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Schaeffer L, Lindner L, Pavlovic G, Hérault Y, Birling MC. CRISMERE Chromosome Engineering in Mouse and Rat. Methods Mol Biol 2023; 2631:277-297. [PMID: 36995673 DOI: 10.1007/978-1-0716-2990-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
CRISPR/Cas9 technology is a versatile tool for engineering biology that has dramatically transformed our ability to manipulate genomes. In this protocol, we use its capacity to generate two double-strand breaks simultaneously, at precise positions in the genome, to generate mouse or rat lines with deletion, inversion, and duplication of a specific genomic segment. The technic is called CRISMERE for CRISpr-MEdiated REarrangement. This protocol describes the different steps to generate and validate the different chromosomal rearrangements that can be obtained with the technology. These new genetic configurations can be useful to model rare diseases with copy number variation, understand the genomic organization, or provide genetic tools (like balancer chromosome) to keep lethal mutations.
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Affiliation(s)
- Laurence Schaeffer
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Loic Lindner
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Yann Hérault
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France.
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2
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Tamada K, Fukumoto K, Toya T, Nakai N, Awasthi JR, Tanaka S, Okabe S, Spitz F, Saitow F, Suzuki H, Takumi T. Genetic dissection identifies Necdin as a driver gene in a mouse model of paternal 15q duplications. Nat Commun 2021; 12:4056. [PMID: 34210967 PMCID: PMC8249516 DOI: 10.1038/s41467-021-24359-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Maternally inherited duplication of chromosome 15q11-q13 (Dup15q) is a pathogenic copy number variation (CNV) associated with autism spectrum disorder (ASD). Recently, paternally derived duplication has also been shown to contribute to the development of ASD. The molecular mechanism underlying paternal Dup15q remains unclear. Here, we conduct genetic and overexpression-based screening and identify Necdin (Ndn) as a driver gene for paternal Dup15q resulting in the development of ASD-like phenotypes in mice. An excess amount of Ndn results in enhanced spine formation and density as well as hyperexcitability of cortical pyramidal neurons. We generate 15q dupΔNdn mice with a normalized copy number of Ndn by excising its one copy from Dup15q mice using a CRISPR-Cas9 system. 15q dupΔNdn mice do not show ASD-like phenotypes and show dendritic spine dynamics and cortical excitatory-inhibitory balance similar to wild type animals. Our study provides an insight into the role of Ndn in paternal 15q duplication and a mouse model of paternal Dup15q syndrome.
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Affiliation(s)
- Kota Tamada
- grid.474690.8RIKEN Brain Science Institute, Wako, Saitama, Japan ,grid.257022.00000 0000 8711 3200Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan ,grid.31432.370000 0001 1092 3077Department of Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, Japan
| | - Keita Fukumoto
- grid.474690.8RIKEN Brain Science Institute, Wako, Saitama, Japan ,grid.257022.00000 0000 8711 3200Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Tsuyoshi Toya
- grid.474690.8RIKEN Brain Science Institute, Wako, Saitama, Japan ,grid.26091.3c0000 0004 1936 9959Graduate School of Pharmaceutical Sciences, Keio University, Minato, Tokyo, Japan
| | - Nobuhiro Nakai
- grid.474690.8RIKEN Brain Science Institute, Wako, Saitama, Japan ,grid.257022.00000 0000 8711 3200Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan ,grid.31432.370000 0001 1092 3077Department of Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, Japan
| | - Janak R. Awasthi
- grid.474690.8RIKEN Brain Science Institute, Wako, Saitama, Japan ,grid.263023.60000 0001 0703 3735Graduate School of Science and Engineering, Saitama University, Sakura, Saitama, Japan
| | - Shinji Tanaka
- grid.26999.3d0000 0001 2151 536XDepartment of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shigeo Okabe
- grid.26999.3d0000 0001 2151 536XDepartment of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - François Spitz
- grid.170205.10000 0004 1936 7822Department of Human Genetics, University of Chicago, Chicago, IL USA
| | - Fumihito Saitow
- grid.410821.e0000 0001 2173 8328Department of Pharmacology, Garduate School of Medicine, Nippon Medical School, Bunkyo, Tokyo, Japan
| | - Hidenori Suzuki
- grid.410821.e0000 0001 2173 8328Department of Pharmacology, Garduate School of Medicine, Nippon Medical School, Bunkyo, Tokyo, Japan
| | - Toru Takumi
- grid.474690.8RIKEN Brain Science Institute, Wako, Saitama, Japan ,grid.257022.00000 0000 8711 3200Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan ,grid.31432.370000 0001 1092 3077Department of Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, Japan ,grid.263023.60000 0001 0703 3735Graduate School of Science and Engineering, Saitama University, Sakura, Saitama, Japan
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3
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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4
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A non-invasive far-red light-induced split-Cre recombinase system for controllable genome engineering in mice. Nat Commun 2020; 11:3708. [PMID: 32709899 PMCID: PMC7381682 DOI: 10.1038/s41467-020-17530-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
The Cre-loxP recombination system is a powerful tool for genetic manipulation. However, there are widely recognized limitations with chemically inducible Cre-loxP systems, and the UV and blue-light induced systems have phototoxicity and minimal capacity for deep tissue penetration. Here, we develop a far-red light-induced split Cre-loxP system (FISC system) based on a bacteriophytochrome optogenetic system and split-Cre recombinase, enabling optogenetical regulation of genome engineering in vivo solely by utilizing a far-red light (FRL). The FISC system exhibits low background and no detectable photocytotoxicity, while offering efficient FRL-induced DNA recombination. Our in vivo studies showcase the strong organ-penetration capacity of FISC system, markedly outperforming two blue-light-based Cre systems for recombination induction in the liver. Demonstrating its strong clinical relevance, we successfully deploy a FISC system using adeno-associated virus (AAV) delivery. Thus, the FISC system expands the optogenetic toolbox for DNA recombination to achieve spatiotemporally controlled, non-invasive genome engineering in living systems. Current light-inducible Cre-loxP systems have minimal capacity for deep tissue penetration. Here, the authors present a far-red light-induced split Cre-loxP system for in vivo genome engineering.
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5
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Muñiz Moreno MDM, Brault V, Birling MC, Pavlovic G, Herault Y. Modeling Down syndrome in animals from the early stage to the 4.0 models and next. PROGRESS IN BRAIN RESEARCH 2019; 251:91-143. [PMID: 32057313 DOI: 10.1016/bs.pbr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genotype-phenotype relationship and the physiopathology of Down Syndrome (DS) have been explored in the last 20 years with more and more relevant mouse models. From the early age of transgenesis to the new CRISPR/CAS9-derived chromosomal engineering and the transchromosomic technologies, mouse models have been key to identify homologous genes or entire regions homologous to the human chromosome 21 that are necessary or sufficient to induce DS features, to investigate the complexity of the genetic interactions that are involved in DS and to explore therapeutic strategies. In this review we report the new developments made, how genomic data and new genetic tools have deeply changed our way of making models, extended our panel of animal models, and increased our understanding of the neurobiology of the disease. But even if we have made an incredible progress which promises to make DS a curable condition, we are facing new research challenges to nurture our knowledge of DS pathophysiology as a neurodevelopmental disorder with many comorbidities during ageing.
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Affiliation(s)
- Maria Del Mar Muñiz Moreno
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Véronique Brault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France.
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6
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Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl HC, Shimizu T, Penninger JM, Pauler FM, Hudson QJ. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genet 2019; 15:e1008268. [PMID: 31329595 PMCID: PMC6675118 DOI: 10.1371/journal.pgen.1008268] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/01/2019] [Accepted: 06/23/2019] [Indexed: 01/08/2023] Open
Abstract
Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established. Long non-coding (lnc) RNAs are numerous in the mammalian genome and many have been implicated in gene regulation. However, the vast majority are uncharacterised and of uncertain function making known functional lncRNAs valuable models for understanding their mechanism of action. One mode of lncRNA action is to recruit epigenetic silencing to target distant genes on the same chromosome. A well-characterized group of lncRNAs that act in this way to silence genes are imprinted lncRNAs. In this study we examined how the imprinted lncRNA Airn silences genes in the Igf2r imprinted cluster, focusing primarily on silencing of the distant imprinted gene Slc22a3. We found that Airn expression blocks chromosome interactions between the Slc22a3 promoter and the Airn gene locus. By making a large genomic deletion including the Airn gene we showed that these interactions are not essential enhancer/promoter interactions, but may help to guide the Airn RNA to target genes to recruit epigenetic silencing. Our study adds to the understanding of how lncRNAs may act to silence distant genes.
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Affiliation(s)
- Daniel Andergassen
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Markus Muckenhuber
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp C. Bammer
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tomasz M. Kulinski
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Takahiko Shimizu
- National Center for Geriatrics and Gerontology, Obu Aichi, Japan
| | - Josef M. Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Florian M. Pauler
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- * E-mail: (QJH); (FMP)
| | - Quanah J. Hudson
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
- * E-mail: (QJH); (FMP)
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7
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Herault Y, Delabar JM, Fisher EMC, Tybulewicz VLJ, Yu E, Brault V. Rodent models in Down syndrome research: impact and future opportunities. Dis Model Mech 2018; 10:1165-1186. [PMID: 28993310 PMCID: PMC5665454 DOI: 10.1242/dmm.029728] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Down syndrome is caused by trisomy of chromosome 21. To date, a multiplicity of mouse models with Down-syndrome-related features has been developed to understand this complex human chromosomal disorder. These mouse models have been important for determining genotype-phenotype relationships and identification of dosage-sensitive genes involved in the pathophysiology of the condition, and in exploring the impact of the additional chromosome on the whole genome. Mouse models of Down syndrome have also been used to test therapeutic strategies. Here, we provide an overview of research in the last 15 years dedicated to the development and application of rodent models for Down syndrome. We also speculate on possible and probable future directions of research in this fast-moving field. As our understanding of the syndrome improves and genome engineering technologies evolve, it is necessary to coordinate efforts to make all Down syndrome models available to the community, to test therapeutics in models that replicate the whole trisomy and design new animal models to promote further discovery of potential therapeutic targets. Summary: Mouse models have boosted therapeutic options for Down syndrome, and improved models are being developed to better understand the pathophysiology of this genetic condition.
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Affiliation(s)
- Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris
| | - Jean M Delabar
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, UMR8251, CNRS, 75205 Paris, France.,INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et la Moelle épinière, ICM, 75013 Paris, France.,Brain and Spine Institute (ICM) CNRS UMR7225, INSERM UMRS 975, 75013 Paris, France
| | - Elizabeth M C Fisher
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, WC1N 3BG, UK.,LonDownS Consortium, London, W1T 7NF UK
| | - Victor L J Tybulewicz
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,LonDownS Consortium, London, W1T 7NF UK.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Eugene Yu
- T21 Research Society, Brain and Spine Institute (ICM), 75013 Paris.,The Children's Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.,Department of Cellular and Molecular Biology, Roswell Park Division of Graduate School, Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
| | - Veronique Brault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
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8
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Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, Murison A, Langenfeld K, Petretich M, Scognamiglio R, Zeisberger P, Benk AS, Amit I, Zandstra PW, Lupien M, Dick JE, Trumpp A, Spitz F. Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature 2018; 558:E4. [PMID: 29769714 DOI: 10.1038/s41586-018-0113-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the originally published version of this Letter, ref. 43 was erroneously provided twice. In the 'Estimation of relative cell-type-specific composition of AML samples' section in the Methods, the citation to ref. 43 after the GEO dataset GSE24759 is correct. However, in the 'Mice' section of the Methods, the citation to ref. 43 after 'TAMERE' should have been associated with a new reference1. The original Letter has been corrected online (with the new reference included as ref. 49).
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Affiliation(s)
- Carsten Bahr
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Lisa von Paleske
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Veli V Uslu
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stanley W Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Katja Langenfeld
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Massimo Petretich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Roberta Scognamiglio
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Petra Zeisberger
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Amelie S Benk
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Michael Smith Laboratories, School of Biomedical Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany. .,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany. .,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,Nationales Zentrum für Tumorerkrankungen (NCT), Heidelberg, Germany.
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,CNRS, UMR3738, 25 Rue du Dr Roux, Paris, France.,(Epi)genomics of Animal Development Unit, Developmental and Stem Cell Biology Department, Institut Pasteur, Paris, France
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9
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A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature 2018; 553:515-520. [PMID: 29342133 DOI: 10.1038/nature25193] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 12/04/2017] [Indexed: 12/11/2022]
Abstract
The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies. Here we show that an evolutionarily conserved region located 1.7 megabases downstream of the Myc gene that has previously been labelled as a 'super-enhancer' is essential for the regulation of Myc expression levels in both normal haematopoietic and leukaemic stem cell hierarchies in mice and humans. Deletion of this region in mice leads to a complete loss of Myc expression in haematopoietic stem cells and progenitors. This caused an accumulation of differentiation-arrested multipotent progenitors and loss of myeloid and B cells, mimicking the phenotype caused by Mx1-Cre-mediated conditional deletion of the Myc gene in haematopoietic stem cells. This super-enhancer comprises multiple enhancer modules with selective activity that recruits a compendium of transcription factors, including GFI1b, RUNX1 and MYB. Analysis of mice carrying deletions of individual enhancer modules suggests that specific Myc expression levels throughout most of the haematopoietic hierarchy are controlled by the combinatorial and additive activity of individual enhancer modules, which collectively function as a 'blood enhancer cluster' (BENC). We show that BENC is also essential for the maintenance of MLL-AF9-driven leukaemia in mice. Furthermore, a BENC module, which controls Myc expression in mouse haematopoietic stem cells and progenitors, shows increased chromatin accessibility in human acute myeloid leukaemia stem cells compared to blasts. This difference correlates with MYC expression and patient outcome. We propose that clusters of enhancers, such as BENC, form highly combinatorial systems that allow precise control of gene expression across normal cellular hierarchies and which also can be hijacked in malignancies.
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10
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Rodríguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev 2017; 31:2264-2281. [PMID: 29273679 PMCID: PMC5769770 DOI: 10.1101/gad.307769.117] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context.
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Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Pierre J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Imane El-Idrissi
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Thi Hanh Nguyen Huynh
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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11
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Abstract
During embryonic development, Hox genes participate in the building of a functional digestive system in metazoans, and genetic conditions involving these genes lead to important, sometimes lethal, growth retardation. Recently, this phenotype was obtained after deletion of Haglr, the Hoxd antisense growth-associated long noncoding RNA (lncRNA) located between Hoxd1 and Hoxd3 In this study, we have analyzed the function of Hoxd genes in delayed growth trajectories by looking at several nested targeted deficiencies of the mouse HoxD cluster. Mutant pups were severely stunted during the suckling period, but many recovered after weaning. After comparing seven distinct HoxD alleles, including CRISPR/Cas9 deletions involving Haglr, we identified Hoxd3 as the critical component for the gut to maintain milk-digestive competence. This essential function could be abrogated by the dominant-negative effect of HOXD10 as shown by a genetic rescue approach, thus further illustrating the importance of posterior prevalence in Hox gene function. A role for the lncRNA Haglr in the control of postnatal growth could not be corroborated.
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12
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Revealing hidden complexities of genomic rearrangements generated with Cas9. Sci Rep 2017; 7:12867. [PMID: 28993641 PMCID: PMC5634419 DOI: 10.1038/s41598-017-12740-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/18/2017] [Indexed: 12/26/2022] Open
Abstract
Modelling human diseases caused by large genomic rearrangements has become more accessible since the utilization of CRISPR/Cas9 in mammalian systems. In a previous study, we showed that genomic rearrangements of up to one million base pairs can be generated by direct injection of CRISPR/Cas9 reagents into mouse zygotes. Although these rearrangements are ascertained by junction PCR, we describe here a variety of unanticipated structural changes often involving reintegration of the region demarcated by the gRNAs in the vicinity of the edited locus. We illustrate here some of this diversity detected by high-resolution fibre-FISH and conclude that extensive molecular analysis is required to fully understand the structure of engineered chromosomes generated by Cas9.
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13
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Birling MC, Herault Y, Pavlovic G. Modeling human disease in rodents by CRISPR/Cas9 genome editing. Mamm Genome 2017; 28:291-301. [PMID: 28677007 PMCID: PMC5569124 DOI: 10.1007/s00335-017-9703-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/21/2017] [Indexed: 02/08/2023]
Abstract
Modeling human disease has proven to be a challenge for the scientific community. For years, generating an animal model was complicated and restricted to very few species. With the rise of CRISPR/Cas9, it is now possible to generate more or less any animal model. In this review, we will show how this technology is and will change our way to obtain relevant disease animal models and how it should impact human health.
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Affiliation(s)
- Marie-Christine Birling
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Guillaume Pavlovic
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
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14
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Efficient and rapid generation of large genomic variants in rats and mice using CRISMERE. Sci Rep 2017; 7:43331. [PMID: 28266534 PMCID: PMC5339700 DOI: 10.1038/srep43331] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/24/2017] [Indexed: 01/05/2023] Open
Abstract
Modelling Down syndrome (DS) in mouse has been crucial for the understanding of the disease and the evaluation of therapeutic targets. Nevertheless, the modelling so far has been limited to the mouse and, even in this model, generating duplication of genomic regions has been labour intensive and time consuming. We developed the CRISpr MEdiated REarrangement (CRISMERE) strategy, which takes advantage of the CRISPR/Cas9 system, to generate most of the desired rearrangements from a single experiment at much lower expenses and in less than 9 months. Deletions, duplications, and inversions of genomic regions as large as 24.4 Mb in rat and mouse founders were observed and germ line transmission was confirmed for fragment as large as 3.6 Mb. Interestingly we have been able to recover duplicated regions from founders in which we only detected deletions. CRISMERE is even more powerful than anticipated it allows the scientific community to manipulate the rodent and probably other genomes in a fast and efficient manner which was not possible before.
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15
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Hasegawa S, Kumagai M, Hagihara M, Nishimaru H, Hirano K, Kaneko R, Okayama A, Hirayama T, Sanbo M, Hirabayashi M, Watanabe M, Hirabayashi T, Yagi T. Distinct and Cooperative Functions for the Protocadherin-α, -β and -γ Clusters in Neuronal Survival and Axon Targeting. Front Mol Neurosci 2016; 9:155. [PMID: 28066179 PMCID: PMC5179546 DOI: 10.3389/fnmol.2016.00155] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/07/2016] [Indexed: 01/29/2023] Open
Abstract
The clustered protocadherin (Pcdh) genes are divided into the Pcdhα, Pcdhβ, and Pcdhγ clusters. Gene-disruption analyses in mice have revealed the in vivo functions of the Pcdhα and Pcdhγ clusters. However, all Pcdh protein isoforms form combinatorial cis-hetero dimers and enter trans-homophilic interactions. Here we addressed distinct and cooperative functions in the Pcdh clusters by generating six cluster-deletion mutants (Δα, Δβ, Δγ, Δαβ, Δβγ, and Δαβγ) and comparing their phenotypes: Δα, Δβ, and Δαβ mutants were viable and fertile; Δγ mutants lived less than 12 h; and Δβγ and Δαβγ mutants died shortly after birth. The Pcdhα, Pcdhβ, and Pcdhγ clusters were individually and cooperatively important in olfactory-axon targeting and spinal-cord neuron survival. Neurodegeneration was most severe in Δαβγ mutants, indicating that Pcdhα and Pcdhβ function cooperatively for neuronal survival. The Pcdhα, Pcdhβ, and Pcdhγ clusters share roles in olfactory-axon targeting and neuronal survival, although to different degrees.
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Affiliation(s)
- Sonoko Hasegawa
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED)Suita, Japan
| | - Makiko Kumagai
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED)Suita, Japan
| | - Mitsue Hagihara
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED)Suita, Japan
| | - Hiroshi Nishimaru
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba Tsukuba, Japan
| | - Keizo Hirano
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University Suita, Japan
| | - Ryosuke Kaneko
- Bioresource Center, Graduate School of Medicine, Gunma University Maebashi, Japan
| | - Atsushi Okayama
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University Suita, Japan
| | - Teruyoshi Hirayama
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED)Suita, Japan
| | - Makoto Sanbo
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences Okazaki, Japan
| | - Masumi Hirabayashi
- AMED-CREST, Japan Agency for Medical Research and Development (AMED)Suita, Japan; Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological SciencesOkazaki, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University Graduate School of Medicine Sapporo, Japan
| | - Takahiro Hirabayashi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED)Suita, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED)Suita, Japan
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16
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Xing Z, Li Y, Pao A, Bennett AS, Tycko B, Mobley WC, Yu YE. Mouse-based genetic modeling and analysis of Down syndrome. Br Med Bull 2016; 120:111-122. [PMID: 27789459 PMCID: PMC5146682 DOI: 10.1093/bmb/ldw040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/07/2016] [Accepted: 10/03/2016] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Down syndrome (DS), caused by human trisomy 21 (Ts21), can be considered as a prototypical model for understanding the effects of chromosomal aneuploidies in other diseases. Human chromosome 21 (Hsa21) is syntenically conserved with three regions in the mouse genome. SOURCES OF DATA A review of recent advances in genetic modeling and analysis of DS. Using Cre/loxP-mediated chromosome engineering, a substantial number of new mouse models of DS have recently been generated, which facilitates better understanding of disease mechanisms in DS. AREAS OF AGREEMENT Based on evolutionary conservation, Ts21 can be modeled by engineered triplication of Hsa21 syntenic regions in mice. The validity of the models is supported by the exhibition of DS-related phenotypes. AREAS OF CONTROVERSY Although substantial progress has been made, it remains a challenge to unravel the relative importance of specific candidate genes and molecular mechanisms underlying the various clinical phenotypes. GROWING POINTS Further understanding of mechanisms based on data from mouse models, in parallel with human studies, may lead to novel therapies for clinical manifestations of Ts21 and insights to the roles of aneuploidies in other developmental disorders and cancers.
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Affiliation(s)
- Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Yichen Li
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Abigail S Bennett
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - William C Mobley
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA .,Cellular and Molecular Biology Program, Roswell Park Division of Graduate School, Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
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17
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Symmons O, Pan L, Remeseiro S, Aktas T, Klein F, Huber W, Spitz F. The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances. Dev Cell 2016; 39:529-543. [PMID: 27867070 PMCID: PMC5142843 DOI: 10.1016/j.devcel.2016.10.015] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/01/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022]
Abstract
Gene expression often requires interaction between promoters and distant enhancers, which occur within the context of highly organized topologically associating domains (TADs). Using a series of engineered chromosomal rearrangements at the Shh locus, we carried out an extensive fine-scale characterization of the factors that govern the long-range regulatory interactions controlling Shh expression. We show that Shh enhancers act pervasively, yet not uniformly, throughout the TAD. Importantly, changing intra-TAD distances had no impact on Shh expression. In contrast, inversions disrupting the TAD altered global folding of the region and prevented regulatory contacts in a distance-dependent manner. Our data indicate that the Shh TAD promotes distance-independent contacts between distant regions that would otherwise interact only sporadically, enabling functional communication between them. In large genomes where genomic distances per se can limit regulatory interactions, this function of TADs could be as essential for gene expression as the formation of insulated neighborhoods.
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Affiliation(s)
- Orsolya Symmons
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Leslie Pan
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tugce Aktas
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Felix Klein
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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18
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Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape. Proc Natl Acad Sci U S A 2016; 113:E7720-E7729. [PMID: 27856734 DOI: 10.1073/pnas.1617141113] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Vertebrate Hox genes encode transcription factors operating during the development of multiple organs and structures. However, the evolutionary mechanism underlying this remarkable pleiotropy remains to be fully understood. Here, we show that Hoxd8 and Hoxd9, two genes of the HoxD complex, are transcribed during mammary bud (MB) development. However, unlike in other developmental contexts, their coexpression does not rely on the same regulatory mechanism. Hoxd8 is regulated by the combined activity of closely located sequences and the most distant telomeric gene desert. On the other hand, Hoxd9 is controlled by an enhancer-rich region that is also located within the telomeric gene desert but has no impact on Hoxd8 transcription, thus constituting an exception to the global regulatory logic systematically observed at this locus. The latter DNA region is also involved in Hoxd gene regulation in other contexts and strongly interacts with Hoxd9 in all tissues analyzed thus far, indicating that its regulatory activity was already operational before the appearance of mammary glands. Within this DNA region and neighboring a strong limb enhancer, we identified a short sequence conserved in therian mammals and capable of enhancer activity in the MBs. We propose that Hoxd gene regulation in embryonic MBs evolved by hijacking a preexisting regulatory landscape that was already at work before the emergence of mammals in structures such as the limbs or the intestinal tract.
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19
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Guerreiro I, Gitto S, Novoa A, Codourey J, Nguyen Huynh TH, Gonzalez F, Milinkovitch MC, Mallo M, Duboule D. Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan. eLife 2016; 5. [PMID: 27476854 PMCID: PMC4969037 DOI: 10.7554/elife.16087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/10/2016] [Indexed: 12/15/2022] Open
Abstract
Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework.
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Affiliation(s)
- Isabel Guerreiro
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Julien Codourey
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Federico Gonzalez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Moises Mallo
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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20
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Ip JY, Sone M, Nashiki C, Pan Q, Kitaichi K, Yanaka K, Abe T, Takao K, Miyakawa T, Blencowe BJ, Nakagawa S. Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine. Sci Rep 2016; 6:27204. [PMID: 27251103 PMCID: PMC4890022 DOI: 10.1038/srep27204] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/12/2016] [Indexed: 02/07/2023] Open
Abstract
The long noncoding RNA Gomafu/MIAT/Rncr2 is thought to function in retinal cell specification, stem cell differentiation and the control of alternative splicing. To further investigate physiological functions of Gomafu, we created mouse knockout (KO) model that completely lacks the Gomafu gene. The KO mice did not exhibit any developmental deficits. However, behavioral tests revealed that the KO mice are hyperactive. This hyperactive behavior was enhanced when the KO mice were treated with the psychostimulant methamphetamine, which was associated with an increase in dopamine release in the nucleus accumbens. RNA sequencing analyses identified a small number of genes affected by the deficiency of Gomafu, a subset of which are known to have important neurobiological functions. These observations suggest that Gomafu modifies mouse behavior thorough a mild modulation of gene expression and/or alternative splicing of target genes.
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Affiliation(s)
- Joanna Y Ip
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Masamitsu Sone
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Chieko Nashiki
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Qun Pan
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Kiyoyuki Kitaichi
- Laboratory of Pharmaceutics, Department of Biomedical Pharmaceutics, Gifu Pharmaceutical University, 1-25-4 Daigakunishi, Gifu 501-1196, Japan
| | - Kaori Yanaka
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Takaya Abe
- Laboratories of Animal Resource Development and Genetic Engineering, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami, Chuou-ku, Kobe 650-0047, Japan
| | - Keizo Takao
- Section of Behavior Patterns, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan.,Division of Animal Resources and Development, Life Science Research Center, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Tsuyoshi Miyakawa
- Section of Behavior Patterns, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan.,Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Benjamin J Blencowe
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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21
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Huang H, Wu Q. CRISPR Double Cutting through the Labyrinthine Architecture of 3D Genomes. J Genet Genomics 2016; 43:273-88. [PMID: 27210040 DOI: 10.1016/j.jgg.2016.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/03/2016] [Accepted: 03/16/2016] [Indexed: 02/06/2023]
Abstract
The genomes are organized into ordered and hierarchical topological structures in interphase nuclei. Within discrete territories of each chromosome, topologically associated domains (TADs) play important roles in various nuclear processes such as gene regulation. Inside TADs separated by relatively constitutive boundaries, distal elements regulate their gene targets through specific chromatin-looping contacts such as long-distance enhancer-promoter interactions. High-throughput sequencing studies have revealed millions of potential regulatory DNA elements, which are much more abundant than the mere ∼20,000 genes they control. The recently emerged CRISPR-Cas9 genome editing technologies have enabled efficient and precise genetic and epigenetic manipulations of genomes. The multiplexed and high-throughput CRISPR capabilities facilitate the discovery and dissection of gene regulatory elements. Here, we describe the applications of CRISPR for genome, epigenome, and 3D genome editing, focusing on CRISPR DNA-fragment editing with Cas9 and a pair of sgRNAs to investigate topological folding of chromatin TADs and developmental gene regulation.
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Affiliation(s)
- Haiyan Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China
| | - Qiang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang, Shanghai 200240, China.
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22
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Boroviak K, Doe B, Banerjee R, Yang F, Bradley A. Chromosome engineering in zygotes with CRISPR/Cas9. Genesis 2016; 54:78-85. [PMID: 26742453 PMCID: PMC4819711 DOI: 10.1002/dvg.22915] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/18/2015] [Accepted: 12/28/2015] [Indexed: 12/26/2022]
Abstract
Deletions, duplications, and inversions of large genomic regions covering several genes are an important class of disease causing variants in humans. Modeling these structural variants in mice requires multistep processes in ES cells, which has limited their availability. Mutant mice containing small insertions, deletions, and single nucleotide polymorphisms can be reliably generated using CRISPR/Cas9 directly in mouse zygotes. Large structural variants can be generated using CRISPR/Cas9 in ES cells, but it has not been possible to generate these directly in zygotes. We now demonstrate the direct generation of deletions, duplications and inversions of up to one million base pairs by zygote injection. genesis 54:78–85, 2016. © 2016 The Authors. genesis Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Katharina Boroviak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridge, United Kingdom
| | - Brendan Doe
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridge, United Kingdom
| | - Ruby Banerjee
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridge, United Kingdom
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridge, United Kingdom
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridge, United Kingdom
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23
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Serth K, Beckers A, Schuster-Gossler K, Pavlova MN, Müller J, Paul MC, Reinhardt R, Gossler A. Generation of an 870 kb deletion encompassing the Skt/Etl4 locus by combination of inter- and intra-chromosomal recombination. BMC Genet 2015; 16:143. [PMID: 26678520 PMCID: PMC4683868 DOI: 10.1186/s12863-015-0302-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/08/2015] [Indexed: 11/13/2022] Open
Abstract
Background Etl4lacZ (Enhancer trap locus 4) and SktGt (Sickle tail) are lacZ reporter gene integrations into the same locus on mouse chromosome 2 targeting a gene that is expressed in the notochord of early embryos and in multiple epithelia during later development. Both insertions caused recessive mutations that resulted exclusively in mild defects in the caudal vertebral column. Since notochord-derived signals are essential for formation of the vertebral column the phenotypes suggested that the lacZ insertions interfered with some notochord-dependent aspect of vertebral development. As both insertions occurred in introns it was unclear whether they represent hypomorphic alleles or abolish gene function. Here, we have generated a definitive null allele of the Skt/Etl4 gene and analysed homozygous mutants. Results We have introduced loxP sites into three positions of the gene based on additional upstream exons that we identified, and deleted approximately 870 kb of the locus by a combination of inter- and intra-chromosomal Cre-mediated recombinations in the female germ line of mice. This deletion removes about 90 % of the coding region and results in the loss of the SKT/ETL4 protein. Similar to the Etl4lacZ and SktGt alleles our deletion mutants are viable and fertile and show only mild defects in caudal vertebrae due to abnormal intervertebral disc development, although with higher penetrance. No other tissue with Skt/Etl4 expression that we analysed showed obvious defects. Conclusion The complete loss of Skt/Etl4 function affects only development of caudal notochord derivatives and is compensated for in its other expression domains. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0302-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katrin Serth
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, 30625, Hannover, Germany.
| | - Anja Beckers
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, 30625, Hannover, Germany.
| | - Karin Schuster-Gossler
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, 30625, Hannover, Germany.
| | - Maria N Pavlova
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, 30625, Hannover, Germany. .,Department of Anaesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98001, USA.
| | - Julia Müller
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, 30625, Hannover, Germany. .,, Gasteiner Str. 31, 10717, Berlin, Germany.
| | - Mariel C Paul
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, 30625, Hannover, Germany. .,Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria.
| | - Richard Reinhardt
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany.
| | - Achim Gossler
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, 30625, Hannover, Germany.
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24
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Raines AM, Magella B, Adam M, Potter SS. Key pathways regulated by HoxA9,10,11/HoxD9,10,11 during limb development. BMC DEVELOPMENTAL BIOLOGY 2015; 15:28. [PMID: 26186931 PMCID: PMC4506574 DOI: 10.1186/s12861-015-0078-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/07/2015] [Indexed: 11/17/2022]
Abstract
Background The 39 mammalian Hox genes show problematic patterns of functional overlap. In order to more fully define the developmental roles of Hox genes it is necessary to remove multiple combinations of paralogous and flanking genes. In addition, the downstream molecular pathways regulated by Hox genes during limb development remain incompletely delineated. Results In this report we examine limb development in mice with frameshift mutations in six Hox genes, Hoxa9,10,11 and Hoxd9,10,11. The mice were made with a novel recombineering method that allows the simultaneous targeting of frameshift mutations into multiple flanking genes. The Hoxa9,10,11−/−/Hoxd9,10,11−/− mutant mice show a reduced ulna and radius that is more severe than seen in Hoxa11−/−/Hoxd11−/− mice, indicating a minor role for the flanking Hox9,10 genes in zeugopod development, as well as their primary function in stylopod development. The mutant mice also show severe reduction of Shh expression in the zone of polarizing activity, and decreased Fgf8 expression in the apical ectodermal ridge, thereby better defining the roles of these specific Hox genes in the regulation of critical signaling centers during limb development. Importantly, we also used laser capture microdissection coupled with RNA-Seq to characterize the gene expression programs in wild type and mutant limbs. Resting, proliferative and hypertrophic compartments of E15.5 forelimb zeugopods were examined. The results provide an RNA-Seq characterization of the progression of gene expression patterns during normal endochondral bone formation. In addition of the Hox mutants showed strongly altered expression of Pknox2, Zfp467, Gdf5, Bmpr1b, Dkk3, Igf1, Hand2, Shox2, Runx3, Bmp7 and Lef1, all of which have been previously shown to play important roles in bone formation. Conclusions The recombineering based frameshift mutation of the six flanking and paralogous Hoxa9,10,11 and Hoxd9,10,11 genes provides a resource for the analysis of their overlapping functions. Analysis of the Hoxa9,10,11−/−/Hoxd9,10,11−/− mutant limbs confirms and extends the results of previous studies using mice with Hox mutations in single paralogous groups or with entire Hox cluster deletions. The RNA-Seq analysis of specific compartments of the normal and mutant limbs defines the multiple key perturbed pathways downstream of these Hox genes. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0078-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna M Raines
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - Bliss Magella
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
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25
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Kishimoto R, Tamada K, Liu X, Okubo H, Ise S, Ohta H, Ruf S, Nakatani J, Kohno N, Spitz F, Takumi T. Model mice for 15q11-13 duplication syndrome exhibit late-onset obesity and altered lipid metabolism. Hum Mol Genet 2015; 24:4559-72. [PMID: 26002101 DOI: 10.1093/hmg/ddv187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 05/18/2015] [Indexed: 12/27/2022] Open
Abstract
Copy number variations on human chromosome 15q11-q13 have been implicated in several neurodevelopmental disorders. A paternal loss or duplication of the Prader-Willi syndrome/Angelman syndrome (PWS/AS) region confers a risk of obesity, although the mechanism remains a mystery due to a lack of an animal model that accurately recreates the obesity phenotype. We performed detailed analyses of mice with duplication of PWS/AS locus (6 Mb) generated by chromosome engineering and found that animals with a paternal duplication of this region (patDp/+) show late-onset obesity, high sensitivity for high-fat diet, high levels of blood leptin and insulin without an increase in food intake. We show that prior to becoming obese, young patDp/+ mice already had enlarged white adipocytes. Transcriptome analysis of adipose tissue revealed an up-regulation of Secreted frizzled-related protein 5 (Sfrp5), known to promote adipogenesis. We additionally generated a new mouse model of paternal duplication focusing on a 3 Mb region (3 Mb patDp/+) within the PWS/AS locus. These mice recapitulate the obese phenotypes including expansion of visceral adipose tissue. Our results suggest paternally expressed genes in PWS/AS locus play a significant role for the obesity and identify new potential targets for future research and treatment of obesity.
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Affiliation(s)
- Rui Kishimoto
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima 734-8553, Japan
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima 734-8553, Japan
| | - Xiaoxi Liu
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Hiroko Okubo
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Satoko Ise
- Banyu Tsukuba Research Institute, Tsukuba, Ibaraki 300-2611, Japan
| | - Hisashi Ohta
- Banyu Tsukuba Research Institute, Tsukuba, Ibaraki 300-2611, Japan
| | - Sandra Ruf
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jin Nakatani
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Ohtsu, Shiga 520-2192, Japan and
| | - Nobuoki Kohno
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima 734-8553, Japan
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima 734-8553, Japan, JST, CREST, Tokyo, Japan
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26
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Kraft K, Geuer S, Will AJ, Chan WL, Paliou C, Borschiwer M, Harabula I, Wittler L, Franke M, Ibrahim DM, Kragesteen BK, Spielmann M, Mundlos S, Lupiáñez DG, Andrey G. Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice. Cell Rep 2015; 10:833-839. [PMID: 25660031 DOI: 10.1016/j.celrep.2015.01.016] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 11/25/2022] Open
Abstract
Structural variations (SVs) contribute to the variability of our genome and are often associated with disease. Their study in model systems was hampered until now by labor-intensive genetic targeting procedures and multiple mouse crossing steps. Here we present the use of CRISPR/Cas for the fast (10 weeks) and efficient generation of SVs in mice. We specifically produced deletions, inversions, and also duplications at six different genomic loci ranging from 1.1 kb to 1.6 Mb with efficiencies up to 42%. After PCR-based selection, clones were successfully used to create mice via aggregation. To test the practicability of the method, we reproduced a human 500 kb disease-associated deletion and were able to recapitulate the human phenotype in mice. Furthermore, we evaluated the regulatory potential of a large genomic interval by deleting a 1.5 Mb fragment. The method presented permits rapid in vivo modeling of genomic rearrangements.
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Affiliation(s)
- Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sinje Geuer
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Anja J Will
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Wing Lee Chan
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Christina Paliou
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Izabela Harabula
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Bjørt K Kragesteen
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Darío G Lupiáñez
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Guillaume Andrey
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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27
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Tsujimura T, Klein FA, Langenfeld K, Glaser J, Huber W, Spitz F. A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. PLoS Genet 2015; 11:e1004897. [PMID: 25569170 PMCID: PMC4288730 DOI: 10.1371/journal.pgen.1004897] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/17/2014] [Indexed: 12/11/2022] Open
Abstract
Despite the well-documented role of remote enhancers in controlling developmental gene expression, the mechanisms that allocate enhancers to genes are poorly characterized. Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. Chromosome conformation capture experiments reveal a corresponding partition of the locus in two distinct structural entities, demarcated by a discrete transition zone. The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation. This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one. Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression. The specificity of enhancer-gene interactions is fundamental to the execution of gene regulatory programs underpinning embryonic development and cell differentiation. However, our understanding of the mechanisms conferring specificity to enhancers and target gene interactions is limited. In this study, we characterize the cis-regulatory organization of a large genomic locus consisting of two developmental genes, Tfap2c and Bmp7. We show that this locus is structurally partitioned into two distinct domains by the constitutive action of a discrete transition zone located between the two genes. This separation restricts selectively the functional action of enhancers to the genes present within the same domain. Interestingly, the effects of this region as a boundary are relative, as it allows some competing interactions to take place across domains. We show that these interactions modulate the functional output of a brain enhancer on its primary target gene resulting in the spatial restriction of its expression domain. These results support a functional link between topological chromatin domains and allocation of enhancers to genes. They further show that a precise adjustment of chromatin interaction levels fine-tunes gene regulation by long-range enhancers.
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Affiliation(s)
- Taro Tsujimura
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Felix A. Klein
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Katja Langenfeld
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Juliane Glaser
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail:
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28
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Expansion of stochastic expression repertoire by tandem duplication in mouse Protocadherin-α cluster. Sci Rep 2014; 4:6263. [PMID: 25179445 PMCID: PMC4151104 DOI: 10.1038/srep06263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/13/2014] [Indexed: 11/08/2022] Open
Abstract
Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive. To investigate the effects of tandem duplication in the Pcdh cluster, here we generated and analyzed a new line of the Pcdh cluster mutant mice. In the mutant allele, a 218-kb region containing the Pcdh-α2 to Pcdh-αc2 variable exons with their promoters was duplicated and the individual duplicated Pcdh isoforms can be disctinguished. The individual duplicated Pcdh-α isoforms showed diverse expression level with stochastic expression manner, even though those have an identical promoter sequence. Interestingly, the 5'-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation. These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence.
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29
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Nolte MJ, Wang Y, Deng JM, Swinton PG, Wei C, Guindani M, Schwartz RJ, Behringer RR. Functional analysis of limb transcriptional enhancers in the mouse. Evol Dev 2014; 16:207-23. [PMID: 24920384 DOI: 10.1111/ede.12084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Transcriptional enhancers are genomic sequences bound by transcription factors that act together with basal transcriptional machinery to regulate gene transcription. Several high-throughput methods have generated large datasets of tissue-specific enhancer sequences with putative roles in developmental processes. However, few enhancers have been deleted from the genome to determine their roles in development. To understand the roles of two enhancers active in the mouse embryonic limb bud we deleted them from the genome. Although the genes regulated by these enhancers are unknown, they were selected because they were identified in a screen for putative limb bud-specific enhancers associated with p300, an acetyltransferase that participates in protein complexes that promote active transcription, and because the orthologous human enhancers (H1442 and H280) drive distinct lacZ expression patterns in limb buds of embryonic day (E) 11.5 transgenic mice. We show that the orthologous mouse sequences, M1442 and M280, regulate dynamic expression in the developing limb. Although significant transcriptional differences in enhancer-proximal genes in embryonic limb buds accompany the deletion of M1442 and M280 no gross limb malformations during embryonic development were observed, demonstrating that M1442 and M280 are not required for mouse limb development. However, M280 is required for the development and/or maintenance of body size; M280 mice are significantly smaller than controls. M280 also harbors an "ultraconserved" sequence that is identical between human, rat, and mouse. This is the first report of a phenotype resulting from the deletion of an ultraconserved element. These studies highlight the importance of determining enhancer regulatory function by experiments that manipulate them in situ and suggest that some of an enhancer's regulatory capacities may be developmentally tolerated rather than developmentally required.
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Affiliation(s)
- Mark J Nolte
- Graduate Program in Genes and Development, University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA; Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
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30
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Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F. Long-range enhancers regulating Myc expression are required for normal facial morphogenesis. Nat Genet 2014; 46:753-8. [DOI: 10.1038/ng.2971] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/08/2014] [Indexed: 12/12/2022]
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31
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Valdez G, Heyer MP, Feng G, Sanes JR. The role of muscle microRNAs in repairing the neuromuscular junction. PLoS One 2014; 9:e93140. [PMID: 24664281 PMCID: PMC3963997 DOI: 10.1371/journal.pone.0093140] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/01/2014] [Indexed: 01/11/2023] Open
Abstract
microRNAs have been implicated in mediating key aspects of skeletal muscle development and responses to diseases and injury. Recently, we demonstrated that a synaptically enriched microRNA, miR-206, functions to promote maintenance and repair of the neuromuscular junction (NMJ); in mutant mice lacking miR-206, reinnervation is impaired following nerve injury and loss of NMJs is accelerated in a mouse model of amyotrophic lateral sclerosis (ALS). Here, we asked whether other microRNAs play similar roles. One attractive candidate is miR-133b because it is in the same transcript that encodes miR-206. Like miR-206, miR-133b is concentrated near NMJs and induced after denervation. In miR-133b null mice, however, NMJ development is unaltered, reinnervation proceeds normally following nerve injury, and disease progression is unaffected in the SOD1(G93A) mouse model of ALS. To determine if miR-206 compensates for the loss of miR-133b, we generated mice lacking both microRNAs. The phenotype of these double mutants resembled that of miR-206 single mutants. Finally, we used conditional mutants of Dicer, an enzyme required for the maturation of most microRNAs, to generate mice in which microRNAs were depleted from skeletal muscle fibers postnatally, thus circumventing a requirement for microRNAs in embryonic muscle development. Reinnervation of muscle fibers following injury was impaired in these mice, but the defect was similar in magnitude to that observed in miR-206 mutants. Together, these results suggest that miR-206 is the major microRNA that regulates repair of the NMJ following nerve injury.
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Affiliation(s)
- Gregorio Valdez
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, Virginia, United States of America
- * E-mail:
| | - Mary P. Heyer
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Therapeutics, The Scripps Research Institute Florida, Jupiter, Florida, United States of America
| | - Guoping Feng
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Joshua R. Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
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32
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Tschopp P, Duboule D. The genetics of murine Hox loci: TAMERE, STRING, and PANTHERE to engineer chromosome variants. Methods Mol Biol 2014; 1196:89-102. [PMID: 25151159 DOI: 10.1007/978-1-4939-1242-1_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Following their duplications at the base of the vertebrate clade, Hox gene clusters underwent remarkable sub- and neo-functionalization events. Many of these evolutionary innovations can be associated with changes in the transcriptional regulation of their genes, where an intricate relationship between the structure of the gene cluster and the architecture of the surrounding genomic landscape is at play. Here, we report on a portfolio of in vivo genome engineering strategies in mice, which have been used to probe and decipher the genetic and molecular underpinnings of the complex regulatory mechanisms implemented at these loci.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
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33
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Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding. Cell Rep 2013; 5:137-50. [DOI: 10.1016/j.celrep.2013.09.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/07/2013] [Accepted: 09/05/2013] [Indexed: 11/23/2022] Open
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34
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Andrey G, Montavon T, Mascrez B, Gonzalez F, Noordermeer D, Leleu M, Trono D, Spitz F, Duboule D. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 2013; 340:1234167. [PMID: 23744951 DOI: 10.1126/science.1234167] [Citation(s) in RCA: 302] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hox genes are major determinants of the animal body plan, where they organize structures along both the trunk and appendicular axes. During mouse limb development, Hoxd genes are transcribed in two waves: early on, when the arm and forearm are specified, and later, when digits form. The transition between early and late regulations involves a functional switch between two opposite topological domains. This switch is reflected by a subset of Hoxd genes mapping centrally into the cluster, which initially interact with the telomeric domain and subsequently swing toward the centromeric domain, where they establish new contacts. This transition between independent regulatory landscapes illustrates both the modularity of the limbs and the distinct evolutionary histories of its various pieces. It also allows the formation of an intermediate area of low HOX proteins content, which develops into the wrist, the transition between our arms and our hands. This regulatory strategy accounts for collinear Hox gene regulation in land vertebrate appendages.
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Affiliation(s)
- Guillaume Andrey
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
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35
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Chen CK, Symmons O, Uslu VV, Tsujimura T, Ruf S, Smedley D, Spitz F. TRACER: a resource to study the regulatory architecture of the mouse genome. BMC Genomics 2013; 14:215. [PMID: 23547943 PMCID: PMC3618316 DOI: 10.1186/1471-2164-14-215] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/22/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Mammalian genes are regulated through the action of multiple regulatory elements, often distributed across large regions. The mechanisms that control the integration of these diverse inputs into specific gene expression patterns are still poorly understood. New approaches enabling the dissection of these mechanisms in vivo are needed. RESULTS Here, we describe TRACER (http://tracerdatabase.embl.de), a resource that centralizes information from a large on-going functional exploration of the mouse genome with different transposon-associated regulatory sensors. Hundreds of insertions have been mapped to specific genomic positions, and their corresponding regulatory potential has been documented by analysis of the expression of the reporter sensor gene in mouse embryos. The data can be easily accessed and provides information on the regulatory activities present in a large number of genomic regions, notably in gene-poor intervals that have been associated with human diseases. CONCLUSIONS TRACER data enables comparisons with the expression pattern of neighbouring genes, activity of surrounding regulatory elements or with other genomic features, revealing the underlying regulatory architecture of these loci. TRACER mouse lines can also be requested for in vivo transposition and chromosomal engineering, to analyse further regions of interest.
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Affiliation(s)
- Chao-Kung Chen
- European Bioinformatics Institute - European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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36
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Marinić M, Aktas T, Ruf S, Spitz F. An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev Cell 2013; 24:530-42. [PMID: 23453598 DOI: 10.1016/j.devcel.2013.01.025] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 11/26/2012] [Accepted: 01/31/2013] [Indexed: 12/26/2022]
Abstract
Fgf8 encodes a key signaling factor, and its precise regulation is essential for embryo patterning. Here, we identified the regulatory modules that control Fgf8 expression during mammalian embryogenesis. These enhancers are interspersed with unrelated genes along a large region of 220 kb; yet they act on Fgf8 only. Intriguingly, this region also contains additional genuine enhancer activities that are not transformed into gene expression. Using genomic engineering strategies, we showed that these multiple and distinct regulatory modules act as a coherent unit and influence genes depending on their position rather than on their promoter sequence. These findings highlight how the structure of a locus regulates the autonomous intrinsic activities of the regulatory elements it contains and contributes to their tissue and target specificities. We discuss the implications of such regulatory systems regarding the evolution of gene expression and the impact of human genomic structural variations.
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Affiliation(s)
- Mirna Marinić
- Developmental Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg 69117, Germany
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37
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Cre-mediated targeted gene activation in the middle silk glands of transgenic silkworms (Bombyx mori). Transgenic Res 2012; 22:607-19. [DOI: 10.1007/s11248-012-9677-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
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38
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Abstract
Gene targeting in embryonic stem (ES) cells coupled with the site-specific Cre/loxP recombination system offers unique opportunities to identify and analyze the roles of cis-acting sequences in the regulation of imprinted gene expression. Although several different approaches have been described to engineer large chromosomal rearrangements in ES cells, these strategies can be labor-intensive and often require several subcloning of the original stem cells, therefore limiting the chances of obtaining germ line transmission of the mutation introduced. Here we describe an alternative approach which is based on in vivo recombination, therefore limiting the number of steps performed in ES cells and allowing to take advantage of the growing number of loxP insertional mutations already available in transgenic mice.
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Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus. Proc Natl Acad Sci U S A 2012; 109:20204-11. [PMID: 23134724 DOI: 10.1073/pnas.1217659109] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Copy number variations are genomic structural variants that are frequently associated with human diseases. Among these copy number variations, duplications of DNA segments are often assumed to lead to dosage effects by increasing the copy number of either genes or their regulatory elements. We produced a series of large targeted duplications within a conserved gene desert upstream of the murine HoxD locus. This DNA region, syntenic to human 2q31-32, contains a range of regulatory elements required for Hoxd gene transcription, and it is often disrupted and/or reorganized in human genetic conditions collectively known as the 2q31 syndrome. Unexpectedly, one such duplication led to a transcriptional down-regulation in developing digits by impairing physical interactions between the target genes and their upstream regulatory elements, thus phenocopying the effect obtained when these enhancer sequences are deleted. These results illustrate the detrimental consequences of interrupting highly conserved regulatory landscapes and reveal a mechanism where genomic duplications lead to partial loss of function of nearby located genes.
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Hasegawa S, Hirabayashi T, Kondo T, Inoue K, Esumi S, Okayama A, Hamada S, Yagi T. Constitutively expressed Protocadherin-α regulates the coalescence and elimination of homotypic olfactory axons through its cytoplasmic region. Front Mol Neurosci 2012; 5:97. [PMID: 23087612 PMCID: PMC3472330 DOI: 10.3389/fnmol.2012.00097] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 09/27/2012] [Indexed: 11/29/2022] Open
Abstract
Olfactory sensory neuron (OSN) axons coalesce into specific glomeruli in the olfactory bulb (OB) according to their odorant receptor (OR) expression. Several guidance molecules enhance the coalescence of homotypic OSN projections, in an OR-specific- and neural-activity-dependent manner. However, the mechanism by which homotypic OSN axons are organized into glomeruli is unsolved. We previously reported that the clustered protocadherin-α (Pcdh-α) family of diverse cadherin-related molecules plays roles in the coalescence and elimination of homotypic OSN axons throughout development. Here we showed that the elimination of small ectopic homotypic glomeruli required the constitutive expression of a Pcdh-α isoform and Pcdh-α's cytoplasmic region, but not OR specificity or neural activity. These results suggest that Pcdh-α proteins provide a cytoplasmic signal to regulate repulsive activity for homotypic OSN axons independently of OR expression and neural activity. The counterbalancing effect of Pcdh-α proteins for the axonal coalescence mechanisms mediated by other olfactory guidance molecules indicate a possible mechanism for the organization of homotypic OSN axons into glomeruli during development.
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Affiliation(s)
- Sonoko Hasegawa
- KOKORO-Biology Group and CREST-JST, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University Osaka, Japan
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41
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Wei Y, Li L, Zhou X, Zhang QY, Dunbar A, Liu F, Kluetzman K, Yang W, Ding X. Generation and characterization of a novel Cyp2a(4/5)bgs-null mouse model. Drug Metab Dispos 2012; 41:132-40. [PMID: 23073733 DOI: 10.1124/dmd.112.048736] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Knockout mouse models targeting various cytochrome P450 (P450 or CYP) genes are valuable for determining P450's biologic functions, including roles in drug metabolism and chemical toxicity. In this study, a novel Cyp2a(4/5)bgs-null mouse model was generated, in which a 1.2-megabase pair genomic fragment containing nine Cyp genes in mouse chromosome 7 (including, sequentially, Cyp2a5, 2g1, 2b19, 2b23, 2a4, 2b9, 2b13, 2b10, and 2s1) are deleted, through Cre-mediated recombination in vivo. The resultant mouse strain was viable and fertile, without any developmental deficits or morphologic abnormalities. Deletion of the constitutive genes in the cluster was confirmed by polymerase chain reaction analysis of the genes and the mRNAs in tissues known to express each gene. The loss of this gene cluster led to significant decreases in microsomal activities toward testosterone hydroxylation in various tissues examined, including olfactory mucosa (OM), lung, liver, and brain. In addition, systemic clearance of pentobarbital was decreased in Cyp2a(4/5)bgs-null mice, as indicated by >60% increases in pentobarbital-induced sleeping time, compared with wild-type (WT) mice. This novel Cyp2a(4/5)bgs-null mouse model will be valuable for in vivo studies of drug metabolism and chemical toxicities in various tissues, including the liver, lung, brain, intestine, kidney, skin, and OM, where one or more of the targeted Cyp genes are known to be expressed in WT mice. The model will also be valuable for preparation of humanized mice that express human CYP2A6, CYP2A13, CYP2B6, or CYP2S1, and as a knockout mouse model for five non-P450 genes (Vmn1r184, Nalp9c, Nalp4a, Nalp9a, and Vmn1r185) that were also deleted.
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Affiliation(s)
- Yuan Wei
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA
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42
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Herault Y, Duchon A, Velot E, Maréchal D, Brault V. The in vivo Down syndrome genomic library in mouse. PROGRESS IN BRAIN RESEARCH 2012; 197:169-97. [PMID: 22541293 DOI: 10.1016/b978-0-444-54299-1.00009-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mouse models are key elements to better understand the genotype-phenotype relationship and the physiopathology of Down syndrome (DS). Even though the mouse will never recapitulate the whole spectrum of intellectual disabilities observed in the DS, mouse models have been developed over the recent decades and have been used extensively to identify homologous genes or entire regions homologous to the human chromosome 21 (Hsa21) that are necessary or sufficient to induce DS cognitive features. In this chapter, we review the principal mouse DS models which have been selected and engineered over the years either for large genomic regions or for a few or a single gene of interest. Their analyses highlight the complexity of the genetic interactions that are involved in DS cognitive phenotypes and also strengthen the hypothesis on the multigenic nature of DS. This review also addresses future research challenges relative to the making of new models and their combination to go further in the characterization of candidates and modifier of the DS features.
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Affiliation(s)
- Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Translational medicine and Neurogenetics program, IGBMC, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, Illkirch, Strasbourg, France.
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43
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Zakany J, Duboule D. A genetic basis for altered sexual behavior in mutant female mice. Curr Biol 2012; 22:1676-80. [PMID: 22863319 DOI: 10.1016/j.cub.2012.06.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/06/2012] [Accepted: 06/26/2012] [Indexed: 12/01/2022]
Abstract
Although neural substrates of mammalian female mating behavior have been described, the association between complex courtship activity and specific underlying mechanisms remains elusive. We have isolated a mouse line that unexpectedly shows altered female social behavior with increased investigation of males and increased genital biting. We investigated adult individuals by behavioral observation and genetic and molecular neuroanatomy methods. We report exacerbated inverse pursuits and incapacitating bites directed at the genitals of stud males. This extreme deviation from wild-type female courtship segregates with a deletion of the Hoxd1 to Hoxd9 genomic region. This dominant Atypical female courtship allele (HoxD(Afc)) induces ectopic Hoxd10 gene expression in several regions in newborn forebrain transitorily and stably in a sparse subpopulation of cells in the cornu ammonis fields of adult hippocampus, which may thus lead to an abnormal modulation in the sexual behavior of mutant females. The resulting compulsive sexual solicitation behavior displayed by the most affected individuals suggests new avenues to study the genetic and molecular bases of normal and pathological mammalian affect and raises the potential involvement of the hippocampus in the control of female courtship behavior. The potential relevance to human 2q.31.1 microdeletion syndrome is discussed.
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Affiliation(s)
- Jozsef Zakany
- National Research Centre Frontiers in Genetics, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland.
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44
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Raveau M, Lignon JM, Nalesso V, Duchon A, Groner Y, Sharp AJ, Dembele D, Brault V, Hérault Y. The App-Runx1 region is critical for birth defects and electrocardiographic dysfunctions observed in a Down syndrome mouse model. PLoS Genet 2012; 8:e1002724. [PMID: 22693452 PMCID: PMC3364940 DOI: 10.1371/journal.pgen.1002724] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 04/05/2012] [Indexed: 01/24/2023] Open
Abstract
Down syndrome (DS) leads to complex phenotypes and is the main genetic cause of birth defects and heart diseases. The Ts65Dn DS mouse model is trisomic for the distal part of mouse chromosome 16 and displays similar features with post-natal lethality and cardiovascular defects. In order to better understand these defects, we defined electrocardiogram (ECG) with a precordial set-up, and we found conduction defects and modifications in wave shape, amplitudes, and durations in Ts65Dn mice. By using a genetic approach consisting of crossing Ts65Dn mice with Ms5Yah mice monosomic for the App-Runx1 genetic interval, we showed that the Ts65Dn viability and ECG were improved by this reduction of gene copy number. Whole-genome expression studies confirmed gene dosage effect in Ts65Dn, Ms5Yah, and Ts65Dn/Ms5Yah hearts and showed an overall perturbation of pathways connected to post-natal lethality (Coq7, Dyrk1a, F5, Gabpa, Hmgn1, Pde10a, Morc3, Slc5a3, and Vwf) and heart function (Tfb1m, Adam19, Slc8a1/Ncx1, and Rcan1). In addition cardiac connexins (Cx40, Cx43) and sodium channel sub-units (Scn5a, Scn1b, Scn10a) were found down-regulated in Ts65Dn atria with additional down-regulation of Cx40 in Ts65Dn ventricles and were likely contributing to conduction defects. All these data pinpoint new cardiac phenotypes in the Ts65Dn, mimicking aspects of human DS features and pathways altered in the mouse model. In addition they highlight the role of the App-Runx1 interval, including Sod1 and Tiam1, in the induction of post-natal lethality and of the cardiac conduction defects in Ts65Dn. These results might lead to new therapeutic strategies to improve the care of DS people.
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Affiliation(s)
- Matthieu Raveau
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, Illkirch, France
| | - Jacques M. Lignon
- Immunologie et Embryologie Moléculaire, CNRS Université d'Orléans, UMR6218, Orléans, France
| | - Valérie Nalesso
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, Illkirch, France
| | - Arnaud Duchon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, Illkirch, France
| | - Yoram Groner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Doulaye Dembele
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, Illkirch, France
| | - Véronique Brault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, Illkirch, France
| | - Yann Hérault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, Illkirch, France
- Transgénèse et Archivage d'Animaux Modèles, CNRS, UPS44, Orléans, France
- Institut Clinique de la Souris, Illkirch, France
- * E-mail:
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45
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Unsuccessful attempt at gene-editing by homologous recombination in the zebrafish germ line using the approach of "Rong and Golic". Transgenic Res 2012; 21:1125-36. [PMID: 22434322 PMCID: PMC3432782 DOI: 10.1007/s11248-012-9607-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 02/22/2012] [Indexed: 10/31/2022]
Abstract
We have investigated the practicality of implementing a strategy for site-specific editing by homologous recombination in zebrafish analogous to that developed by Rong and Golic (Rong and Golic in Genetics 157:1307-1312, 2001) in Drosophila melanogaster. We analysed approximately 7,300 offspring from 22 crosses and demonstrated successful excision of the gene editing construct but failed to detect either gene editing or the random integration of the intact editing construct subsequent to excision. The clustering of events in our data set demonstrates that the excision events are not occurring independently and emphasise that a promoter driving high level, tissue-specific transcription in meiotic cells is likely to be necessary if this general approach to site-specific editing by homologous recombination is to fulfil its potential.
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46
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Delpretti S, Zakany J, Duboule D. A function for all posterior Hoxd genes during digit development? Dev Dyn 2012; 241:792-802. [PMID: 22374744 DOI: 10.1002/dvdy.23756] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Four posterior Hoxd genes, from Hoxd13 to Hoxd10, are collectively regulated during the development of tetrapod digits. Besides the well-documented role of Hoxd13, the function of the neighboring genes has been difficult to evaluate due to the close genetic linkage and potential regulatory interferences. We used a combination of five small nested deletions in cis, involving from two to four consecutive genes of the Hoxd13 to Hoxd9 loci, in mice, to evaluate their combined functional importance. RESULTS We show that deletions leading to a gain of function of Hoxd13, via regulatory re-allocation, generate abnormal phenotypes, in agreement with the dominant negative role of this gene. We also show that Hoxd10, Hoxd11, and Hoxd12 all seem to play a genuine role in digit development, though less compelling than that of Hoxd13. In contrast, the nearby Hoxd9 contributed no measurable function in digits. CONCLUSIONS We conclude that a slight and transient deregulation of Hoxd13 expression can readily affect the relative lengths of limb segments and that all posterior Hoxd genes likely contribute to the final limb morphology. We discuss the difficulty to clearly assess the functional share of individual genes within such a gene family, where closely located neighbors, coding for homologous proteins, are regulated by a unique circuitry and all contribute to shape the distal parts of our appendages.
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Affiliation(s)
- Saskia Delpretti
- National Research Centre Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, Switzerland
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47
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Tschopp P, Duboule D. A genetic approach to the transcriptional regulation of Hox gene clusters. Annu Rev Genet 2012; 45:145-66. [PMID: 22060042 DOI: 10.1146/annurev-genet-102209-163429] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of vertebrate genomes was accompanied by an astounding increase in the complexity of their regulatory modalities. Genetic redundancy resulting from large-scale genome duplications at the base of the chordate tree was repeatedly exploited by the functional redeployment of paralogous genes via innovations in their regulatory circuits. As a paradigm of such regulatory evolution, we have extensively studied those control mechanisms at work in-cis over vertebrate Hox gene clusters. Here, we review the portfolio of genetic strategies that have been developed to tackle the intricate relationship between genomic topography and the transcriptional activities in this gene family, and we describe some of the mechanistic insights we gained by using the HoxD cluster as an example. We discuss the high heuristic value of this system in our general understanding of how changes in transcriptional regulation can diversify gene function and thereby fuel morphological evolution.
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Affiliation(s)
- Patrick Tschopp
- National Center of Competence in Research, Frontiers in Genetics, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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48
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Tschopp P, Christen AJ, Duboule D. Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters. Development 2012; 139:929-39. [PMID: 22278926 DOI: 10.1242/dev.076794] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The importance of Hox genes in the specification of neuronal fates in the spinal cord has long been recognized. However, the transcriptional controls underlying their collinear expression domains remain largely unknown. Here we show in mice that the correspondence between the physical order of Hoxd genes and their rostral expression boundaries, although respecting spatial collinearity, does not display a fully progressive distribution. Instead, two major anteroposterior boundaries are detected, coinciding with the functional subdivision of the spinal cord. Tiling array analyses reveal two distinct blocks of transcription, regulated independently from one another, that define the observed expression boundaries. Targeted deletions in vivo that remove the genomic fragments separating the two blocks induce ectopic expression of posterior genes. We further evaluate the independent regulatory potential and transcription profile of each gene locus by a tiling array approach using a contiguous series of transgenes combined with locus-specific deletions. Our work uncovers a bimodal type of HoxD spatial collinearity in the developing spinal cord that relies on two separate 'enhancer mini-hubs' to ensure correct Hoxd gene expression levels while maintaining their appropriate anteroposterior boundaries.
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Affiliation(s)
- Patrick Tschopp
- National Research Centre Frontiers in Genetics at Department of Genetics and Evolution, University of Geneva, Sciences III, Quai Ernest-Ansermet 30, Geneva 4, Switzerland
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49
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A regulatory archipelago controls Hox genes transcription in digits. Cell 2012; 147:1132-45. [PMID: 22118467 DOI: 10.1016/j.cell.2011.10.023] [Citation(s) in RCA: 363] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 06/11/2011] [Accepted: 10/07/2011] [Indexed: 11/22/2022]
Abstract
The evolution of digits was an essential step in the success of tetrapods. Among the key players, Hoxd genes are coordinately regulated in developing digits, where they help organize growth and patterns. We identified the distal regulatory sites associated with these genes by probing the three-dimensional architecture of this regulatory unit in developing limbs. This approach, combined with in vivo deletions of distinct regulatory regions, revealed that the active part of the gene cluster contacts several enhancer-like sequences. These elements are dispersed throughout the nearby gene desert, and each contributes either quantitatively or qualitatively to Hox gene transcription in presumptive digits. We propose that this genetic system, which we call a "regulatory archipelago," provides an inherent flexibility that may partly underlie the diversity in number and morphology of digits across tetrapods, as well as their resilience to drastic variations.
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50
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Scotti M, Kmita M. Recruitment of 5' Hoxa genes in the allantois is essential for proper extra-embryonic function in placental mammals. Development 2012; 139:731-9. [PMID: 22219351 DOI: 10.1242/dev.075408] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Hox gene family is well known for its functions in establishing morphological diversity along the anterior-posterior axis of developing embryos. In mammals, one of these genes, Hoxa13, is crucial for embryonic survival, as its function is required for the proper expansion of the fetal vasculature in the placenta. Thus, it appears that the developmental strategy specific to placental mammals is linked, at least in part, to the recruitment of Hoxa13 function in developing extra-embryonic tissues. Yet, the mechanism underlying this extra-embryonic recruitment is unknown. Here, we provide evidence that this functional novelty is not exclusive to Hoxa13 but is shared with its neighboring Hoxa11 and Hoxa10 genes. We show that the extra-embryonic function of these three Hoxa genes stems from their specific expression in the allantois, an extra-embryonic hallmark of amniote vertebrates. Interestingly, Hoxa10-13 expression in the allantois is conserved in chick embryos, which are non-placental amniotes, suggesting that the extra-embryonic recruitment of Hoxa10, Hoxa11 and Hoxa13 most likely arose in amniotes, i.e. prior to the emergence of placental mammals. Finally, using a series of targeted recombination and transgenic assays, we provide evidence that the regulatory mechanism underlying Hoxa expression in the allantois is extremely complex and relies on several cis-regulatory sequences.
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Affiliation(s)
- Martina Scotti
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal, Université de Montréal, 110 avenue des Pins Ouest, Montréal, Québec, Canada
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