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Farhadova S, Ghousein A, Charon F, Surcis C, Gomez-Velazques M, Roidor C, Di Michele F, Borensztein M, De Sario A, Esnault C, Noordermeer D, Moindrot B, Feil R. The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation. Nucleic Acids Res 2024; 52:6183-6200. [PMID: 38613389 PMCID: PMC11194098 DOI: 10.1093/nar/gkae247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain's imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse embryonic stem cells (mESCs) that carry an ectopic poly(A) signal, reducing RNA levels along the polycistron, and generated Rian-/- mESCs as well. Upon ESC differentiation, we found that Meg3 lncRNA (but not Rian) is required for Dlk1 repression on the maternal chromosome. Biallelic Meg3 expression acquired through CRISPR-mediated demethylation of the paternal Meg3 promoter led to biallelic Dlk1 repression, and to loss of Rtl1 expression. lncRNA expression also correlated with DNA hypomethylation and CTCF binding at the 5'-side of Meg3. Using Capture Hi-C, we found that this creates a Topologically Associating Domain (TAD) organization that brings Meg3 close to Dlk1 on the maternal chromosome. The requirement of Meg3 for gene repression and TAD structure may explain how aberrant MEG3 expression at the human DLK1-DIO3 locus associates with imprinting disorders.
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Affiliation(s)
- Sabina Farhadova
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
- Genetic Resources Research Institute, Azerbaijan National Academy of Sciences (ANAS), AZ1106 Baku, Azerbaijan
| | - Amani Ghousein
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - François Charon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Caroline Surcis
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
| | - Melisa Gomez-Velazques
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Clara Roidor
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Maud Borensztein
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Albertina De Sario
- University of Montpellier, 34090 Montpellier, France
- PhyMedExp, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, 34295 Montpellier, France
| | - Cyril Esnault
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
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2
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Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-Dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. Mol Cell 2024; 84:1842-1854.e7. [PMID: 38759624 PMCID: PMC11104518 DOI: 10.1016/j.molcel.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024]
Abstract
Genomic context critically modulates regulatory function but is difficult to manipulate systematically. The murine insulin-like growth factor 2 (Igf2)/H19 locus is a paradigmatic model of enhancer selectivity, whereby CTCF occupancy at an imprinting control region directs downstream enhancers to activate either H19 or Igf2. We used synthetic regulatory genomics to repeatedly replace the native locus with 157-kb payloads, and we systematically dissected its architecture. Enhancer deletion and ectopic delivery revealed previously uncharacterized long-range regulatory dependencies at the native locus. Exchanging the H19 enhancer cluster with the Sox2 locus control region (LCR) showed that the H19 enhancers relied on their native surroundings while the Sox2 LCR functioned autonomously. Analysis of regulatory DNA actuation across cell types revealed that these enhancer clusters typify broader classes of context sensitivity genome wide. These results show that unexpected dependencies influence even well-studied loci, and our approach permits large-scale manipulation of complete loci to investigate the relationship between regulatory architecture and function.
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Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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3
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Cortes DE, Escudero M, Korgan AC, Mitra A, Edwards A, Aydin SC, Munger SC, Charland K, Zhang ZW, O'Connell KMS, Reinholdt LG, Pera MF. An in vitro neurogenetics platform for precision disease modeling in the mouse. SCIENCE ADVANCES 2024; 10:eadj9305. [PMID: 38569042 PMCID: PMC10990289 DOI: 10.1126/sciadv.adj9305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
The power and scope of disease modeling can be markedly enhanced through the incorporation of broad genetic diversity. The introduction of pathogenic mutations into a single inbred mouse strain sometimes fails to mimic human disease. We describe a cross-species precision disease modeling platform that exploits mouse genetic diversity to bridge cell-based modeling with whole organism analysis. We developed a universal protocol that permitted robust and reproducible neural differentiation of genetically diverse human and mouse pluripotent stem cell lines and then carried out a proof-of-concept study of the neurodevelopmental gene DYRK1A. Results in vitro reliably predicted the effects of genetic background on Dyrk1a loss-of-function phenotypes in vivo. Transcriptomic comparison of responsive and unresponsive strains identified molecular pathways conferring sensitivity or resilience to Dyrk1a1A loss and highlighted differential messenger RNA isoform usage as an important determinant of response. This cross-species strategy provides a powerful tool in the functional analysis of candidate disease variants identified through human genetic studies.
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Affiliation(s)
| | | | | | - Arojit Mitra
- The Jackson Laboratory, Bar Harbor, ME 04660, USA
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4
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Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.02.547201. [PMID: 37781588 PMCID: PMC10541140 DOI: 10.1101/2023.07.02.547201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the murine Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting activity of payloads delivered at the endogenous Igf2/H19 locus or ectopically at Hprt revealed that the Igf2/H19 locus includes additional, previously unknown long-range regulatory elements. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate the relationship between locus architecture and function.
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Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- These authors contributed equally
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- These authors contributed equally
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J. Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Highmark Health, Pittsburgh, PA 15222, USA
| | - Megan S. Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Neochromosome Inc., Long Island City, NY 11101, USA
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Lead contact
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5
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Suita K, Ishikawa K, Kaneko M, Wataki A, Takahashi M, Kiyonari H, Sunagawa GA. Mouse embryonic stem cells embody organismal-level cold resistance. Cell Rep 2023; 42:112954. [PMID: 37595588 DOI: 10.1016/j.celrep.2023.112954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/02/2023] [Accepted: 07/22/2023] [Indexed: 08/20/2023] Open
Abstract
During hibernation, some mammals show low body temperatures (<10°C). Tissues from hibernators exhibit cold resistance even when the animal is not hibernating. Mice can also enter hypothermic fasting-induced torpor (FIT), but the cold resistance of FIT has never been related to their tissues. Here, we show that an inbred mouse STM2 exhibits lower body temperature during FIT than C57BL/6J or MYS/Mz. Thus, STM2 resists the cold more than other strains. Analysis of strain-specific mouse embryonic stem (ES) cells shows that STM2 ES cells are more cold-resistant than others and rely on the oxidative phosphorylation (OXPHOS) pathway but respire independently of the electron transfer chain complex I in the cold. We also found that the liver of STM2 uses OXPHOS more in cold than other strains. This study demonstrates that an organismal phenotype associated with torpor can be effectively studied in an in vitro setup using mouse cells.
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Affiliation(s)
- Koukyou Suita
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Biology of Aging, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Hibernation Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Anesthesiology and Resuscitology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Okayama City, Okayama 700-8558, Japan
| | - Kiyomi Ishikawa
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Biology of Aging, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Hibernation Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Ayaka Wataki
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Biology of Aging, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Hibernation Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Masayo Takahashi
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Genshiro A Sunagawa
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Biology of Aging, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Hibernation Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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6
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Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation. Nat Commun 2022; 13:5432. [PMID: 36114205 PMCID: PMC9481624 DOI: 10.1038/s41467-022-33013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalised approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. Epigenetic fidelity can be tracked by genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unknown reasons. To try to understand the causes underlying these defects, we conducted a thorough imprinting analysis using IMPLICON, a high-throughput method measuring DNA methylation levels, in multiple female and male murine iPSC lines generated under different experimental conditions. Our results show that imprinting defects are remarkably common in iPSCs, but their nature depends on the sex of donor cells and their response to culture conditions. Imprints in female iPSCs resist the initial genome-wide DNA demethylation wave during reprogramming, but ultimately cells accumulate hypomethylation defects irrespective of culture medium formulations. In contrast, imprinting defects on male iPSCs depends on the experimental conditions and arise during reprogramming, being mitigated by the addition of vitamin C (VitC). Our findings are fundamental to further optimise reprogramming strategies and generate iPSCs with a stable epigenome. Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is associated with epigenetic alterations. Here the authors assess DNA methylation in detail in multiple female and male mouse iPSC lines generated with different protocols and find that defects depend on the sex of donor cells and can be partially mitigated by Vitamin C.
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7
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Kojima S, Shiochi N, Sato K, Yamaura M, Ito T, Yamamura N, Goto N, Odamoto M, Kobayashi S, Kimura T, Sekita Y. Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain. Nucleic Acids Res 2022; 50:5080-5094. [PMID: 35544282 PMCID: PMC9122602 DOI: 10.1093/nar/gkac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/03/2022] [Accepted: 04/24/2022] [Indexed: 11/12/2022] Open
Abstract
The Dlk1-Dio3 imprinted domain is controlled by an imprinting control region (ICR) called IG-DMR that is hypomethylated on the maternal allele and hypermethylated on the paternal allele. Although several genetic mutation experiments have shown that IG-DMR is essential for imprinting control of the domain, how DNA methylation itself functions has not been elucidated. Here, we performed both gain and loss of DNA methylation experiments targeting IG-DMR by transiently introducing CRISPR/Cas9 based-targeted DNA methylation editing tools along with one guide RNA into mouse ES cells. Altered DNA methylation, particularly at IG-DMR-Rep, which is a tandem repeat containing ZFP57 methylated DNA-binding protein binding motifs, affected the imprinting state of the whole domain, including DNA methylation, imprinted gene expression, and histone modifications. Moreover, the altered imprinting states were persistent through neuronal differentiation. Our results suggest that the DNA methylation state at IG-DMR-Rep, but not other sites in IG-DMR, is a master element to determine whether the allele behaves as the intrinsic maternal or paternal allele. Meanwhile, this study provides a robust strategy and methodology to study core DNA methylation in cis-regulatory elements, such as ICRs and enhancers.
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Affiliation(s)
- Shin Kojima
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoya Shiochi
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuki Sato
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mamiko Yamaura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Toshiaki Ito
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Nodoka Yamamura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoki Goto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mika Odamoto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Shin Kobayashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo 135-0064, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yoichi Sekita
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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8
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Byers C, Spruce C, Fortin HJ, Hartig EI, Czechanski A, Munger SC, Reinholdt LG, Skelly DA, Baker CL. Genetic control of the pluripotency epigenome determines differentiation bias in mouse embryonic stem cells. EMBO J 2022; 41:e109445. [PMID: 34931323 PMCID: PMC8762565 DOI: 10.15252/embj.2021109445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023] Open
Abstract
Genetically diverse pluripotent stem cells display varied, heritable responses to differentiation cues. Here, we harnessed these disparities through derivation of mouse embryonic stem cells from the BXD genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, to identify loci regulating cell state transitions. Upon transition to formative pluripotency, B6 stem cells quickly dissolved naïve networks adopting gene expression modules indicative of neuroectoderm lineages, whereas D2 retained aspects of naïve pluripotency. Spontaneous formation of embryoid bodies identified divergent differentiation where B6 showed a propensity toward neuroectoderm and D2 toward definitive endoderm. Genetic mapping identified major trans-acting loci co-regulating chromatin accessibility and gene expression in both naïve and formative pluripotency. These loci distally modulated occupancy of pluripotency factors at hundreds of regulatory elements. One trans-acting locus on Chr 12 primarily impacted chromatin accessibility in embryonic stem cells, while in epiblast-like cells, the same locus subsequently influenced expression of genes enriched for neurogenesis, suggesting early chromatin priming. These results demonstrate genetically determined biases in lineage commitment and identify major regulators of the pluripotency epigenome.
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Affiliation(s)
- Candice Byers
- The Jackson LaboratoryBar HarborMEUSA,Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | - Haley J Fortin
- The Jackson LaboratoryBar HarborMEUSA,Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | - Ellen I Hartig
- The Jackson LaboratoryBar HarborMEUSA,Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | - Steven C Munger
- The Jackson LaboratoryBar HarborMEUSA,Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | | | - Christopher L Baker
- The Jackson LaboratoryBar HarborMEUSA,Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
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9
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Aronson BE, Scourzic L, Shah V, Swanzey E, Kloetgen A, Polyzos A, Sinha A, Azziz A, Caspi I, Li J, Pelham-Webb B, Glenn RA, Vierbuchen T, Wichterle H, Tsirigos A, Dawlaty MM, Stadtfeld M, Apostolou E. A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus. Dev Cell 2021; 56:3052-3065.e5. [PMID: 34710357 PMCID: PMC8628258 DOI: 10.1016/j.devcel.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Loss of imprinting (LOI) results in severe developmental defects, but the mechanisms preventing LOI remain incompletely understood. Here, we dissect the functional components of the imprinting control region of the essential Dlk1-Dio3 locus (called IG-DMR) in pluripotent stem cells. We demonstrate that the IG-DMR consists of two antagonistic elements: a paternally methylated CpG island that prevents recruitment of TET dioxygenases and a maternally unmethylated non-canonical enhancer that ensures expression of the Gtl2 lncRNA by counteracting de novo DNA methyltransferases. Genetic or epigenetic editing of these elements leads to distinct LOI phenotypes with characteristic alternations of allele-specific gene expression, DNA methylation, and 3D chromatin topology. Although repression of the Gtl2 promoter results in dysregulated imprinting, the stability of LOI phenotypes depends on the IG-DMR, suggesting a functional hierarchy. These findings establish the IG-DMR as a bipartite control element that maintains imprinting by allele-specific restriction of the DNA (de)methylation machinery.
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Affiliation(s)
- Boaz E Aronson
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Laurianne Scourzic
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Veevek Shah
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Emily Swanzey
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jackson Laboratory, Bar Harbor, ME, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Alexander Polyzos
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Abhishek Sinha
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annabel Azziz
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Inbal Caspi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiexi Li
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Bobbie Pelham-Webb
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY, USA
| | - Rachel A Glenn
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, Neuroscience and Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, Center for Motor Neuron Biology and Disease and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Institute for Computational Medicine and Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY 10016, USA
| | - Meelad M Dawlaty
- Ruth L and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, NY 10461, USA; Department of Genetics, Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthias Stadtfeld
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Effie Apostolou
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA.
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10
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Takeda I, Araki M, Ishiguro KI, Ohga T, Takada K, Yamaguchi Y, Hashimoto K, Kai T, Nakagata N, Imasaka M, Yoshinobu K, Araki K. Gene trapping reveals a new transcriptionally active genome element: The chromosome-specific clustered trap region. Genes Cells 2021; 26:874-890. [PMID: 34418226 DOI: 10.1111/gtc.12890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/01/2022]
Abstract
Nearly half of the human genome consists of repetitive sequences such as long interspersed nuclear elements. The relationship between these repeating sequences and diseases has remained unclear. Gene trapping is a useful technique for disrupting a gene and expressing a reporter gene by using the promoter activity of the gene. The analysis of trapped genes revealed a new genome element-the chromosome-specific clustered trap (CSCT) region. For any examined sequence within this region, an equivalent was found using the BLAT of the University of California, Santa Cruz (UCSC) Genome Browser. CSCT13 mapped to chromosome 13 and contained only three genes. To elucidate its in vivo function, the whole CSCT13 region (1.6 Mbp) was deleted using the CRISPR/Cas9 system in mouse embryonic stem cells, and subsequently, a CSCT13 knockout mouse line was established. The rate of homozygotes was significantly lower than expected according to Mendel's laws. In addition, the number of offspring obtained by mating homozygotes was significantly smaller than that obtained by crossing controls. Furthermore, CSCT13 might have an effect on meiotic homologous recombination. This study identifies a transcriptionally active CSCT with an important role in mouse development.
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Affiliation(s)
- Iyo Takeda
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Masatake Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kei-Ichiro Ishiguro
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Toshinori Ohga
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kouki Takada
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Yusuke Yamaguchi
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Koichi Hashimoto
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Takuma Kai
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Naomi Nakagata
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Mai Imasaka
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kumiko Yoshinobu
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
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11
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Swanzey E, O'Connor C, Reinholdt LG. Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics. Trends Genet 2021; 37:251-265. [PMID: 33010949 PMCID: PMC7889615 DOI: 10.1016/j.tig.2020.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023]
Abstract
Interrogation of disease-relevant cellular and molecular traits exhibited by genetically diverse cell populations enables in vitro systems genetics approaches for uncovering the basic properties of cellular function and identity. Primary cells, stem cells, and organoids derived from genetically diverse mouse strains, such as Collaborative Cross and Diversity Outbred populations, offer the opportunity for parallel in vitro/in vivo screening. These panels provide genetic resolution for variant discovery and functional characterization, as well as disease modeling and in vivo validation capabilities. Here we review mouse cellular systems genetics approaches for characterizing the influence of genetic variation on signaling networks and phenotypic diversity, and we discuss approaches for data integration and cross-species validation.
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Affiliation(s)
| | - Callan O'Connor
- The Jackson Laboratory, Bar Harbor, ME, USA; Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
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12
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Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. Viruses 2020; 12:v12101089. [PMID: 32993145 PMCID: PMC7650545 DOI: 10.3390/v12101089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.
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13
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Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:v12080810. [PMID: 32727076 PMCID: PMC7472028 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
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