1
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Chen Y, Li M, Wu Y. The occurrence and development of induced pluripotent stem cells. Front Genet 2024; 15:1389558. [PMID: 38699229 PMCID: PMC11063328 DOI: 10.3389/fgene.2024.1389558] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
The ectopic expression of four transcription factors, Oct3/4, Sox2, Klf4, and c-Myc (OSKM), known as "Yamanaka factors," can reprogram or stimulate the production of induced pluripotent stem cells (iPSCs). Although OSKM is still the gold standard, there are multiple ways to reprogram cells into iPSCs. In recent years, significant progress has been made in improving the efficiency of this technology. Ten years after the first report was published, human pluripotent stem cells have gradually been applied in clinical settings, including disease modeling, cell therapy, new drug development, and cell derivation. Here, we provide a review of the discovery of iPSCs and their applications in disease and development.
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Affiliation(s)
| | - Meng Li
- Department of Cardiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yanqing Wu
- Department of Cardiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
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2
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Wille CK, Neumann EN, Deshpande AJ, Sridharan R. DOT1L interaction partner AF10 controls patterning of H3K79 methylation and RNA polymerase II to maintain cell identity. Stem Cell Reports 2023; 18:2451-2463. [PMID: 37995701 PMCID: PMC10724070 DOI: 10.1016/j.stemcr.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/16/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Histone 3 lysine 79 methylation (H3K79me) is enriched on gene bodies proportional to gene expression levels and serves as a strong barrier for the reprogramming of somatic cells to induced pluripotent stem cells (iPSCs). DOT1L is the sole histone methyltransferase that deposits all three orders-mono (me1), di (me2), and tri (me3) methylation-at H3K79. Here, we leverage genetic and chemical approaches to parse the specific functions of orders of H3K79me in maintaining cell identity. DOT1L interacts with AF10 (Mllt10), which recognizes unmodified H3K27 and boosts H3K79me2/3 methylation. AF10 deletion evicts H3K79me2/3 and reorganizes H3K79me1 to the transcription start site to facilitate iPSC formation in the absence of steady-state transcriptional changes. Instead, AF10 loss redistributes RNA polymerase II to a uniquely pluripotent pattern at highly expressed, rapidly transcribed housekeeping genes. Taken together, we reveal a specific mechanism for H3K79me2/3 located at the gene body in reinforcing cell identity.
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Affiliation(s)
- Coral K Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Edwin N Neumann
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Aniruddha J Deshpande
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA.
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3
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Wille CK, Zhang X, Haws SA, Denu JM, Sridharan R. DOT1L is a barrier to histone acetylation during reprogramming to pluripotency. Sci Adv 2023; 9:eadf3980. [PMID: 37976354 PMCID: PMC10656071 DOI: 10.1126/sciadv.adf3980] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Embryonic stem cells (ESCs) have transcriptionally permissive chromatin enriched for gene activation-associated histone modifications. A striking exception is DOT1L-mediated H3K79 dimethylation (H3K79me2) that is considered a positive regulator of transcription. We find that ESCs are depleted for H3K79me2 at shared locations of enrichment with somatic cells, which are highly and ubiquitously expressed housekeeping genes, and have lower RNA polymerase II (RNAPII) at the transcription start site (TSS) despite greater nascent transcription. Inhibiting DOT1L increases the efficiency of reprogramming of somatic to induced pluripotent stem cells, enables an ESC-like RNAPII pattern at the TSS, and functionally compensates for enforced RNAPII pausing. DOT1L inhibition increases H3K27 methylation and RNAPII elongation-enhancing histone acetylation without changing the expression of the causal histone-modifying enzymes. Only the maintenance of elevated histone acetylation is essential for enhanced reprogramming and occurs at loci that are depleted for H3K79me2. Thus, DOT1L inhibition promotes the hyperacetylation and hypertranscription pluripotent properties.
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Affiliation(s)
- Coral K. Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Xiaoya Zhang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Haws
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
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4
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Abstract
DOT1-Like (DOT1L) is the sole methyltransferase of histone H3K79, a modification enriched mainly on the bodies of actively transcribing genes. DOT1L has been extensively studied in leukemia were some of the most frequent onco-fusion proteins contain portions of DOT1L associated factors that mislocalize H3K79 methylation and drive oncogenesis. However, the role of DOT1L in non-transformed, developmental contexts is less clear. Here we assess the known functional roles of DOT1L both in vitro cell culture and in vivo models of mammalian development. DOT1L is evicted during the 2-cell stage when cells are totipotent and massive epigenetic and transcriptional alterations occur. Embryonic stem cell lines that are derived from the blastocyst tolerate the loss of DOT1L, while the reduction of DOT1L protein levels or its catalytic activity greatly enhances somatic cell reprogramming to induced pluripotent stem cells. DOT1L knockout mice are embryonically lethal when organogenesis commences. We catalog the rapidly increasing studies of total and lineage specific knockout model systems that show that DOT1L is broadly required for differentiation. Reduced DOT1L activity is concomitant with increased developmental potential. Contrary to what would be expected of a modification that is associated with active transcription, loss of DOT1L activity results in more upregulated than downregulated genes. DOT1L also participates in various epigenetic networks that are both cell type and developmental stage specific. Taken together, the functions of DOT1L during development are pleiotropic and involve gene regulation at the locus specific and global levels.
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Affiliation(s)
- Coral K. Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Coral K. Wille, , Rupa Sridharan,
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Coral K. Wille, , Rupa Sridharan,
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5
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Wille CK, Sridharan R. DOT1L inhibition enhances pluripotency beyond acquisition of epithelial identity and without immediate suppression of the somatic transcriptome. Stem Cell Reports 2021; 17:384-396. [PMID: 34995500 PMCID: PMC8828533 DOI: 10.1016/j.stemcr.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/24/2020] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
Inhibiting the histone 3 lysine 79 (H3K79) methyltransferase, disruptor of telomeric silencing 1-like (DOT1L), increases the efficiency of reprogramming somatic cells to induced pluripotent stem cells (iPSCs). Here, we find that, despite the enrichment of H3K79 methylation on thousands of actively transcribed genes in somatic cells, DOT1L inhibition (DOT1Li) does not immediately cause the shutdown of the somatic transcriptional profile to enable transition to pluripotency. Contrary to the prevalent view, DOT1Li promotes iPSC generation beyond the mesenchymal to epithelial transition and even from already epithelial cell types. DOT1Li is most potent at the midpoint of reprogramming in part by repressing Nfix that persists at late stages of reprogramming. Importantly, regulation of single genes cannot substitute for DOT1Li, demonstrating that H3K79 methylation has pleiotropic effects in maintaining cell identity. DOT1L is a barrier of reprogramming, especially at the mid-point DOT1L inhibition increases pluripotency beyond MET DOT1L inhibition does not immediately suppress somatic expression Single factors cannot replace the pleiotropic effects of DOT1L inhibition
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Affiliation(s)
- Coral K Wille
- Wisconsin Institute for Discovery, University of Wisconsin, 330 North Orchard Street, Room 2118, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin, 330 North Orchard Street, Room 2118, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA.
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6
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Uğurlu-Çimen D, Odluyurt D, Sevinç K, Özkan-Küçük NE, Özçimen B, Demirtaş D, Enüstün E, Aztekin C, Philpott M, Oppermann U, Özlü N, Önder TT. AF10 (MLLT10) prevents somatic cell reprogramming through regulation of DOT1L-mediated H3K79 methylation. Epigenetics Chromatin 2021; 14:32. [PMID: 34215314 PMCID: PMC8254283 DOI: 10.1186/s13072-021-00406-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/01/2021] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background The histone H3 lysine 79 (H3K79) methyltransferase DOT1L is a key chromatin-based barrier to somatic cell reprogramming. However, the mechanisms by which DOT1L safeguards cell identity and somatic-specific transcriptional programs remain unknown. Results We employed a proteomic approach using proximity-based labeling to identify DOT1L-interacting proteins and investigated their effects on reprogramming. Among DOT1L interactors, suppression of AF10 (MLLT10) via RNA interference or CRISPR/Cas9, significantly increases reprogramming efficiency. In somatic cells and induced pluripotent stem cells (iPSCs) higher order H3K79 methylation is dependent on AF10 expression. In AF10 knock-out cells, re-expression wild-type AF10, but not a DOT1L binding-impaired mutant, rescues overall H3K79 methylation and reduces reprogramming efficiency. Transcriptomic analyses during reprogramming show that AF10 suppression results in downregulation of fibroblast-specific genes and accelerates the activation of pluripotency-associated genes. Conclusions Our findings establish AF10 as a novel barrier to reprogramming by regulating H3K79 methylation and thereby sheds light on the mechanism by which cell identity is maintained in somatic cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00406-7.
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Affiliation(s)
| | - Deniz Odluyurt
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Kenan Sevinç
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | | | - Burcu Özçimen
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Deniz Demirtaş
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Eray Enüstün
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Can Aztekin
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | | | - Udo Oppermann
- Botnar Research Centre, University of Oxford, Oxford, UK.,Centre for Medicine Discovery, University of Oxford, Oxford, UK
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
| | - Tamer T Önder
- School of Medicine, Koc University, Istanbul, 34450, Turkey.
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7
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Arabacı DH, Terzioğlu G, Bayırbaşı B, Önder TT. Going up the hill: chromatin-based barriers to epigenetic reprogramming. FEBS J 2020; 288:4798-4811. [PMID: 33190371 DOI: 10.1111/febs.15628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 08/20/2020] [Revised: 10/20/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022]
Abstract
The establishment and maintenance of cellular identity are crucial during development and tissue homeostasis. Epigenetic mechanisms based largely on DNA methylation and histone modifications serve to reinforce and safeguard differentiated cell states. Somatic cell nuclear transfer (SCNT) or transcription factors such as Oct4, Sox2, Klf4, c-MYC (OSKM) can erase somatic cell identity and reprogram the cells to a pluripotent state. In doing so, reprogramming must reset the chromatin landscape, silence somatic-specific gene expression programs, and, in their place, activate the pluripotency network. In this viewpoint, we consider the major chromatin-based barriers for reprogramming of somatic cells to pluripotency. Among these, repressive chromatin modifications such as DNA methylation, H3K9 methylation, variant histone deposition, and histone deacetylation generally block the activation of pluripotency genes. In contrast, active transcription-associated chromatin marks such as DOT1L-catalyzed H3K79 methylation, FACT-mediated histone turnover, active enhancer SUMOylation, and EP300/CBP bromodomain-mediated interactions act to maintain somatic-specific gene expression programs. We highlight how genetic or chemical inhibition of both types of barriers can enhance the kinetics and/or efficiency of reprogramming. Understanding the mechanisms by which these barriers function provides insight into how chromatin marks help maintain cell identity.
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Affiliation(s)
| | | | | | - Tamer T Önder
- School of Medicine, Koç University, Istanbul, Turkey
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8
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Tran KA, Pietrzak SJ, Zaidan NZ, Siahpirani AF, McCalla SG, Zhou AS, Iyer G, Roy S, Sridharan R. Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency. Cell Rep 2019; 27:1726-1741.e5. [PMID: 31067459 DOI: 10.1016/j.celrep.2019.04.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 03/04/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
Elucidating the mechanism of reprogramming is confounded by heterogeneity due to the low efficiency and differential kinetics of obtaining induced pluripotent stem cells (iPSCs) from somatic cells. Therefore, we increased the efficiency with a combination of epigenomic modifiers and signaling molecules and profiled the transcriptomes of individual reprogramming cells. Contrary to the established temporal order, somatic gene inactivation and upregulation of cell cycle, epithelial, and early pluripotency genes can be triggered independently such that any combination of these events can occur in single cells. Sustained co-expression of Epcam, Nanog, and Sox2 with other genes is required to progress toward iPSCs. Ehf, Phlda2, and translation initiation factor Eif4a1 play functional roles in robust iPSC generation. Using regulatory network analysis, we identify a critical role for signaling inhibition by 2i in repressing somatic expression and synergy between the epigenomic modifiers ascorbic acid and a Dot1L inhibitor for pluripotency gene activation.
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9
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Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J. Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2. EMBO J 2019; 39:e102591. [PMID: 31782544 DOI: 10.15252/embj.2019102591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 06/03/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
Developmental cell fate specification is a unidirectional process that can be reverted in response to injury or experimental reprogramming. Whether differentiation and de-differentiation trajectories intersect mechanistically is unclear. Here, we performed comparative screening in lineage-related mouse naïve embryonic stem cells (ESCs) and primed epiblast stem cells (EpiSCs), and identified the constitutively expressed zinc finger transcription factor (TF) Zfp281 as a bidirectional regulator of cell state interconversion. We showed that subtle chromatin binding changes in differentiated cells translate into activation of the histone H3 lysine 9 (H3K9) methyltransferase Ehmt1 and stabilization of the zinc finger TF Zic2 at enhancers and promoters. Genetic gain-of-function and loss-of-function experiments confirmed a critical role of Ehmt1 and Zic2 downstream of Zfp281 both in driving exit from the ESC state and in restricting reprogramming of EpiSCs. Our study reveals that cell type-invariant chromatin association of Zfp281 provides an interaction platform for remodeling the cis-regulatory network underlying cellular plasticity.
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Affiliation(s)
- Daniela Mayer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Melanie Rittirsch
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ilya Lukonin
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Maria Winzi
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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10
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Franz H, Villarreal A, Heidrich S, Videm P, Kilpert F, Mestres I, Calegari F, Backofen R, Manke T, Vogel T. DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex. Nucleic Acids Res 2019; 47:168-183. [PMID: 30329130 PMCID: PMC6326801 DOI: 10.1093/nar/gky953] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 07/24/2018] [Accepted: 10/04/2018] [Indexed: 01/01/2023] Open
Abstract
Cortical development is controlled by transcriptional programs, which are orchestrated by transcription factors. Yet, stable inheritance of spatio-temporal activity of factors influencing cell fate and localization in different layers is only partly understood. Here we find that deletion of Dot1l in the murine telencephalon leads to cortical layering defects, indicating DOT1L activity and chromatin methylation at H3K79 impact on the cell cycle, and influence transcriptional programs conferring upper layer identity in early progenitors. Specifically, DOT1L prevents premature differentiation by increasing expression of genes that regulate asymmetric cell division (Vangl2, Cenpj). Loss of DOT1L results in reduced numbers of progenitors expressing genes including SoxB1 gene family members. Loss of DOT1L also leads to altered cortical distribution of deep layer neurons that express either TBR1, CTIP2 or SOX5, and less activation of transcriptional programs that are characteristic for upper layer neurons (Satb2, Pou3f3, Cux2, SoxC family members). Data from three different mouse models suggest that DOT1L balances transcriptional programs necessary for proper neuronal composition and distribution in the six cortical layers. Furthermore, because loss of DOT1L in the pre-neurogenic phase of development impairs specifically generation of SATB2-expressing upper layer neurons, our data suggest that DOT1L primes upper layer identity in cortical progenitors.
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Affiliation(s)
- Henriette Franz
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Alejandro Villarreal
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Stefanie Heidrich
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany
| | - Fabian Kilpert
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ivan Mestres
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany
| | - Federico Calegari
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Center for non-coding RNA in Technology and Health, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Tanja Vogel
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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11
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Ebrahimi A, Sevinç K, Gürhan Sevinç G, Cribbs AP, Philpott M, Uyulur F, Morova T, Dunford JE, Göklemez S, Arı Ş, Oppermann U, Önder TT. Bromodomain inhibition of the coactivators CBP/EP300 facilitate cellular reprogramming. Nat Chem Biol 2019; 15:519-28. [PMID: 30962627 DOI: 10.1038/s41589-019-0264-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/27/2019] [Indexed: 01/09/2023]
Abstract
Silencing of the somatic cell type-specific genes is a critical yet poorly understood step in reprogramming. To uncover pathways that maintain cell identity, we performed a reprogramming screen using inhibitors of chromatin factors. Here, we identify acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators CREB (cyclic-AMP response element binding protein) binding protein (CBP) and E1A binding protein of 300 kDa (EP300) as potent enhancers of reprogramming. These inhibitors accelerate reprogramming, are critical during its early stages and, when combined with DOT1L inhibition, enable efficient derivation of human induced pluripotent stem cells (iPSCs) with OCT4 and SOX2. In contrast, catalytic inhibition of CBP/EP300 prevents iPSC formation, suggesting distinct functions for different coactivator domains in reprogramming. CBP/EP300 bromodomain inhibition decreases somatic-specific gene expression, histone H3 lysine 27 acetylation (H3K27Ac) and chromatin accessibility at target promoters and enhancers. The master mesenchymal transcription factor PRRX1 is one such functionally important target of CBP/EP300 bromodomain inhibition. Collectively, these results show that CBP/EP300 bromodomains sustain cell-type-specific gene expression and maintain cell identity.
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12
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Apostolou E, Stadtfeld M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev 2018; 52:77-85. [PMID: 29925040 DOI: 10.1016/j.gde.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022]
Abstract
The discovery of induced pluripotent stem cells (iPSCs) has solidified the concept of transcription factors as major players in controlling cell identity and provided a tractable tool to study how somatic cell identity can be dismantled and pluripotency established. A number of landmark studies have established hallmarks and roadmaps of iPSC formation by describing relative kinetics of transcriptional, protein and epigenetic changes, including alterations in DNA methylation and histone modifications. Recently, technological advancements such as single-cell analyses, high-resolution genome-wide chromatin assays and more efficient reprogramming systems have been used to challenge and refine our understanding of the reprogramming process. Here, we will outline novel insights into the molecular mechanisms underlying iPSC formation, focusing on how the core reprogramming factors OCT4, KLF4, SOX2 and MYC (OKSM) drive changes in gene expression, chromatin state and 3D genome topology. In addition, we will discuss unexpected consequences of reprogramming factor expression in in vitro and in vivo systems that may point towards new applications of iPSC technology.
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Affiliation(s)
- Effie Apostolou
- Edward and Sandra Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA.
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13
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Nefzger CM, Rossello FJ, Chen J, Liu X, Knaupp AS, Firas J, Paynter JM, Pflueger J, Buckberry S, Lim SM, Williams B, Alaei S, Faye-chauhan K, Petretto E, Nilsson SK, Lister R, Ramialison M, Powell DR, Rackham OJ, Polo JM. Cell Type of Origin Dictates the Route to Pluripotency. Cell Rep 2017; 21:2649-60. [DOI: 10.1016/j.celrep.2017.11.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/02/2017] [Accepted: 11/08/2017] [Indexed: 11/23/2022] Open
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14
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Teshigawara R, Cho J, Kameda M, Tada T. Mechanism of human somatic reprogramming to iPS cell. J Transl Med 2017; 97:1152-7. [PMID: 28530648 DOI: 10.1038/labinvest.2017.56] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/10/2017] [Accepted: 04/17/2017] [Indexed: 01/09/2023] Open
Abstract
Somatic reprogramming to induced pluripotent stem cells (iPSC) was realized in the year 2006 in mice, and in 2007 in humans, by transiently forced expression of a combination of exogenous transcription factors. Human and mouse iPSCs are distinctly reprogrammed into a 'primed' and a 'naïve' state, respectively. In the last decade, puzzle pieces of somatic reprogramming have been collected with difficulty. Collectively, dissecting reprogramming events and identification of the hallmark of sequentially activated/silenced genes have revealed mouse somatic reprogramming in fragments, but there is a long way to go toward understanding the molecular mechanisms of human somatic reprogramming, even with developing technologies. Recently, an established human intermediately reprogrammed stem cell (iRSC) line, which has paused reprogramming at the endogenous OCT4-negative/exogenous transgene-positive pre-MET (mesenchymal-to-epithelial-transition) stage can resume reprogramming into endogenous OCT4-positive iPSCs only by change of culture conditions. Genome-editing-mediated visualization of endogenous OCT4 activity with GFP in living iRSCs demonstrates the timing of OCT4 activation and entry to MET in the reprogramming toward iPSCs. Applications of genome-editing technology to pluripotent stem cells will reshape our approaches for exploring molecular mechanisms.
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