1
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Wilkinson AL, Zorzan I, Rugg-Gunn PJ. Epigenetic regulation of early human embryo development. Cell Stem Cell 2023; 30:1569-1584. [PMID: 37858333 DOI: 10.1016/j.stem.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Studies of mammalian development have advanced our understanding of the genetic, epigenetic, and cellular processes that orchestrate embryogenesis and have uncovered new insights into the unique aspects of human embryogenesis. Recent studies have now produced the first epigenetic maps of early human embryogenesis, stimulating new ideas about epigenetic reprogramming, cell fate control, and the potential mechanisms underpinning developmental plasticity in human embryos. In this review, we discuss these new insights into the epigenetic regulation of early human development and the importance of these processes for safeguarding development. We also highlight unanswered questions and key challenges that remain to be addressed.
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Affiliation(s)
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
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2
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Giuliani A, Licursi V, Nisi PS, Fiore M, D'Angelo S, Biagioni S, Negri R, Rugg-Gunn PJ, Cacci E, Lupo G. Dbx2, an Aging-Related Homeobox Gene, Inhibits the Proliferation of Adult Neural Progenitors. Stem Cell Rev Rep 2023; 19:2837-2851. [PMID: 37605090 PMCID: PMC10661760 DOI: 10.1007/s12015-023-10600-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 08/23/2023]
Abstract
In the adult mouse brain, the subventricular zone (SVZ) underlying the lateral ventricles harbours a population of quiescent neural stem cells, which can be activated (aNSCs) to initiate proliferation and generate a neurogenic lineage consisting of transit amplifying progenitors (TAPs), neuroblasts (NBs) and newborn neurons. This process is markedly reduced during aging. Recent studies suggest that the aged SVZ niche decreases the pool of proliferating neural/stem progenitor cells (NSPCs), and hence adult neurogenesis, by causing transcriptomic changes that promote NSC quiescence. The transcription factors that mediate these changes, however, remain unclear. We previously found that the homeobox gene Dbx2 is upregulated in NSPCs of the aged mouse SVZ and can inhibit the growth of NSPC cultures. Here, we further investigate its role as a candidate transcriptional regulator of neurogenic decline. We show that Dbx2 expression is downregulated by Epidermal Growth Factor receptor signaling, which promotes NSPC proliferation and decreases in the aged SVZ. By means of transgenic NSPC lines overexpressing Dbx2, we also show that this gene inhibits NSPC proliferation by hindering the G2/M transition. Furthermore, we exploit RNA sequencing of transgenic NSPCs to elucidate the transcriptomic networks modulated by Dbx2. Among the top hits, we report the downregulation of the molecular pathways implicated in cell cycle progression. Accordingly, we find that Dbx2 function is negatively correlated with the transcriptional signatures of proliferative NSPCs (aNSCs, TAPs and early NBs). These results point to Dbx2 as a transcription factor relaying the anti-neurogenic input of the aged niche to the NSPC transcriptome.
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Affiliation(s)
- Andrea Giuliani
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
| | - Valerio Licursi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, Italy.
| | - Paola S Nisi
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
| | - Mario Fiore
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, Italy
| | - Sara D'Angelo
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
| | - Stefano Biagioni
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, Italy
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Emanuele Cacci
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
| | - Giuseppe Lupo
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy.
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3
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Rugg-Gunn PJ, Moris N, Tam PPL. Technical challenges of studying early human development. Development 2023; 150:dev201797. [PMID: 37260362 PMCID: PMC10281548 DOI: 10.1242/dev.201797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent years have seen exciting progress across human embryo research, including new methods for culturing embryos, transcriptional profiling of embryogenesis and gastrulation, mapping lineage trajectories, and experimenting on stem cell-based embryo models. These advances are beginning to define the dynamical principles of development across stages, tissues and organs, enabling a better understanding of human development before birth in health and disease, and potentially leading to improved treatments for infertility and developmental disorders. However, there are still significant roadblocks en route to this goal. Here, we highlight technical challenges to studying early human development and propose ways and means to overcome some of these constraints.
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Affiliation(s)
- Peter J. Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
| | - Naomi Moris
- The Francis Crick Institute, London NW1 1AT, UK
| | - Patrick P. L. Tam
- Embryology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead NSW 2145, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney NSW 2006, Australia
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4
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Maskalenka K, Alagöz G, Krueger F, Wright J, Rostovskaya M, Nakhuda A, Bendall A, Krueger C, Walker S, Scally A, Rugg-Gunn PJ. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells. Development 2023; 150:286291. [PMID: 36621005 PMCID: PMC10110494 DOI: 10.1242/dev.201155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023]
Abstract
Gene duplication events can drive evolution by providing genetic material for new gene functions, and they create opportunities for diverse developmental strategies to emerge between species. To study the contribution of duplicated genes to human early development, we examined the evolution and function of NANOGP1, a tandem duplicate of the transcription factor NANOG. We found that NANOGP1 and NANOG have overlapping but distinct expression profiles, with high NANOGP1 expression restricted to early epiblast cells and naïve-state pluripotent stem cells. Sequence analysis and epitope-tagging revealed that NANOGP1 is protein coding with an intact homeobox domain. The duplication that created NANOGP1 occurred earlier in primate evolution than previously thought and has been retained only in great apes, whereas Old World monkeys have disabled the gene in different ways, including homeodomain point mutations. NANOGP1 is a strong inducer of naïve pluripotency; however, unlike NANOG, it is not required to maintain the undifferentiated status of human naïve pluripotent cells. By retaining expression, sequence and partial functional conservation with its ancestral copy, NANOGP1 exemplifies how gene duplication and subfunctionalisation can contribute to transcription factor activity in human pluripotency and development.
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Affiliation(s)
| | - Gökberk Alagöz
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Joshua Wright
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Asif Nakhuda
- Gene Targeting Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Christel Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
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5
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von Meyenn F, Berrens RV, Andrews S, Santos F, Collier AJ, Krueger F, Osorno R, Dean W, Rugg-Gunn PJ, Reik W. Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification. Dev Cell 2022; 57:2669-2671. [DOI: 10.1016/j.devcel.2022.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Rostovskaya M, Andrews S, Reik W, Rugg-Gunn PJ. Amniogenesis occurs in two independent waves in primates. Cell Stem Cell 2022; 29:744-759.e6. [PMID: 35439430 DOI: 10.1016/j.stem.2022.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/16/2022] [Accepted: 03/24/2022] [Indexed: 01/28/2023]
Abstract
In primates, the amnion emerges through cavitation of the epiblast during implantation, whereas in other species it does so later at gastrulation by the folding of the ectoderm. How the mechanisms of amniogenesis diversified during evolution remains unknown. Unexpectedly, single-cell analysis of primate embryos uncovered two transcriptionally and temporally distinct amniogenesis waves. To study this, we employed the naive-to-primed transition of human pluripotent stem cells (hPSCs) to model peri-implantation epiblast development. Partially primed hPSCs transiently gained the ability to differentiate into cavitating epithelium that transcriptionally and morphologically matched the early amnion, whereas fully primed hPSCs produced cells resembling the late amnion instead, thus recapitulating the two independent differentiation waves. The early wave follows a trophectoderm-like pathway and encompasses cavitation, whereas the late wave resembles an ectoderm-like route during gastrulation. The discovery of two independent waves explains how amniogenesis through cavitation could emerge during evolution via duplication of the pre-existing trophectoderm program.
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Affiliation(s)
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Altoslabs Cambridge Institute, Cambridge CB21 6GP, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1QR, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome-MRC Stem Cell Institute, Cambridge CB2 0AW, UK.
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome-MRC Stem Cell Institute, Cambridge CB2 0AW, UK.
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7
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Collier AJ, Bendall A, Fabian C, Malcolm AA, Tilgner K, Semprich CI, Wojdyla K, Nisi PS, Kishore K, Roamio Franklin VN, Mirshekar-Syahkal B, D’Santos C, Plath K, Yusa K, Rugg-Gunn PJ. Genome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human naïve pluripotent cell reprogramming. Sci Adv 2022; 8:eabk0013. [PMID: 35333572 PMCID: PMC8956265 DOI: 10.1126/sciadv.abk0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Uncovering the mechanisms that establish naïve pluripotency in humans is crucial for the future applications of pluripotent stem cells including the production of human blastoids. However, the regulatory pathways that control the establishment of naïve pluripotency by reprogramming are largely unknown. Here, we use genome-wide screening to identify essential regulators as well as major impediments of human primed to naïve pluripotent stem cell reprogramming. We discover that factors essential for cell state change do not typically undergo changes at the level of gene expression but rather are repurposed with new functions. Mechanistically, we establish that the variant Polycomb complex PRC1.3 and PRDM14 jointly repress developmental and gene regulatory factors to ensure naïve cell reprogramming. In addition, small-molecule inhibitors of reprogramming impediments improve naïve cell reprogramming beyond current methods. Collectively, this work defines the principles controlling the establishment of human naïve pluripotency and also provides new insights into mechanisms that destabilize and reconfigure cell identity during cell state transitions.
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Affiliation(s)
- Amanda J. Collier
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | - Andrew A. Malcolm
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Katarzyna Tilgner
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Clive D’Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kosuke Yusa
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Stem Cell Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Peter J. Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
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8
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Abstract
Human pluripotent stem cells exist in naïve and primed states that recapitulate the distinct molecular and cellular properties of pre- and post-implantation epiblast cells, respectively. Naïve pluripotent stem cells can be captured directly from blastocysts but, more commonly, the cells are reprogrammed from primed cells in a process called "resetting". Several methods to achieve resetting have been described. Chemical resetting of primed cells to a naïve pluripotent state is one such method and has come to the forefront as a simple, efficient, and transgene-free method to induce naïve pluripotency. The process involves the transient application of a histone deacetylase inhibitor to initiate resetting, followed by the emergence of nascent naïve pluripotent stem cells in supportive conditions, and finally the stabilization and expansion of naïve pluripotent stem cell cultures. Here, a detailed protocol is provided for chemical resetting starting from plating primed cells until a stable culture of naïve pluripotent stem cells is established.
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9
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Rugg-Gunn PJ. Flow Cytometry Analysis of Cell-Surface Markers to Identify Human Naïve Pluripotent Stem Cells. Methods Mol Biol 2022; 2416:257-265. [PMID: 34870841 DOI: 10.1007/978-1-0716-1908-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-surface proteins provide excellent biomarkers to identify specific cell types and resolve heterogeneous cell populations. The analysis of cell-surface proteins by flow cytometry produces robust and quantitative information with single-cell resolution, and allows live target cells to be purified and characterized or re-cultured. Studies using antibody screens, proteomics, and candidate analysis have identified a comprehensive set of proteins that are expressed on the surface of naïve and primed human pluripotent stem cells. These findings have led to the development of suitable protein markers and antibodies to accurately distinguish between these two cell types. Here, a detailed protocol is provided that uses multi-color flow cytometry to analyze cell-surface protein expression in naïve and primed human pluripotent stem cells. This method enables the unambiguous identification of pluripotent cell types and the opportunity to sort target cells including during cell state transitions. The protocol can be combined to additionally investigate the expression of reporter genes and other informative features, such as DNA content.
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10
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Tomimatsu K, Bihary D, Olan I, Parry AJ, Schoenfelder S, Chan ASL, Slater GSC, Ito Y, Rugg-Gunn PJ, Kirschner K, Bermejo-Rodriguez C, Seko T, Kugoh H, Shiraishi K, Sayama K, Kimura H, Fraser P, Narita M, Samarajiwa SA, Narita M. Locus-specific induction of gene expression from heterochromatin loci during cellular senescence. Nat Aging 2022; 2:31-45. [PMID: 37118356 DOI: 10.1038/s43587-021-00147-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/04/2021] [Indexed: 04/30/2023]
Abstract
Senescence is a fate-determined state, accompanied by reorganization of heterochromatin. Although lineage-appropriate genes can be temporarily repressed through facultative heterochromatin, stable silencing of lineage-inappropriate genes often involves the constitutive heterochromatic mark, histone H3 lysine 9 trimethylation (H3K9me3). The fate of these heterochromatic genes during senescence is unclear. In the present study, we show that a small number of lineage-inappropriate genes, exemplified by the LCE2 skin genes, are derepressed during senescence from H3K9me3 regions in fibroblasts. DNA FISH experiments reveal that these gene loci, which are condensed at the nuclear periphery in proliferative cells, are decompacted during senescence. Decompaction of the locus is not sufficient for LCE2 expression, which requires p53 and C/EBPβ signaling. NLRP3, which is predominantly expressed in macrophages from an open topologically associated domain (TAD), is also derepressed in senescent fibroblasts due to the local disruption of the H3K9me3-rich TAD that contains it. NLRP3 has been implicated in the amplification of inflammatory cytokine signaling in senescence and aging, highlighting the functional relevance of gene induction from 'permissive' H3K9me3 regions in senescent cells.
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Affiliation(s)
- Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Shiga University of Medical Science, Shiga, Japan
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Dóra Bihary
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Ioana Olan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Aled J Parry
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Stefan Schoenfelder
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Adelyne S L Chan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Guy St C Slater
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- International University of Health and Welfare, Tochigi, Japan
| | | | - Kristina Kirschner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Institute for Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Camino Bermejo-Rodriguez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Tomomi Seko
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
- Chromosome Engineering Research Center, Tottori University, Yonago, Japan
| | - Hiroyuki Kugoh
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
- Chromosome Engineering Research Center, Tottori University, Yonago, Japan
| | - Ken Shiraishi
- Department of Dermatology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Koji Sayama
- Department of Dermatology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Hiroshi Kimura
- Tokyo Tech World Research Hub Initiative and Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Masako Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Shamith A Samarajiwa
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK.
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Tokyo Tech World Research Hub Initiative and Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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11
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Osnato A, Brown S, Krueger C, Andrews S, Collier AJ, Nakanoh S, Quiroga Londoño M, Wesley BT, Muraro D, Brumm AS, Niakan KK, Vallier L, Ortmann D, Rugg-Gunn PJ. TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells. eLife 2021; 10:e67259. [PMID: 34463252 PMCID: PMC8410071 DOI: 10.7554/elife.67259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022] Open
Abstract
The signalling pathways that maintain primed human pluripotent stem cells (hPSCs) have been well characterised, revealing a critical role for TGFβ/Activin/Nodal signalling. In contrast, the signalling requirements of naive human pluripotency have not been fully established. Here, we demonstrate that TGFβ signalling is required to maintain naive hPSCs. The downstream effector proteins - SMAD2/3 - bind common sites in naive and primed hPSCs, including shared pluripotency genes. In naive hPSCs, SMAD2/3 additionally bind to active regulatory regions near to naive pluripotency genes. Inhibiting TGFβ signalling in naive hPSCs causes the downregulation of SMAD2/3-target genes and pluripotency exit. Single-cell analyses reveal that naive and primed hPSCs follow different transcriptional trajectories after inhibition of TGFβ signalling. Primed hPSCs differentiate into neuroectoderm cells, whereas naive hPSCs transition into trophectoderm. These results establish that there is a continuum for TGFβ pathway function in human pluripotency spanning a developmental window from naive to primed states.
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Affiliation(s)
- Anna Osnato
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Stephanie Brown
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Christel Krueger
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Amanda J Collier
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
| | - Shota Nakanoh
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Division of Embryology, National Institute for Basic BiologyOkazakiJapan
| | - Mariana Quiroga Londoño
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Brandon T Wesley
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniele Muraro
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, HinxtonCambridgeUnited Kingdom
| | - A Sophie Brumm
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
| | - Ludovic Vallier
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniel Ortmann
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Peter J Rugg-Gunn
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
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12
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Chovanec P, Collier AJ, Krueger C, Várnai C, Semprich CI, Schoenfelder S, Corcoran AE, Rugg-Gunn PJ. Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states. Nat Commun 2021; 12:2098. [PMID: 33828098 PMCID: PMC8026613 DOI: 10.1038/s41467-021-22201-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 03/05/2021] [Indexed: 01/10/2023] Open
Abstract
The transition from naive to primed pluripotency is accompanied by an extensive reorganisation of transcriptional and epigenetic programmes. However, the role of transcriptional enhancers and three-dimensional chromatin organisation in coordinating these developmental programmes remains incompletely understood. Here, we generate a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells, and develop a network-graph approach to examine the atlas at multiple spatial scales. We uncover highly connected promoter hubs that change substantially in interaction frequency and in transcriptional co-regulation between pluripotent states. Small hubs frequently merge to form larger networks in primed cells, often linked by newly-formed Polycomb-associated interactions. We identify widespread state-specific differences in enhancer activity and interactivity that correspond with an extensive reconfiguration of OCT4, SOX2 and NANOG binding and target gene expression. These findings provide multilayered insights into the chromatin-based gene regulatory control of human pluripotent states.
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Affiliation(s)
- Peter Chovanec
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | | | - Stefan Schoenfelder
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Anne E Corcoran
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
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13
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Ortmann D, Brown S, Czechanski A, Aydin S, Muraro D, Huang Y, Tomaz RA, Osnato A, Canu G, Wesley BT, Skelly DA, Stegle O, Choi T, Churchill GA, Baker CL, Rugg-Gunn PJ, Munger SC, Reinholdt LG, Vallier L. Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation. Cell Stem Cell 2020; 27:470-481.e6. [PMID: 32795399 PMCID: PMC7487768 DOI: 10.1016/j.stem.2020.07.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/10/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022]
Abstract
Variability among pluripotent stem cell (PSC) lines is a prevailing issue that hampers not only experimental reproducibility but also large-scale applications and personalized cell-based therapy. This variability could result from epigenetic and genetic factors that influence stem cell behavior. Naive culture conditions minimize epigenetic fluctuation, potentially overcoming differences in PSC line differentiation potential. Here we derived PSCs from distinct mouse strains under naive conditions and show that lines from distinct genetic backgrounds have divergent differentiation capacity, confirming a major role for genetics in PSC phenotypic variability. This is explained in part through inconsistent activity of extra-cellular signaling, including the Wnt pathway, which is modulated by specific genetic variants. Overall, this study shows that genetic background plays a dominant role in driving phenotypic variability of PSCs.
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Affiliation(s)
- Daniel Ortmann
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK.
| | - Stephanie Brown
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | | | | | - Daniele Muraro
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yuanhua Huang
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rute A Tomaz
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Anna Osnato
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Giovanni Canu
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Brandon T Wesley
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | | | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Ted Choi
- Jackson Laboratory, Bar Harbor, ME, USA
| | | | | | - Peter J Rugg-Gunn
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Ludovic Vallier
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK.
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14
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Wojdyla K, Collier AJ, Fabian C, Nisi PS, Biggins L, Oxley D, Rugg-Gunn PJ. Cell-Surface Proteomics Identifies Differences in Signaling and Adhesion Protein Expression between Naive and Primed Human Pluripotent Stem Cells. Stem Cell Reports 2020; 14:972-988. [PMID: 32302559 PMCID: PMC7220956 DOI: 10.1016/j.stemcr.2020.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified over 1,700 plasma membrane proteins, including those involved in cell adhesion, signaling, and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signaling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signaling pathway activity and has identified new markers to define human pluripotent states.
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Affiliation(s)
- Katarzyna Wojdyla
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Mass Spectrometry Facility, The Babraham Institute, Cambridge, UK
| | | | - Charlene Fabian
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Paola S Nisi
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Laura Biggins
- Bioinformatics Group, The Babraham Institute, Cambridge, UK
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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15
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Goodwin J, Laslett AL, Rugg-Gunn PJ. The application of cell surface markers to demarcate distinct human pluripotent states. Exp Cell Res 2020; 387:111749. [PMID: 31790696 PMCID: PMC6983944 DOI: 10.1016/j.yexcr.2019.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 01/24/2023]
Abstract
Recent advances in human pluripotent stem cell (hPSC) research have uncovered different subpopulations within stem cell cultures and have captured a range of pluripotent states that hold distinct molecular and functional properties. At the two ends of the pluripotency spectrum are naïve and primed hPSC, whereby naïve hPSC grown in stringent conditions recapitulate features of the preimplantation human embryo, and the conventionally grown primed hPSC align closer to the early postimplantation embryo. Investigating these cell types will help to define the mechanisms that control early development and should provide new insights into stem cell properties such as cell identity, differentiation and reprogramming. Monitoring cell surface marker expression provides a valuable approach to resolve complex cell populations, to directly compare between cell types, and to isolate viable cells for functional experiments. This review discusses the discovery and applications of cell surface markers to study human pluripotent cell types with a particular focus on the transitions between naïve and primed states. Highlighted areas for future study include the potential functions for the identified cell surface proteins in pluripotency, the production of new high-quality monoclonal antibodies to naïve-specific protein epitopes and the use of cell surface markers to characterise subpopulations within pluripotent states.
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Affiliation(s)
- Jacob Goodwin
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Andrew L Laslett
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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16
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Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Xie W, Krueger F, Göttgens B, Rugg-Gunn PJ, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature 2019; 576:487-491. [PMID: 31827285 PMCID: PMC6924995 DOI: 10.1038/s41586-019-1825-8] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 10/22/2019] [Indexed: 12/28/2022]
Abstract
Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with major transcriptional changes1-5. Global epigenetic reprogramming accompanies these changes6-8, but the role of the epigenome in regulating early cell-fate choice remains unresolved, and the coordination between different molecular layers is unclear. Here we describe a single-cell multi-omics map of chromatin accessibility, DNA methylation and RNA expression during the onset of gastrulation in mouse embryos. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements at enhancer marks, driven by ten-eleven translocation (TET)-mediated demethylation and a concomitant increase of accessibility. By contrast, the methylation and accessibility landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or remodelled before cell-fate decisions, providing the molecular framework for a hierarchical emergence of the primary germ layers.
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Affiliation(s)
| | | | | | | | | | - Chantriolnt-Andreas Kapourani
- School of Informatics, University of Edinburgh, Edinburgh, UK
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ivan Imaz-Rosshandler
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Tim Lohoff
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Yunlong Xiang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China
| | - Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Florian Buettner
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | | | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Wendy Dean
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Oliver Stegle
- European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - John C Marioni
- European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
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17
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Novo CL, Javierre BM, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJ. Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition. Cell Rep 2019. [PMID: 29514091 PMCID: PMC5863031 DOI: 10.1016/j.celrep.2018.02.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs). We found that SEs form complex, spatial networks in which individual SEs contact multiple promoters, and a rewiring of promoter-SE interactions occurs between pluripotent states. We also show that long-range promoter-SE interactions are more prevalent in ESCs than in epiblast stem cells (EpiSCs) or Nanog-deficient ESCs. We conclude that SEs form cell-type-specific interaction networks that are partly dependent on core transcription factors, thereby providing insights into the gene regulatory organization of pluripotent cells. Promoter-capture Hi-C identifies 3D interactions in mouse pluripotent cells Super-enhancers (SEs) form complex spatial networks contacting multiple promoters Rewiring of promoter-SE interactions between ESC and EpiSC pluripotent states Long-range SE interactions are a hallmark of mouse ESCs
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Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Steven W Wingett
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | | | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
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18
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Choy MK, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P, Keavney BD. Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks. Nat Commun 2018; 9:2526. [PMID: 29955040 PMCID: PMC6023870 DOI: 10.1038/s41467-018-04931-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 05/29/2018] [Indexed: 12/21/2022] Open
Abstract
Long-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression quantitative trait loci (eQTLs) in cardiac left ventricular tissue; captures the dynamic process of genome reorganisation after hESC-CM differentiation; overlaps genome-wide association study (GWAS) regions associated with heart rate; and identifies new candidate genes in such regions. These findings indicate that regulatory elements in hESC-CMs identified by our approach control gene expression involved in ventricular conduction and rhythm of the heart. The study of promoter interactions in other hESC-derived cell types may be of utility in functional investigation of GWAS-associated regions.
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Affiliation(s)
- Mun-Kit Choy
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK.
| | - Biola M Javierre
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias I Pujol, Badalona, 08916, Barcelona, Spain
| | - Simon G Williams
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Stephanie L Baross
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Yingjuan Liu
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Chris Wallace
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Paula Freire-Pritchett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
- Department of Biological Science, Florida State University, Tallahassee, 32306, FL, USA.
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK.
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19
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Lupo G, Nisi PS, Esteve P, Paul YL, Novo CL, Sidders B, Khan MA, Biagioni S, Liu HK, Bovolenta P, Cacci E, Rugg-Gunn PJ. Molecular profiling of aged neural progenitors identifies Dbx2 as a candidate regulator of age-associated neurogenic decline. Aging Cell 2018; 17:e12745. [PMID: 29504228 PMCID: PMC5946077 DOI: 10.1111/acel.12745] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2018] [Indexed: 12/22/2022] Open
Abstract
Adult neurogenesis declines with aging due to the depletion and functional impairment of neural stem/progenitor cells (NSPCs). An improved understanding of the underlying mechanisms that drive age‐associated neurogenic deficiency could lead to the development of strategies to alleviate cognitive impairment and facilitate neuroregeneration. An essential step towards this aim is to investigate the molecular changes that occur in NSPC aging on a genomewide scale. In this study, we compare the transcriptional, histone methylation and DNA methylation signatures of NSPCs derived from the subventricular zone (SVZ) of young adult (3 months old) and aged (18 months old) mice. Surprisingly, the transcriptional and epigenomic profiles of SVZ‐derived NSPCs are largely unchanged in aged cells. Despite the global similarities, we detect robust age‐dependent changes at several hundred genes and regulatory elements, thereby identifying putative regulators of neurogenic decline. Within this list, the homeobox gene Dbx2 is upregulated in vitro and in vivo, and its promoter region has altered histone and DNA methylation levels, in aged NSPCs. Using functional in vitro assays, we show that elevated Dbx2 expression in young adult NSPCs promotes age‐related phenotypes, including the reduced proliferation of NSPC cultures and the altered transcript levels of age‐associated regulators of NSPC proliferation and differentiation. Depleting Dbx2 in aged NSPCs caused the reverse gene expression changes. Taken together, these results provide new insights into the molecular programmes that are affected during mouse NSPC aging, and uncover a new functional role for Dbx2 in promoting age‐related neurogenic decline.
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Affiliation(s)
- Giuseppe Lupo
- Department of Chemistry; Sapienza University of Rome; Rome Italy
| | - Paola S. Nisi
- Department of Biology and Biotechnology “C. Darwin”; Sapienza University of Rome; Rome Italy
| | - Pilar Esteve
- Centro de Biologia Molecular “Severo Ochoa”; Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid; Madrid Spain
- CIBER of Rare Diseases; ISCIII; Madrid Spain
| | - Yu-Lee Paul
- Epigenetics Programme; The Babraham Institute; Cambridge UK
| | | | - Ben Sidders
- Bioscience; Oncology; IMED Biotech Unit; AstraZeneca; Cambridge UK
| | - Muhammad A. Khan
- Division of Molecular Neurogenetics; German Cancer Research Centre (DKFZ); DKFZ-ZMBH Alliance; Heidelberg Germany
| | - Stefano Biagioni
- Department of Biology and Biotechnology “C. Darwin”; Sapienza University of Rome; Rome Italy
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics; German Cancer Research Centre (DKFZ); DKFZ-ZMBH Alliance; Heidelberg Germany
| | - Paola Bovolenta
- Centro de Biologia Molecular “Severo Ochoa”; Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid; Madrid Spain
- CIBER of Rare Diseases; ISCIII; Madrid Spain
| | - Emanuele Cacci
- Department of Biology and Biotechnology “C. Darwin”; Sapienza University of Rome; Rome Italy
| | - Peter J. Rugg-Gunn
- Epigenetics Programme; The Babraham Institute; Cambridge UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute; University of Cambridge; Cambridge UK
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20
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Andrews PW, Ben-David U, Benvenisty N, Coffey P, Eggan K, Knowles BB, Nagy A, Pera M, Reubinoff B, Rugg-Gunn PJ, Stacey GN. Assessing the Safety of Human Pluripotent Stem Cells and Their Derivatives for Clinical Applications. Stem Cell Reports 2018; 9:1-4. [PMID: 28700896 DOI: 10.1016/j.stemcr.2017.05.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 01/09/2023] Open
Abstract
Pluripotent stem cells may acquire genetic and epigenetic variants during culture following their derivation. At a conference organized by the International Stem Cell Initiative, and held at The Jackson Laboratory, Bar Harbor, Maine, October 2016, participants discussed how the appearance of such variants can be monitored and minimized and, crucially, how their significance for the safety of therapeutic applications of these cells can be assessed. A strong recommendation from the meeting was that an international advisory group should be set up to review the genetic and epigenetic changes observed in human pluripotent stem cell lines and establish a framework for evaluating the risks that they may pose for clinical use.
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Affiliation(s)
- Peter W Andrews
- Department of Biomedical Science, Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK.
| | | | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Peter Coffey
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Neuroscience Research Institute, University of California, Santa Barbara, CA 93117, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Barbara B Knowles
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Siriraj Center of Excellence for Stem Cell Research, Mahidol University, Bangkok 10700, Thailand
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada; Monash University, ARMI, Melbourne, Victoria 3800, Australia
| | - Martin Pera
- Stem Cells Australia, Melbourne Brain Centre, The University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Anatomy and Neurosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Florey Neuroscience & Mental Health Institute, Melbourne, VIC 3052, Australia; Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
| | - Benjamin Reubinoff
- Department of Obstetrics and Gynecology, Hadassah Human Embryonic Stem Cells Research Center, The Goldyne-Savad Institute of Gene Therapy, Hadassah-Hebrew University Hospital, Jerusalem 91120, Israel
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Glyn N Stacey
- UK Stem Cell Bank, Advanced Therapies Division, NIBSC-MHRA, London EN6 3QG, UK
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21
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Collier AJ, Rugg-Gunn PJ. Identifying Human Naïve Pluripotent Stem Cells - Evaluating State-Specific Reporter Lines and Cell-Surface Markers. Bioessays 2018; 40:e1700239. [PMID: 29574793 DOI: 10.1002/bies.201700239] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/11/2018] [Indexed: 12/11/2022]
Abstract
Recent reports that human pluripotent stem cells can be captured in a spectrum of states with variable properties has prompted a re-evaluation of how pluripotency is acquired and stabilised. The latest additions to the stem cell hierarchy open up opportunities for understanding human development, reprogramming, and cell state transitions more generally. Many of the new cell lines have been collectively termed 'naïve' human pluripotent stem cells to distinguish them from the conventional 'primed' cells. Here, several transcriptional and epigenetic hallmarks of human pluripotent states in the recently described cell lines are reviewed and evaluated. Methods to derive and identify human naïve pluripotent stem cells are also discussed, with a focus on the uses and future developments of state-specific reporter cell lines and cell-surface proteins. Finally, opportunities and uncertainties in naïve stem cell biology are highlighted, and the current limitations of human naïve pluripotent stem cells considered, particularly in the context of differentiation.
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Affiliation(s)
- Amanda J Collier
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Collinson A, Collier AJ, Morgan NP, Sienerth AR, Chandra T, Andrews S, Rugg-Gunn PJ. Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells. Cell Rep 2017; 17:2700-2714. [PMID: 27926872 PMCID: PMC5177603 DOI: 10.1016/j.celrep.2016.11.032] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/11/2016] [Accepted: 11/09/2016] [Indexed: 12/11/2022] Open
Abstract
Through the histone methyltransferase EZH2, the Polycomb complex PRC2 mediates H3K27me3 and is associated with transcriptional repression. PRC2 regulates cell-fate decisions in model organisms; however, its role in regulating cell differentiation during human embryogenesis is unknown. Here, we report the characterization of EZH2-deficient human embryonic stem cells (hESCs). H3K27me3 was lost upon EZH2 deletion, identifying an essential requirement for EZH2 in methylating H3K27 in hESCs, in contrast to its non-essential role in mouse ESCs. Developmental regulators were derepressed in EZH2-deficient hESCs, and single-cell analysis revealed an unexpected acquisition of lineage-restricted transcriptional programs. EZH2-deficient hESCs show strongly reduced self-renewal and proliferation, thereby identifying a more severe phenotype compared to mouse ESCs. EZH2-deficient hESCs can initiate differentiation toward developmental lineages; however, they cannot fully differentiate into mature specialized tissues. Thus, EZH2 is required for stable ESC self-renewal, regulation of transcriptional programs, and for late-stage differentiation in this model of early human development. Comprehensive examination of EZH2 function in human ESC regulation EZH2 deficiency causes lineage-restricted derepression of developmental regulators More severe self-renewal and growth defects in EZH2-deficient hESCs than in mESCs EZH2-deficient hESCs can differentiate to early lineages but cannot form mature tissues
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Affiliation(s)
- Adam Collinson
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Amanda J Collier
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Natasha P Morgan
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Arnold R Sienerth
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Tamir Chandra
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.
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24
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Carucci N, Cacci E, Nisi PS, Licursi V, Paul YL, Biagioni S, Negri R, Rugg-Gunn PJ, Lupo G. Transcriptional response of Hoxb genes to retinoid signalling is regionally restricted along the neural tube rostrocaudal axis. R Soc Open Sci 2017; 4:160913. [PMID: 28484611 PMCID: PMC5414248 DOI: 10.1098/rsos.160913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
During vertebrate neural development, positional information is largely specified by extracellular morphogens. Their distribution, however, is very dynamic due to the multiple roles played by the same signals in the developing and adult neural tissue. This suggests that neural progenitors are able to modify their competence to respond to morphogen signalling and autonomously maintain positional identities after their initial specification. In this work, we take advantage of in vitro culture systems of mouse neural stem/progenitor cells (NSPCs) to show that NSPCs isolated from rostral or caudal regions of the mouse neural tube are differentially responsive to retinoic acid (RA), a pivotal morphogen for the specification of posterior neural fates. Hoxb genes are among the best known RA direct targets in the neural tissue, yet we found that RA could promote their transcription only in caudal but not in rostral NSPCs. Correlating with these effects, key RA-responsive regulatory regions in the Hoxb cluster displayed opposite enrichment of activating or repressing histone marks in rostral and caudal NSPCs. Finally, RA was able to strengthen Hoxb chromatin activation in caudal NSPCs, but was ineffective on the repressed Hoxb chromatin of rostral NSPCs. These results suggest that the response of NSPCs to morphogen signalling across the rostrocaudal axis of the neural tube may be gated by the epigenetic configuration of target patterning genes, allowing long-term maintenance of intrinsic positional values in spite of continuously changing extrinsic signals.
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Affiliation(s)
- Nicoletta Carucci
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Emanuele Cacci
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Paola S. Nisi
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Yu-Lee Paul
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Stefano Biagioni
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
- Istituto Pasteur— Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Giuseppe Lupo
- Istituto Pasteur— Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
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25
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Freire-Pritchett P, Schoenfelder S, Várnai C, Wingett SW, Cairns J, Collier AJ, García-Vílchez R, Furlan-Magaril M, Osborne CS, Fraser P, Rugg-Gunn PJ, Spivakov M. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. eLife 2017; 6:21926. [PMID: 28332981 PMCID: PMC5407860 DOI: 10.7554/elife.21926] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/22/2017] [Indexed: 12/19/2022] Open
Abstract
Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells. DOI:http://dx.doi.org/10.7554/eLife.21926.001 Virtually every cell in the body contains the same set of DNA, which encodes thousands of genes. The activities of these genes vary between different types of cells and at different points in time. As a result, our DNA contains a complex array of molecular switches that instruct genes to switch on and off at the right time and in the right cells. These molecular switches, termed regulatory elements, are often a long way away from the genes that they control, and this can make it difficult to find out which switch controls which genes. DNA is made up of several different building blocks known as bases and the order of these bases encodes specific information about the gene. Every human cell contains approximately two meters of DNA, which is highly folded in the cell nucleus. This three-dimensional folding allows regions that are far apart on the DNA thread to physically contact each other. To reach the genes they control, regulatory elements form loops on the DNA that are near-impossible to predict from looking at the sequence of bases alone. Mapping the locations of these loops can reveal the hidden circuitry within our DNA and help us to understand how unwanted changes (mutations) within regulatory elements may cause disease. Freire-Pritchett, Schoenfelder et al. set out to reveal how loops between genes and their regulatory elements change as the stem cells specialise into immature brain cells. The experiments show that the pattern of DNA loops is extensively altered after the stem cells specialise into brain cells, that is, some loops are lost and new ones form. Furthermore, the regulatory elements themselves were often toggled between “on” and “off” states. These two processes tend to occur together, so that new loops are formed at the same time as the switch is activated. Freire-Pritchett, Schoenfelder et al. also show that individual genes are often connected to many different regulatory elements. The next step is to understand how these multiple connections work together to coordinate gene activity, and whether this information could be used to control how stem cells specialise. This knowledge may lead to the development of stem cell-based therapies for stroke, Parkinson’s disease and other conditions. DOI:http://dx.doi.org/10.7554/eLife.21926.002
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Affiliation(s)
| | | | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Steven W Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Amanda J Collier
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Cameron S Osborne
- Department of Genetics and Molecular Medicine, King's College London School of Medicine, London, United Kingdom
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
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26
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Vallot C, Patrat C, Collier AJ, Huret C, Casanova M, Liyakat Ali TM, Tosolini M, Frydman N, Heard E, Rugg-Gunn PJ, Rougeulle C. XACT Noncoding RNA Competes with XIST in the Control of X Chromosome Activity during Human Early Development. Cell Stem Cell 2016; 20:102-111. [PMID: 27989768 PMCID: PMC5222720 DOI: 10.1016/j.stem.2016.10.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/23/2016] [Accepted: 10/19/2016] [Indexed: 12/28/2022]
Abstract
Sex chromosome dosage compensation is essential in most metazoans, but the developmental timing and underlying mechanisms vary significantly, even among placental mammals. Here we identify human-specific mechanisms regulating X chromosome activity in early embryonic development. Single-cell RNA sequencing and imaging revealed co-activation and accumulation of the long noncoding RNAs (lncRNAs) XACT and XIST on active X chromosomes in both early human pre-implantation embryos and naive human embryonic stem cells. In these contexts, the XIST RNA adopts an unusual, highly dispersed organization, which may explain why it does not trigger X chromosome inactivation at this stage. Functional studies in transgenic mouse cells show that XACT influences XIST accumulation in cis. Our findings therefore suggest a mechanism involving antagonistic activity of XIST and XACT in controlling X chromosome activity in early human embryos, and they highlight the contribution of rapidly evolving lncRNAs to species-specific developmental mechanisms. XACT and XIST simultaneously coat active X chromosomes in human embryos Naive hESCs capture the pre-inactive state with XIST and XACT co-accumulation XIST adopts a dispersed configuration in pre-inactive cells in vitro and in vivo XACT prevents XIST accumulation in cis in a mouse heterologous system
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Affiliation(s)
- Céline Vallot
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, 75013 Paris, France.
| | - Catherine Patrat
- Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75005 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, 75018 Paris, France; Reproductive Biology Department, AP-HP, Bichat-Claude Bernard Hospital, 75018 Paris, France
| | - Amanda J Collier
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Christophe Huret
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, 75013 Paris, France
| | - Miguel Casanova
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, 75013 Paris, France
| | - Tharvesh M Liyakat Ali
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, 75013 Paris, France
| | - Matteo Tosolini
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, 75013 Paris, France
| | - Nelly Frydman
- Université Paris-Sud, Clamart 92140, France; Unit of Reproductive Biology, AP-HP, Hôpital Antoine Béclère, Clamart 92141, France
| | - Edith Heard
- Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75005 Paris, France
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Claire Rougeulle
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, 75013 Paris, France.
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27
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Novo CL, Tang C, Ahmed K, Djuric U, Fussner E, Mullin NP, Morgan NP, Hayre J, Sienerth AR, Elderkin S, Nishinakamura R, Chambers I, Ellis J, Bazett-Jones DP, Rugg-Gunn PJ. The pluripotency factor Nanog regulates pericentromeric heterochromatin organization in mouse embryonic stem cells. Genes Dev 2016; 30:1101-15. [PMID: 27125671 PMCID: PMC4863740 DOI: 10.1101/gad.275685.115] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022]
Abstract
Here, Novo et al. identify a new critical role for the transcription factor Nanog in maintaining an open heterochromatin state in pluripotent mouse embryonic stem cells and demonstrate that forced expression of Nanog is sufficient to remodel and decondense chromatin in more developmentally advanced mammalian cell types. This study delineates a direct connection between the pluripotency network and chromatin organization and shows that maintainence of an open heterochromatin architecture is highly regulated in embryonic stem cells. An open and decondensed chromatin organization is a defining property of pluripotency. Several epigenetic regulators have been implicated in maintaining an open chromatin organization, but how these processes are connected to the pluripotency network is unknown. Here, we identified a new role for the transcription factor NANOG as a key regulator connecting the pluripotency network with constitutive heterochromatin organization in mouse embryonic stem cells. Deletion of Nanog leads to chromatin compaction and the remodeling of heterochromatin domains. Forced expression of NANOG in epiblast stem cells is sufficient to decompact chromatin. NANOG associates with satellite repeats within heterochromatin domains, contributing to an architecture characterized by highly dispersed chromatin fibers, low levels of H3K9me3, and high major satellite transcription, and the strong transactivation domain of NANOG is required for this organization. The heterochromatin-associated protein SALL1 is a direct cofactor for NANOG, and loss of Sall1 recapitulates the Nanog-null phenotype, but the loss of Sall1 can be circumvented through direct recruitment of the NANOG transactivation domain to major satellites. These results establish a direct connection between the pluripotency network and chromatin organization and emphasize that maintaining an open heterochromatin architecture is a highly regulated process in embryonic stem cells.
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Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Calvin Tang
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Kashif Ahmed
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada
| | - Ugljesa Djuric
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Eden Fussner
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nicholas P Mullin
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - Natasha P Morgan
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Jasvinder Hayre
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Arnold R Sienerth
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, United Kingdom
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - James Ellis
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David P Bazett-Jones
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom
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28
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Abstract
Translating the vast amounts of genomic and epigenomic information accumulated on the linear genome into three-dimensional models of nuclear organization is a current major challenge. In response to this challenge, recent technological innovations based on chromosome conformation capture methods in combination with increasingly powerful functional approaches have revealed exciting insights into key aspects of genome regulation. These findings have led to an emerging model where the genome is folded and compartmentalized into highly conserved topological domains that are further divided into functional subdomains containing physical loops that bring cis-regulatory elements to close proximity. Targeted functional experiments, largely based on designable DNA-binding proteins, have begun to define the major architectural proteins required to establish and maintain appropriate genome regulation. Here, we focus on the accessible and well-characterized system of pluripotent cells to review the functional role of chromatin organization in regulating pluripotency, differentiation and reprogramming.
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29
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Rugg-Gunn PJ, Cox BJ, Lanner F, Sharma P, Ignatchenko V, McDonald ACH, Garner J, Gramolini AO, Rossant J, Kislinger T. Cell-surface proteomics identifies lineage-specific markers of embryo-derived stem cells. Dev Cell 2012; 22:887-901. [PMID: 22424930 PMCID: PMC3405530 DOI: 10.1016/j.devcel.2012.01.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 10/20/2011] [Accepted: 01/11/2012] [Indexed: 11/30/2022]
Abstract
The advent of reprogramming and its impact on stem cell biology has renewed interest in lineage restriction in mammalian embryos, the source of embryonic (ES), epiblast (EpiSC), trophoblast (TS), and extraembryonic endoderm (XEN) stem cell lineages. Isolation of specific cell types during stem cell differentiation and reprogramming, and also directly from embryos, is a major technical challenge because few cell-surface proteins are known that can distinguish each cell type. We provide a large-scale proteomic resource of cell-surface proteins for the four embryo-derived stem cell lines. We validated 27 antibodies against lineage-specific cell-surface markers, which enabled investigation of specific cell populations during ES-EpiSC reprogramming and ES-to-XEN differentiation. Identified markers also allowed prospective isolation and characterization of viable lineage progenitors from blastocysts by flow cytometry. These results provide a comprehensive stem cell proteomic resource and enable new approaches to interrogate the mechanisms that regulate cell fate specification.
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Affiliation(s)
- Peter J Rugg-Gunn
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, 555 University Avenue, Toronto, ON M5G 1X8, Canada
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30
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Abstract
Trophoblast cells are required for the growth and survival of the fetus during pregnancy, and failure to maintain appropriate trophoblast regulation is associated with placental insufficiencies and intrauterine growth restriction. Development of the trophoblast lineage is mediated by interactions between genetic and epigenetic factors. This review will focus on new insights that have been gained from analysis of mouse models into the epigenetic mechanisms that are required for the early establishment of the trophoblast lineage and for the development of specialized cell types of the fetal placenta. In particular, the importance of DNA methylation, 5-hydroxymethylcytosine and histone modifications in orchestrating trophoblast gene expression and functional outcome will be discussed. These insights are beginning to be extended towards human studies and initial results suggest that the causes and consequences of a variety of placental pathologies are related to epigenetic processes. Furthermore, the epigenetic landscape that regulates trophoblast cells seems to be particularly vulnerable to perturbation during development. This has major implications for diet and other environmental factors during pregnancy.
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Affiliation(s)
- Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK.
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31
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Rugg-Gunn PJ, Ferguson-Smith AC, Pedersen RA. Status of genomic imprinting in human embryonic stem cells as revealed by a large cohort of independently derived and maintained lines. Hum Mol Genet 2007; 16 Spec No. 2:R243-51. [PMID: 17911167 DOI: 10.1093/hmg/ddm245] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Investigation of the epigenetic stability of human embryonic stem cells (hESCs) is a crucial step for their use in cell-replacement therapies, as well as for assessing whether hESCs model epigenetic regulation in human pre-implantation cell types. To address these issues, we have examined the expression of imprinted genes in a previous study and more recently in 46 individual hESC lines as part of the International Stem Cell Initiative. Our results show that nearly all hESC lines examined possessed a substantial degree of epigenetic stability, despite differences in genetic background and in their derivation and initial propagation conditions. However, some hESCs did show loss of allele-specific expression, which could have implications for hESC differentiation and epigenetic stability (both in vitro and after clinical transplantation). A benefit of our and other recent studies of genomic imprinting in hESCs was the identification of imprinted genes that provide a useful indication of epigenetic stability. SNRPN, IPW and KCNQ1OT1 were highly stable and thus appeared insensitive to perturbation; in contrast, H19, IGF2 and MEG3 were more variable and thus could potentially provide a sensitive indication of epigenetic status. In this review, we examine the differences between imprinted genes in their susceptibility to perturbation and discuss the potential molecular basis for these differences. This examination provides insight into the regulation of genomic imprinting in hESCs and the corresponding peri-implantation stages of human development.
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Affiliation(s)
- Peter J Rugg-Gunn
- Department of Surgery and Cambridge Institute for Medical Research, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 OXY, UK.
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32
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Kim K, Ng K, Rugg-Gunn PJ, Shieh JH, Kirak O, Jaenisch R, Wakayama T, Moore MA, Pedersen RA, Daley GQ. Recombination signatures distinguish embryonic stem cells derived by parthenogenesis and somatic cell nuclear transfer. Cell Stem Cell 2007; 1:346-52. [PMID: 18371368 DOI: 10.1016/j.stem.2007.07.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/01/2007] [Accepted: 07/03/2007] [Indexed: 11/17/2022]
Abstract
Parthenogenesis and somatic cell nuclear transfer (SCNT) are two methods for deriving embryonic stem (ES) cells that are genetically matched to the oocyte donor or somatic cell donor, respectively. Using genome-wide single nucleotide polymorphism (SNP) analysis, we demonstrate distinct signatures of genetic recombination that distinguish parthenogenetic ES cells from those generated by SCNT. We applied SNP analysis to the human ES cell line SCNT-hES-1, previously claimed to have been derived by SCNT, and present evidence that it represents a human parthenogenetic ES cell line. Genome-wide SNP analysis represents a means to validate the genetic provenance of an ES cell line.
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Affiliation(s)
- Kitai Kim
- Division of Pediatric Hematology/Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115, USA
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33
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Abstract
In order to exploit the exceptional potential of human embryonic stem cells (hESCs) in cell-replacement therapies, the genetic and epigenetic factors controlling early human development must be better defined. Limitations in human embryonic material restrict the scale of studies that can be performed, and therefore an in vitro model in which to study epigenetic regulation in human preimplantation cell types would be desirable. HESCs could provide such a model, but since they are derived from a stage in mammalian development when the genome is undergoing global epigenetic remodelling, it is unclear whether their epigenetic status would be stable or subject to variation. Herein, we discuss recent work that examines allele-specific imprinted gene expression and methylation patterns, thereby demonstrating that hESCs maintain a substantial degree of epigenetic stability during culture. Therefore, we suggest that hESCs could provide a model for studying epigenetic regulation during the early stages of human cellular pluripotency and differentiation. Furthermore, we propose specific experiments using such a model to address important questions pertaining to epigenetic mechanisms of certain human disorders.
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Affiliation(s)
- Peter J Rugg-Gunn
- Department of Surgery, Cambridge Institute for Medical Research, UK.
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34
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Rugg-Gunn PJ, Ferguson-Smith AC, Pedersen RA. Epigenetic status of human embryonic stem cells. Nat Genet 2005; 37:585-7. [PMID: 15864307 DOI: 10.1038/ng1556] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Accepted: 04/01/2005] [Indexed: 11/08/2022]
Abstract
We examined the allele-specific expression of six imprinted genes and the methylation profiles of three imprinting control regions to assess the epigenetic status of human embryonic stem cells. We identified generally monoallelic gene expression and normal methylation patterns. During prolonged passage, one cell line became biallelic with respect to H19, but without loss of the gametic methylation imprint. These data argue for a substantial degree of epigenetic stability in human embryonic stem cells.
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Affiliation(s)
- Peter J Rugg-Gunn
- Department of Surgery, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK.
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35
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Abstract
It is widely recognized that gain- and loss-of-function approaches are essential for understanding the functions of specific genes, and such approaches would be particularly valuable in studies involving human embryonic stem (hES) cells. We describe a simple and efficient approach using lipofection to transfect hES cells, which enabled us to generate hES cell lines expressing naturally fluorescent green or red proteins without affecting cell pluripotency. We used these cell lines to establish a means of diminishing gene function using small interfering (si)RNAs, which were effective at knocking down gene expression in hES cells. We then demonstrated that stable expression of siRNA could knock down the expression of endogenous genes. Application of these gain- and loss-of-function approaches should have widespread use, not only in revealing the developmental roles of specific human genes, but also for their utility in modulating differentiation.
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Affiliation(s)
- Ludovic Vallier
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
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