1
|
Manti PG, Darbellay F, Leleu M, Coughlan AY, Moret B, Cuennet J, Droux F, Stoudmann M, Mancini GF, Hautier A, Sordet-Dessimoz J, Vincent SD, Testa G, Cossu G, Barrandon Y. The Transcriptional Regulator Prdm1 Is Essential for the Early Development of the Sensory Whisker Follicle and Is Linked to the Beta-Catenin First Dermal Signal. Biomedicines 2022; 10:2647. [PMID: 36289911 PMCID: PMC9599752 DOI: 10.3390/biomedicines10102647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/18/2022] Open
Abstract
Prdm1 mutant mice are one of the rare mutant strains that do not develop whisker hair follicles while still displaying a pelage. Here, we show that Prdm1 is expressed at the earliest stage of whisker development in clusters of mesenchymal cells before placode formation. Its conditional knockout in the murine soma leads to the loss of expression of Bmp2, Shh, Bmp4, Krt17, Edar, and Gli1, though leaving the β-catenin-driven first dermal signal intact. Furthermore, we show that Prdm1 expressing cells not only act as a signaling center but also as a multipotent progenitor population contributing to the several lineages of the adult whisker. We confirm by genetic ablation experiments that the absence of macro vibrissae reverberates on the organization of nerve wiring in the mystacial pads and leads to the reorganization of the barrel cortex. We demonstrate that Lef1 acts upstream of Prdm1 and identify a primate-specific deletion of a Lef1 enhancer named Leaf. This loss may have been significant in the evolutionary process, leading to the progressive defunctionalization and disappearance of vibrissae in primates.
Collapse
Affiliation(s)
- Pierluigi G Manti
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Fabrice Darbellay
- Laboratory of Developmental Genomics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Marion Leleu
- BioInformatics Competence Center, UNIL-EPFL, 1015 Lausanne, Switzerland
| | - Aisling Y Coughlan
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Bernard Moret
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Julien Cuennet
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Frederic Droux
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Magali Stoudmann
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Gian-Filippo Mancini
- Histology Core Facility, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Agnès Hautier
- Histology Core Facility, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | | | - Stephane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Giuseppe Testa
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Giulio Cossu
- Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester M139PL, UK
- Division of Neuroscience, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Yann Barrandon
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
- Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
- Department of Plastic, Reconstructive and Aesthetic Surgery, Singapore General Hospital, Singapore 169608, Singapore
- A*STAR Skin Research Labs, Singapore 138648, Singapore
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Abstract
The use of 3C-based methods has revealed the importance of the 3D organization of the chromatin for key aspects of genome biology. However, the different caveats of the variants of 3C techniques have limited their scope and the range of scientific fields that could benefit from these approaches. To address these limitations, we present 4Cin, a method to generate 3D models and derive virtual Hi-C (vHi-C) heat maps of genomic loci based on 4C-seq or any kind of 4C-seq-like data, such as those derived from NG Capture-C. 3D genome organization is determined by integrative consideration of the spatial distances derived from as few as four 4C-seq experiments. The 3D models obtained from 4C-seq data, together with their associated vHi-C maps, allow the inference of all chromosomal contacts within a given genomic region, facilitating the identification of Topological Associating Domains (TAD) boundaries. Thus, 4Cin offers a much cheaper, accessible and versatile alternative to other available techniques while providing a comprehensive 3D topological profiling. By studying TAD modifications in genomic structural variants associated to disease phenotypes and performing cross-species evolutionary comparisons of 3D chromatin structures in a quantitative manner, we demonstrate the broad potential and novel range of applications of our method. Chromatin conformation capture (3C) methods have revealed the importance of the 3D organization of the chromatin, which is key to understand many aspects of genome biology. But each of these methods have their own limitations. Here we present 4Cin, a software that generates 3D models of the chromatin from a small number of 4C-seq experiments, a 3C-based method that provides the frequency of contacts between one fragments and the genome (one vs all). These 3D models are used to infer all chromosomal contacts within a given genomic region (many vs many). The contact maps facilitate the identification of Topological Associating Domains boundaries. Our software offers a much cheaper, accessible and versatile alternative to other available techniques while providing a comprehensive 3D topological profiling. We applied our software to two different loci to study modifications in genomic structural variants associated to disease phenotypes and to compare the chromatin organization in two different species in a quantitative manner.
Collapse
|
5
|
Neijts R, Deschamps J. At the base of colinear Hox gene expression: cis -features and trans -factors orchestrating the initial phase of Hox cluster activation. Dev Biol 2017; 428:293-299. [DOI: 10.1016/j.ydbio.2017.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/16/2017] [Indexed: 10/19/2022]
|
6
|
Armit C, Richardson L, Venkataraman S, Graham L, Burton N, Hill B, Yang Y, Baldock RA. eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis. Dev Biol 2017; 423:1-11. [PMID: 28161522 PMCID: PMC5442644 DOI: 10.1016/j.ydbio.2017.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/23/2022]
Abstract
The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expression data for the mouse embryo. In this resource article we describe the novel web-based tools we have developed for 3D visualisation of embryo anatomy and gene expression. We show how mapping of gene expression data onto spatial models delivers a framework for capturing gene expression that enhances our understanding of development, and we review the exploratory tools utilised by the EMAGE gene expression database as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ-omic expression patterns. We report on recent developments of the eHistology atlas and our use of web-services to support embedding of the online 'The Atlas of Mouse Development' in the context of other resources such as the DMDD mouse phenotype database. In addition, we discuss new developments including a cellular-resolution placental atlas, third-party atlas models, clonal analysis data and a new interactive eLearning resource for developmental processes.
Collapse
Affiliation(s)
- Chris Armit
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Lorna Richardson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Shanmugasundaram Venkataraman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Liz Graham
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Nicholas Burton
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Bill Hill
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Yiya Yang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Richard A Baldock
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| |
Collapse
|
7
|
Adebayo S, McLeod K, Tudose I, Osumi-Sutherland D, Burdett T, Baldock R, Burger A, Parkinson H. PhenoImageShare: an image annotation and query infrastructure. J Biomed Semantics 2016; 7:35. [PMID: 27267125 PMCID: PMC4896029 DOI: 10.1186/s13326-016-0072-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/05/2016] [Indexed: 01/12/2023] Open
Abstract
Background High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to the community are all challenges that come with these methods. Results PhenoImageShare provides an ontology-enabled lightweight image data query, annotation service and a single point of access backed by a Solr server for programmatic access to an integrated image collection enabling improved community access. PhenoImageShare also provides an easy to use online image annotation tool with functionality to draw regions of interest on images and to annotate them with terms from an autosuggest-enabled ontology-lookup widget. The provenance of each image, and annotation, is kept and links to original resources are provided. The semantic and intuitive search interface is species and imaging technology neutral. PhenoImageShare now provides access to annotation for over 100,000 images for 2 species. Conclusion The PhenoImageShare platform provides underlying infrastructure for both programmatic access and user-facing tools for biologists enabling the query and annotation of federated images. PhenoImageShare is accessible online at http://www.phenoimageshare.org.
Collapse
Affiliation(s)
- Solomon Adebayo
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh, UK
| | - Kenneth McLeod
- Department of Computer Science, Heriot-Watt University, Edinburgh, UK
| | - Ilinca Tudose
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Tony Burdett
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Richard Baldock
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh, UK
| | - Albert Burger
- Department of Computer Science, Heriot-Watt University, Edinburgh, UK
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Abstract
Transcriptional regulation of thousands of genes instructs complex morphogenetic and molecular events for heart development. Cardiac transcription factors choreograph gene expression at each stage of differentiation by interacting with cofactors, including chromatin-modifying enzymes, and by binding to a constellation of regulatory DNA elements. Here, we present salient examples relevant to cardiovascular development and heart disease, and review techniques that can sharpen our understanding of cardiovascular biology. We discuss the interplay between cardiac transcription factors, cis-regulatory elements, and chromatin as dynamic regulatory networks, to orchestrate sequential deployment of the cardiac gene expression program.
Collapse
Affiliation(s)
- Irfan S Kathiriya
- From the Gladstone Institute of Cardiovascular Disease and the Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (I.S.K., E.P.N., B.G.B.); and Department of Anesthesia and Perioperative Care (I.S.K.), Department of Pediatrics (B.G.B.), Cardiovascular Research Institute (B.G.B.), and Institute for Regeneration Medicine (B.G.B.), University of California, San Francisco.
| | - Elphège P Nora
- From the Gladstone Institute of Cardiovascular Disease and the Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (I.S.K., E.P.N., B.G.B.); and Department of Anesthesia and Perioperative Care (I.S.K.), Department of Pediatrics (B.G.B.), Cardiovascular Research Institute (B.G.B.), and Institute for Regeneration Medicine (B.G.B.), University of California, San Francisco.
| | - Benoit G Bruneau
- From the Gladstone Institute of Cardiovascular Disease and the Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (I.S.K., E.P.N., B.G.B.); and Department of Anesthesia and Perioperative Care (I.S.K.), Department of Pediatrics (B.G.B.), Cardiovascular Research Institute (B.G.B.), and Institute for Regeneration Medicine (B.G.B.), University of California, San Francisco.
| |
Collapse
|
10
|
Hoxa2 selectively enhances Meis binding to change a branchial arch ground state. Dev Cell 2015; 32:265-77. [PMID: 25640223 PMCID: PMC4333904 DOI: 10.1016/j.devcel.2014.12.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/18/2014] [Accepted: 12/23/2014] [Indexed: 02/07/2023]
Abstract
Hox transcription factors (TFs) are essential for vertebrate development, but how these evolutionary conserved proteins function in vivo remains unclear. Because Hox proteins have notoriously low binding specificity, they are believed to bind with cofactors, mainly homeodomain TFs Pbx and Meis, to select their specific targets. We mapped binding of Meis, Pbx, and Hoxa2 in the branchial arches, a series of segments in the developing vertebrate head. Meis occupancy is largely similar in Hox-positive and -negative arches. Hoxa2, which specifies second arch (IIBA) identity, recognizes a subset of Meis prebound sites that contain Hox motifs. Importantly, at these sites Meis binding is strongly increased. This enhanced Meis binding coincides with active enhancers, which are linked to genes highly expressed in the IIBA and regulated by Hoxa2. These findings show that Hoxa2 operates as a tissue-specific cofactor, enhancing Meis binding to specific sites that provide the IIBA with its anatomical identity. Meis provides a ground state that is common to all the branchial arches Hoxa2 recognizes Meis prebound sites in the second arch that contain Hox motifs Hoxa2 enhances Meis binding, which coincides with active enhancers, at these sites Hoxa2 modulates the ground-state binding of Meis to instruct second arch identity
Collapse
|
11
|
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.
Collapse
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:
| |
Collapse
|
12
|
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]
|
13
|
Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F. Functional and topological characteristics of mammalian regulatory domains. Genome Res 2014; 24:390-400. [PMID: 24398455 PMCID: PMC3941104 DOI: 10.1101/gr.163519.113] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/19/2013] [Indexed: 01/04/2023]
Abstract
Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene regulatory activities along the mouse genome, using hundreds of insertions of a regulatory sensor. We found that enhancers distribute their activities along broad regions and not in a gene-centric manner, defining large regulatory domains. Remarkably, these domains correlate strongly with the recently described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within large domains. These findings support a model of genomic organization where TADs confine regulatory activities to specific but large regulatory domains, contributing to the establishment of specific gene expression profiles.
Collapse
Affiliation(s)
- Orsolya Symmons
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Veli Vural Uslu
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Taro Tsujimura
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sandra Ruf
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sonya Nassari
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Wibke Schwarzer
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Laurence Ettwiller
- Centre for Organismal Studies, University of Heidelberg, 69111 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| |
Collapse
|