Between Mouse Epiblast Stem Cells Derived From Nuclear Transfer and Naturally Fertilized Embryos. Front Mol Neurosci 2018; 11:392. [PMID: 30425619 PMCID: PMC6218595 DOI: 10.3389/fnmol.2018.00392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/09/2018] [Indexed: 11/18/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) can give rise to fertile adults, but the successful perinatal and postnatal developmental rates are inefficient, including delayed developmental behaviors, and respiratory failure. However, the molecular and cellular mechanisms remain elusive. Mouse epiblast stem cells (mEpiSCs) from E5.5-6.5 epiblasts share defining features with human embryonic stem cells (hESCs), providing a new opportunity to study early mammalian development in vitro. In this study, mEpiSCs were established from naturally fertilized mouse embryos (F-mEpiSCs) and SCNT mouse embryos (NT-mEpiSCs). Also, the in vitro neuronal differentiation capacity of F-mEpiSCs and NT-mEpiSCs was compared. Morphology analysis showed less and smaller neurospheres formation and lower percentage of early neurons generation in NT-mEpiSCs. The immunocytochemical analysis and altered mRNA expression levels of the neuronal markers in differentiated cells further confirmed that neurogenesis was slower in NT-mEpiSCs than in F-mEpiSCs. Moreover, neuronal differentiation capacity was correlated with the basal expression levels of Atox1 and Vinculin but not Brachyury and Otx2, emphasizing that developmental aberrations in neurogenesis were associated with the NT technique but not random variations between clones. This study provided an important in vitro platform using mEpiSCs to study early epigenetic and developmental processes associated with neurogenesis.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology and Vision Science, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yi Zheng
- Department of Reproductive Medical Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yan Li
- Department of Reproductive Medical Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Danna Ye
- Department of Reproductive Medical Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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3
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Vitamin C and l-Proline Antagonistic Effects Capture Alternative States in the Pluripotency Continuum. Stem Cell Reports 2016; 8:1-10. [PMID: 28017658 PMCID: PMC5233408 DOI: 10.1016/j.stemcr.2016.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 11/24/2016] [Accepted: 11/25/2016] [Indexed: 12/14/2022] Open
Abstract
Metabolites and cofactors are emerging as key regulators of cell plasticity and reprogramming, and their role in the control of pluripotency is just being discovered. Here we provide unprecedented evidence that embryonic stem cell (ESC) pluripotency relies on the relative levels of two physiological metabolites, namely ascorbic acid (vitamin C, VitC) and l-proline (l-Pro), which affect global DNA methylation, transcriptional profile, and energy metabolism. Specifically, while a high VitC/l-Pro ratio drives ESCs toward a naive state, the opposite condition (l-Pro excess) captures a fully reversible early primed pluripotent state, which depends on autocrine fibroblast growth factor and transforming growth factor β signaling pathways. Our findings highlight the pivotal role of metabolites availability in controlling the pluripotency continuum from naive to primed states. Global DNA methylation is modulated by l-Pro and VitC availability in ESCs l-Pro and VitC relative levels induce naive and reversible primed pluripotency High l-Pro/low VitC levels induce metabolic reprogramming in ESCs l-Pro induces and sustains autocrine FGF and TGF-β signaling in ESCs
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4
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Hosseini SM, Dufort I, Nieminen J, Moulavi F, Ghanaei HR, Hajian M, Jafarpour F, Forouzanfar M, Gourbai H, Shahverdi AH, Nasr-Esfahani MH, Sirard MA. Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors. BMC Genomics 2016; 17:16. [PMID: 26725231 PMCID: PMC4698792 DOI: 10.1186/s12864-015-2264-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 12/01/2015] [Indexed: 12/27/2022] Open
Abstract
Background The limited duration and compromised efficiency of oocyte-mediated reprogramming, which occurs during the early hours following somatic cell nuclear transfer (SCNT), may significantly interfere with epigenetic reprogramming, contributing to the high incidence of ill/fatal transcriptional phenotypes and physiological anomalies occurring later during pre- and post-implantation events. A potent histone deacetylase inhibitor, trichostatin A (TSA), was used to understand the effects of assisted epigenetic modifications on transcriptional profiles of SCNT blastocysts and to identify specific or categories of genes affected. Results TSA improved the yield and quality of in vitro embryo development compared to control (CTR-NT). Significance analysis of microarray results revealed that of 37,238 targeted gene transcripts represented on the microarray slide, a relatively small number of genes were differentially expressed in CTR-NT (1592 = 4.3 %) and TSA-NT (1907 = 5.1 %) compared to IVF embryos. For both SCNT groups, the majority of downregulated and more than half of upregulated genes were common and as much as 15 % of all deregulated transcripts were located on chromosome X. Correspondence analysis clustered CTR-NT and IVF transcriptomes close together regardless of the embryo production method, whereas TSA changed SCNT transcriptome to a very clearly separated cluster. Ontological classification of deregulated genes using IPA uncovered a variety of functional categories similarly affected in both SCNT groups with a preponderance of genes required for biological processes. Examination of genes involved in different canonical pathways revealed that the WNT and FGF pathways were similarly affected in both SCNT groups. Although TSA markedly changed epigenetic reprogramming of donor cells (DNA-methylation, H3K9 acetylation), reconstituted oocytes (5mC, 5hmC), and blastocysts (DNA-methylation, H3K9 acetylation), these changes did not recapitulate parallel marked changes in chromatin remodeling, and nascent mRNA and OCT4-EGFP expression of TSA-NT vs. CRT-NT embryos. Conclusions The results obtained suggest that despite the extensive reprogramming of donor cells that occurred by the blastocyst stage, SCNT-specific errors are of a non-random nature in bovine and are not responsive to epigenetic modifications by TSA. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2264-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sayyed Morteza Hosseini
- Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. .,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Isabelle Dufort
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Julie Nieminen
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Fariba Moulavi
- Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Hamid Reza Ghanaei
- Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Mahdi Hajian
- Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Farnoosh Jafarpour
- Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Mohsen Forouzanfar
- Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Hamid Gourbai
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Abdol Hossein Shahverdi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Mohammad Hossein Nasr-Esfahani
- Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. .,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Marc-André Sirard
- Centre de Recherche en Biologie de la Reproduction, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon INAF, Université Laval, Québec, QC, G1V 0A6, Canada.
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5
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Marks H, Kerstens HHD, Barakat TS, Splinter E, Dirks RAM, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG. Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. Genome Biol 2015; 16:149. [PMID: 26235224 PMCID: PMC4546214 DOI: 10.1186/s13059-015-0698-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/18/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells, which contain a single X chromosome. Here, we use mouse female embryonic stem cells (ESCs) with non-random X chromosome inactivation (XCI) and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome by high-resolution allele-specific RNA-seq. RESULTS Induction of XCI by differentiation of female ESCs shows that genes proximal to the X-inactivation center are silenced earlier than distal genes, while lowly expressed genes show faster XCI dynamics than highly expressed genes. The active X chromosome shows a minor but significant increase in gene activity during differentiation, resulting in complete dosage compensation in differentiated cell types. Genes escaping XCI show little or no silencing during early propagation of XCI. Allele-specific RNA-seq of neural progenitor cells generated from the female ESCs identifies three regions distal to the X-inactivation center that escape XCI. These regions, which stably escape during propagation and maintenance of XCI, coincide with topologically associating domains (TADs) as present in the female ESCs. Also, the previously characterized gene clusters escaping XCI in human fibroblasts correlate with TADs. CONCLUSIONS The gene silencing observed during XCI provides further insight in the establishment of the repressive complex formed by the inactive X chromosome. The association of escape regions with TADs, in mouse and human, suggests that TADs are the primary targets during propagation of XCI over the X chromosome.
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Affiliation(s)
- Hendrik Marks
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Hindrik H D Kerstens
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tahsin Stefan Barakat
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Erik Splinter
- Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
| | - René A M Dirks
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Guido van Mierlo
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Onkar Joshi
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Shuang-Yin Wang
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tomas Babak
- Biology Department, Queen's University, Kingston, ON, Canada.
| | - Cornelis A Albers
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tüzer Kalkan
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Alice Jouneau
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Wouter de Laat
- Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Hendrik G Stunnenberg
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
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Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation. Mol Cell Biol 2015; 35:1026-42. [PMID: 25582196 DOI: 10.1128/mcb.01172-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Tet 5-methylcytosine dioxygenases catalyze DNA demethylation by producing 5-hydroxymethylcytosine and further oxidized products. Tet1 and Tet2 are highly expressed in mouse pluripotent cells and downregulated to different extents in somatic cells, but the transcriptional mechanisms are unclear. Here we defined the promoter and enhancer domains in Tet1 and Tet2. Within a 15-kb "superenhancer" of Tet1, there are two transcription start sites (TSSs) with different activation patterns during development. A 6-kb promoter region upstream of the distal TSS is highly active in naive pluripotent cells, autonomously reports Tet1 expression in a transgenic system, and rapidly undergoes DNA methylation and silencing upon differentiation in cultured cells and native epiblast. A second TSS downstream, associated with a constitutively weak CpG-rich promoter, is activated by a neighboring enhancer in naive embryonic stem cells (ESCs) and primed epiblast-like cells (EpiLCs). Tet2 has a CpG island promoter with pluripotency-independent activity and an ESC-specific distal intragenic enhancer; the latter is rapidly downregulated in EpiLCs. Our study reveals distinct modes of transcriptional regulation at Tet1 and Tet2 during cell state transitions of early development. New transgenic reporters using Tet1 and Tet2 cis-regulatory domains may serve to distinguish nuanced changes in pluripotent states and the underlying epigenetic variations.
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Abstract
Somatic cell nuclear transfer (SCNT) has a low success rate that rarely exceeds 5 %. Moreover, SCNT requires highly technical skills and may be influenced by the biological material used (oocyte and donor cell quality). Hence, it is crucial to check the normality of the donor cell's karyotype. Numerical and structural chromosome abnormalities are detected by cytogenetic analysis at minimum using G-banding to identify the chromosomes. Here, we describe the classical protocols that are needed to perform complete cytogenetic analyses, i.e., G-banding to identify chromosome aberrations, followed by Fluorescent In Situ Hybridization (FISH) of specific probes for a more sensitive detection and precise identification of the rearrangement.
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8
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Veillard AC, Marks H, Bernardo AS, Jouneau L, Laloë D, Boulanger L, Kaan A, Brochard V, Tosolini M, Pedersen R, Stunnenberg H, Jouneau A. Stable methylation at promoters distinguishes epiblast stem cells from embryonic stem cells and the in vivo epiblasts. Stem Cells Dev 2014; 23:2014-29. [PMID: 24738887 DOI: 10.1089/scd.2013.0639] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs) are the in vitro representatives of naïve and primed pluripotency, respectively. It is currently unclear how their epigenomes underpin the phenotypic and molecular characteristics of these distinct pluripotent states. Here, we performed a genome-wide comparison of DNA methylation between ESCs and EpiSCs by MethylCap-Seq. We observe that promoters are preferential targets for methylation in EpiSC compared to ESCs, in particular high CpG island promoters. This is in line with upregulation of the de novo methyltransferases Dnmt3a1 and Dnmt3b in EpiSC, and downregulation of the demethylases Tet1 and Tet2. Remarkably, the observed DNA methylation signature is specific to EpiSCs and differs from that of their in vivo counterpart, the postimplantation epiblast. Using a subset of promoters that are differentially methylated, we show that DNA methylation is established within a few days during in vitro outgrowth of the epiblast, and also occurs when ESCs are converted to EpiSCs in vitro. Once established, this methylation is stable, as ES-like cells obtained by in vitro reversion of EpiSCs display an epigenetic memory that only extensive passaging and sub-cloning are able to almost completely erase.
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9
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Fröhlich T, Kösters M, Graf A, Wolf E, Kobolak J, Brochard V, Dinnyés A, Jouneau A, Arnold GJ. iTRAQ proteome analysis reflects a progressed differentiation state of epiblast derived versus inner cell mass derived murine embryonic stem cells. J Proteomics 2013; 90:38-51. [DOI: 10.1016/j.jprot.2013.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/26/2013] [Accepted: 03/19/2013] [Indexed: 12/26/2022]
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10
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Habibi E, Brinkman AB, Arand J, Kroeze LI, Kerstens HHD, Matarese F, Lepikhov K, Gut M, Brun-Heath I, Hubner NC, Benedetti R, Altucci L, Jansen JH, Walter J, Gut IG, Marks H, Stunnenberg HG. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 2013; 13:360-9. [PMID: 23850244 DOI: 10.1016/j.stem.2013.06.002] [Citation(s) in RCA: 343] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/03/2013] [Accepted: 06/07/2013] [Indexed: 12/22/2022]
Abstract
The use of two kinase inhibitors (2i) enables derivation of mouse embryonic stem cells (ESCs) in the pluripotent ground state. Using whole-genome bisulfite sequencing (WGBS), we show that male 2i ESCs are globally hypomethylated compared to conventional ESCs maintained in serum. In serum, female ESCs are hypomethyated similarly to male ESCs in 2i, and DNA methylation is further reduced in 2i. Regions with elevated DNA methylation in 2i strongly correlate with the presence of H3K9me3 on endogenous retroviruses (ERVs) and imprinted loci. The methylome of male ESCs in serum parallels postimplantation blastocyst cells, while 2i stalls ESCs in a hypomethylated, ICM-like state. WGBS analysis during adaptation of 2i ESCs to serum suggests that deposition of DNA methylation is largely random, while loss of DNA methylation during reversion to 2i occurs passively, initiating at TET1 binding sites. Together, our analysis provides insight into DNA methylation dynamics in cultured ESCs paralleling early developmental processes.
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Affiliation(s)
- Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences NCMLS, Radboud University, 6525GA, Nijmegen, The Netherlands
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11
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Narbonne P, Miyamoto K, Gurdon JB. Reprogramming and development in nuclear transfer embryos and in interspecific systems. Curr Opin Genet Dev 2012; 22:450-8. [PMID: 23062626 PMCID: PMC3654497 DOI: 10.1016/j.gde.2012.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/29/2012] [Accepted: 09/17/2012] [Indexed: 11/18/2022]
Abstract
Nuclear transfer (NT) remains the most effective method to reprogram somatic cells to totipotency. Somatic cell nuclear transfer (SCNT) efficiency however remains low, but recurrent problems occurring in partially reprogrammed cloned embryos have recently been identified and some remedied. In particular, the trophectoderm has been identified as a lineage whose reprogramming success has a large influence on SCNT embryo development. Several interspecific hybrid and cybrid reprogramming systems have been developed as they offer various technical advantages and potential applications, and together with SCNT, they have led to the identification of a series of reprogramming events and responsible reprogramming factors. Interspecific incompatibilities hinder full exploitation of cross-species reprogramming systems, yet recent findings suggest that these may not constitute insurmountable obstacles.
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Affiliation(s)
- Patrick Narbonne
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
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12
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Androgenetic haploid embryonic stem cells produce live transgenic mice. Nature 2012; 490:407-11. [PMID: 23023130 DOI: 10.1038/nature11435] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/23/2012] [Indexed: 12/24/2022]
Abstract
Haploids and double haploids are important resources for studying recessive traits and have large impacts on crop breeding, but natural haploids are rare in animals. Mammalian haploids are restricted to germline cells and are occasionally found in tumours with massive chromosome loss. Recent success in establishing haploid embryonic stem (ES) cells in medaka fish and mice raised the possibility of using engineered mammalian haploid cells in genetic studies. However, the availability and functional characterization of mammalian haploid ES cells are still limited. Here we show that mouse androgenetic haploid ES (ahES) cell lines can be established by transferring sperm into an enucleated oocyte. The ahES cells maintain haploidy and stable growth over 30 passages, express pluripotent markers, possess the ability to differentiate into all three germ layers in vitro and in vivo, and contribute to germlines of chimaeras when injected into blastocysts. Although epigenetically distinct from sperm cells, the ahES cells can produce viable and fertile progenies after intracytoplasmic injection into mature oocytes. The oocyte-injection procedure can also produce viable transgenic mice from genetically engineered ahES cells. Our findings show the developmental pluripotency of androgenentic haploids and provide a new tool to quickly produce genetic models for recessive traits. They may also shed new light on assisted reproduction.
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13
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Degrelle SA, Jaffrezic F, Campion E, Lê Cao KA, Le Bourhis D, Richard C, Rodde N, Fleurot R, Everts RE, Lecardonnel J, Heyman Y, Vignon X, Yang X, Tian XC, Lewin HA, Renard JP, Hue I. Uncoupled embryonic and extra-embryonic tissues compromise blastocyst development after somatic cell nuclear transfer. PLoS One 2012; 7:e38309. [PMID: 22701625 PMCID: PMC3368877 DOI: 10.1371/journal.pone.0038309] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 05/04/2012] [Indexed: 02/04/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) is the most efficient cell reprogramming technique available, especially when working with bovine species. Although SCNT blastocysts performed equally well or better than controls in the weeks following embryo transfer at Day 7, elongation and gastrulation defects were observed prior to implantation. To understand the developmental implications of embryonic/extra-embryonic interactions, the morphological and molecular features of elongating and gastrulating tissues were analysed. At Day 18, 30 SCNT conceptuses were compared to 20 controls (AI and IVP: 10 conceptuses each); one-half of the SCNT conceptuses appeared normal while the other half showed signs of atypical elongation and gastrulation. SCNT was also associated with a high incidence of discordance in embryonic and extra-embryonic patterns, as evidenced by morphological and molecular “uncoupling”. Elongation appeared to be secondarily affected; only 3 of 30 conceptuses had abnormally elongated shapes and there were very few differences in gene expression when they were compared to the controls. However, some of these differences could be linked to defects in microvilli formation or extracellular matrix composition and could thus impact extra-embryonic functions. In contrast to elongation, gastrulation stages included embryonic defects that likely affected the hypoblast, the epiblast, or the early stages of their differentiation. When taking into account SCNT conceptus somatic origin, i.e. the reprogramming efficiency of each bovine ear fibroblast (Low: 0029, Med: 7711, High: 5538), we found that embryonic abnormalities or severe embryonic/extra-embryonic uncoupling were more tightly correlated to embryo loss at implantation than were elongation defects. Alternatively, extra-embryonic differences between SCNT and control conceptuses at Day 18 were related to molecular plasticity (high efficiency/high plasticity) and subsequent pregnancy loss. Finally, because it alters re-differentiation processes in vivo, SCNT reprogramming highlights temporally and spatially restricted interactions among cells and tissues in a unique way.
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Affiliation(s)
- Séverine A. Degrelle
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Florence Jaffrezic
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Evelyne Campion
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Kim-Anh Lê Cao
- INRA, UR631, Station d’Amélioration Génétique des Animaux, Castanet, France
| | - Daniel Le Bourhis
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
- UNCEIA, R&D Department, Maisons Alfort, France
| | | | - Nathalie Rodde
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Renaud Fleurot
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Robin E. Everts
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | | | - Yvan Heyman
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Xavier Vignon
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Xiangzhong Yang
- Department of Animal Science and Center for Regenerative Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Xiuchun C. Tian
- Department of Animal Science and Center for Regenerative Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Harris A. Lewin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jean-Paul Renard
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Isabelle Hue
- INRA, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
- * E-mail:
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Maruotti J, Muñoz M, Degrelle SA, Gómez E, Louet C, Díez C, Monforte CD, de Longchamp PH, Brochard V, Hue I, Caamaño JN, Jouneau A. Efficient derivation of bovine embryonic stem cells needs more than active core pluripotency factors. Mol Reprod Dev 2012; 79:461-77. [PMID: 22573702 DOI: 10.1002/mrd.22051] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 05/01/2012] [Indexed: 12/20/2022]
Abstract
Pluripotency can be captured in vitro, providing that the culture environment meets the requirements that avoid differentiation while stimulating self-renewal. From studies in the mouse embryo, two kinds of pluripotent stem cells have been obtained from the early and late epiblast, embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs), representing the naive and primed states, respectively. All attempts to derive convincing ESCs in ungulates have been unsuccessful, although all attempts were based on the assumption that the conditions used to derive mouse ESCs or human ESC could be applied in other species. Pluripotent cells derived in primates, rabbit, and pig strongly indicate that the state of pluripotency of these cells is, in fact, closer to EpiSCs than to ESCs, and thus depend on fibroblast growth factor (FGF) and Activin signaling pathways. Based on this observation, we have tried to derive EpiSC from the epiblast of bovine elongated embryos as well as ESCs from Day-8 blastocysts. We here show that the core transcription factors Oct4/Sox2/Nanog can be used as markers of pluripotency in the bovine since their expression was restricted to the developing epiblast after Day 8, and disappeared following differentiation of both the ESC-like and EpiSC-like cultures. Although FGF and Activin pathways are indeed present and active in the bovine, it is not sufficient/enough to maintain a long-term pluripotency ex vivo, as was reported for mouse and pig EpiSCs.
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Affiliation(s)
- Julien Maruotti
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
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15
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Sun B, Ito M, Mendjan S, Ito Y, Brons IGM, Murrell A, Vallier L, Ferguson-Smith AC, Pedersen RA. Status of genomic imprinting in epigenetically distinct pluripotent stem cells. Stem Cells 2012; 30:161-8. [PMID: 22109880 DOI: 10.1002/stem.793] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mouse epiblast stem cells (EpiSCs) derived from postimplantation embryos are developmentally and functionally different from embryonic stem cells (ESCs) generated from blastocysts. EpiSCs require Activin A and FGF2 signaling for self-renewal, similar to human ESCs (hESCs), while mouse ESCs require LIF and BMP4. Unlike ESCs, EpiSCs have undergone X-inactivation, similar to the tendency of hESCs. The shared self-renewal and X-inactivation properties of EpiSCs and hESCs suggest that they have an epigenetic state distinct from ESCs. This hypothesis predicts that EpiSCs would have monoallelic expression of most imprinted genes, like that observed in hESCs. Here, we confirm this prediction. By contrast, we find that mouse induced pluripotent stem cells (iPSCs) tend to lose imprinting similar to mouse ESCs. These findings reveal that iPSCs have an epigenetic status associated with their pluripotent state rather than their developmental origin. Our results also reinforce the view that hESCs and EpiSCs are in vitro counterparts, sharing an epigenetic status distinct from ESCs and iPSCs.
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Affiliation(s)
- Bowen Sun
- The Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery, University of Cambridge, Cambridge, United Kingdom
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16
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Jouneau A, Ciaudo C, Sismeiro O, Brochard V, Jouneau L, Vandormael-Pournin S, Coppée JY, Zhou Q, Heard E, Antoniewski C, Cohen-Tannoudji M. Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA (NEW YORK, N.Y.) 2012; 18:253-264. [PMID: 22201644 PMCID: PMC3264912 DOI: 10.1261/rna.028878.111] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 11/06/2011] [Indexed: 05/31/2023]
Abstract
Over the last years, the microRNA (miRNA) pathway has emerged as a key component of the regulatory network of pluripotency. Although clearly distinct states of pluripotency have been described in vivo and ex vivo, differences in miRNA expression profiles associated with the developmental modulation of pluripotency have not been extensively studied so far. Here, we performed deep sequencing to profile miRNA expression in naive (embryonic stem cell [ESC]) and primed (epiblast stem cell [EpiSC]) pluripotent stem cells derived from mouse embryos of identical genetic background. We developed a graphical representation method allowing the rapid identification of miRNAs with an atypical profile including mirtrons, a small nucleolar RNA (snoRNA)-derived miRNA, and miRNAs whose biogenesis may differ between ESC and EpiSC. Comparison of mature miRNA profiles revealed that ESCs and EpiSCs exhibit very different miRNA signatures with one third of miRNAs being differentially expressed between the two cell types. Notably, differential expression of several clusters, including miR290-295, miR17-92, miR302/367, and a large repetitive cluster on chromosome 2, was observed. Our analysis also showed that differentiation priming of EpiSC compared to ESC is evidenced by changes in miRNA expression. These dynamic changes in miRNAs signature are likely to reflect both redundant and specific roles of miRNAs in the fine-tuning of pluripotency during development.
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Affiliation(s)
- Alice Jouneau
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78352 Jouy-en-Josas, France
- ENVA, F-94704 Maisons Alfort, France
| | - Constance Ciaudo
- CNRS UMR3215, INSERM U934, Institut Curie, F-75248 Paris, France
| | | | - Vincent Brochard
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78352 Jouy-en-Josas, France
- ENVA, F-94704 Maisons Alfort, France
| | - Luc Jouneau
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78352 Jouy-en-Josas, France
- ENVA, F-94704 Maisons Alfort, France
| | - Sandrine Vandormael-Pournin
- Département de Biologie du Développement, Institut Pasteur, Unité de Génétique Fonctionnelle de la Souris, F-75015 Paris, France
- CNRS URA 2578, F-75015 Paris, France
| | | | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
| | - Edith Heard
- CNRS UMR3215, INSERM U934, Institut Curie, F-75248 Paris, France
| | - Christophe Antoniewski
- CNRS URA 2578, F-75015 Paris, France
- Drosophila Genetics and Epigenetics, Institut Pasteur, F-75015 Paris, France
| | - Michel Cohen-Tannoudji
- Département de Biologie du Développement, Institut Pasteur, Unité de Génétique Fonctionnelle de la Souris, F-75015 Paris, France
- CNRS URA 2578, F-75015 Paris, France
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18
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Hai T, Hao J, Wang L, Jouneau A, Zhou Q. Pluripotency maintenance in mouse somatic cell nuclear transfer embryos and its improvement by treatment with the histone deacetylase inhibitor TSA. Cell Reprogram 2011; 13:47-56. [PMID: 21241188 DOI: 10.1089/cell.2010.0042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Reprogramming of somatic cells to pluripotency can be achieved by nuclear transfer into enucleated oocytes (SCNT). A key event of this process is the demethylation of the Oct4 gene and its temporally and spatially regulated expression. Different studies have shown that it occurs abnormally in some SCNT embryos. TSA is a histone deacetylase inhibitor known to increase the efficiency of development to term of SCNT embryos, but its impact on the developmental features of SCNT embryos is poorly understood. Here, we have followed the fate of the pluripotent cells within SCNT embryos, from the late blastocyst to the early epiblast prior to gastrulation. Our data show a delay in development correlated with a defect in forming and maintaining a correct number of Oct4 expressing ICM and epiblast cells in SCNT embryos. As a consequence, during the outgrowth phase of embryonic stem cell derivation as well as during diapause in vivo, part of the SCNT blastocysts completely lose their ICM cells. Meanwhile, the others display a correctly reprogrammed ICM compatible with the derivation of ES cells and development of the epiblast. Our data also indicate that TSA favors the establishment of pluripotency in SCNT embryos.
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Affiliation(s)
- Tang Hai
- State Key Laboratory of Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, People's Republic of China
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19
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Sullivan GJ, Bai Y, Fletcher J, Wilmut I. Induced pluripotent stem cells: epigenetic memories and practical implications. Mol Hum Reprod 2010; 16:880-5. [PMID: 21059705 DOI: 10.1093/molehr/gaq091] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) may be obtained by direct reprogramming of different somatic cells to a pluripotent state by forced expression of a handful of transcription factors. It was generally assumed that iPSCs are functionally equivalent to their embryonic stem cell (ESC) counterparts. Recently, a number of research groups have demonstrated that this is not the case, showing that iPSCs retain 'epigenetic memory' of the donor tissue from which they were derived and display skewed differentiation potential. This raises the question whether such cells are fit for experimental, diagnostic or therapeutic purpose. A brief survey of the literature illustrates that differences at both epigenetic and transcriptome level are observed between various pluripotent stem cell populations. Interestingly, iPSC populations with perceived 'anomalies' can be coaxed to a more ESC-like cellular state either by continuous passaging--which attenuates these epigenetic differences--or treatment with small molecules that target the machinery responsible for remodelling the genome. This suggests that the establishment of an epigenetic status approximating an ESC counterpart is largely a passive process. The mechanisms responsible remain to be established. Meanwhile, other areas of reprogramming are rapidly evolving such as, trans-differentiation of one somatic cell type to another by the forced expression of key transcription factors. When it comes to assessing their practical usefulness, the same question will also apply.
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Affiliation(s)
- G J Sullivan
- MRC Centre for Regenerative Medicine, University of Edinburgh, Chancellors Building, 49, Little France Crescent, Edinburgh EH16 4SB, UK
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20
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Jouneau A. [Nuclear reprogramming and pluripotency: the case of epiblast stem cells]. Med Sci (Paris) 2010; 26:792-4. [PMID: 20929663 DOI: 10.1051/medsci/20102610792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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