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García-Padilla C, Lozano-Velasco E, García-López V, Aránega A, Franco D, García-Martínez V, López-Sánchez C. miR-1 as a Key Epigenetic Regulator in Early Differentiation of Cardiac Sinoatrial Region. Int J Mol Sci 2024; 25:6608. [PMID: 38928314 PMCID: PMC11204236 DOI: 10.3390/ijms25126608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
A large diversity of epigenetic factors, such as microRNAs and histones modifications, are known to be capable of regulating gene expression without altering DNA sequence itself. In particular, miR-1 is considered the first essential microRNA in cardiac development. In this study, miR-1 potential role in early cardiac chamber differentiation was analyzed through specific signaling pathways. For this, we performed in chick embryos functional experiments by means of miR-1 microinjections into the posterior cardiac precursors-of both primitive endocardial tubes-committed to sinoatrial region fates. Subsequently, embryos were subjected to whole mount in situ hybridization, immunohistochemistry and RT-qPCR analysis. As a relevant novelty, our results revealed that miR-1 increased Amhc1, Tbx5 and Gata4, while this microRNA diminished Mef2c and Cripto expressions during early differentiation of the cardiac sinoatrial region. Furthermore, we observed in this developmental context that miR-1 upregulated CrabpII and Rarß and downregulated CrabpI, which are three crucial factors in the retinoic acid signaling pathway. Interestingly, we also noticed that miR-1 directly interacted with Hdac4 and Calm1/Calmodulin, as well as with Erk2/Mapk1, which are three key factors actively involved in Mef2c regulation. Our study shows, for the first time, a key role of miR-1 as an epigenetic regulator in the early differentiation of the cardiac sinoatrial region through orchestrating opposite actions between retinoic acid and Mef2c, fundamental to properly assign cardiac cells to their respective heart chambers. A better understanding of those molecular mechanisms modulated by miR-1 will definitely help in fields applied to therapy and cardiac regeneration and repair.
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Affiliation(s)
- Carlos García-Padilla
- Department of Human Anatomy and Embryology, Faculty of Medicine and Health Sciences, Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (C.G.-P.); (E.L.-V.); (V.G.-L.); (V.G.-M.)
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (A.A.); (D.F.)
| | - Estefanía Lozano-Velasco
- Department of Human Anatomy and Embryology, Faculty of Medicine and Health Sciences, Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (C.G.-P.); (E.L.-V.); (V.G.-L.); (V.G.-M.)
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (A.A.); (D.F.)
- Medina Foundation, 18016 Granada, Spain
| | - Virginio García-López
- Department of Human Anatomy and Embryology, Faculty of Medicine and Health Sciences, Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (C.G.-P.); (E.L.-V.); (V.G.-L.); (V.G.-M.)
- Department of Medical and Surgical Therapeutics, Pharmacology Area, Faculty of Medicine and Health Sciences, University of Extremadura, 06006 Badajoz, Spain
| | - Amelia Aránega
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (A.A.); (D.F.)
- Medina Foundation, 18016 Granada, Spain
| | - Diego Franco
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (A.A.); (D.F.)
- Medina Foundation, 18016 Granada, Spain
| | - Virginio García-Martínez
- Department of Human Anatomy and Embryology, Faculty of Medicine and Health Sciences, Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (C.G.-P.); (E.L.-V.); (V.G.-L.); (V.G.-M.)
| | - Carmen López-Sánchez
- Department of Human Anatomy and Embryology, Faculty of Medicine and Health Sciences, Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (C.G.-P.); (E.L.-V.); (V.G.-L.); (V.G.-M.)
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2
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Baldarelli RM, Smith CL, Ringwald M, Richardson JE, Bult CJ. Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse. Genetics 2024; 227:iyae031. [PMID: 38531069 PMCID: PMC11075557 DOI: 10.1093/genetics/iyae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/13/2024] [Indexed: 03/28/2024] Open
Abstract
Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic and genomic aspects of human biology and disease using the laboratory mouse as a model system. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are core MGI databases that share data and system architecture. MGI serves as the central community resource of integrated information about mouse genome features, variation, expression, gene function, phenotype, and human disease models acquired from peer-reviewed publications, author submissions, and major bioinformatics resources. To facilitate integration and standardization of data, biocuration scientists annotate using terms from controlled metadata vocabularies and biological ontologies (e.g. Mammalian Phenotype Ontology, Mouse Developmental Anatomy, Disease Ontology, Gene Ontology, etc.), and by applying international community standards for gene, allele, and mouse strain nomenclature. MGI serves basic scientists, translational researchers, and data scientists by providing access to FAIR-compliant data in both human-readable and compute-ready formats. The MGI resource is accessible at https://informatics.jax.org. Here, we present an overview of the core data types represented in MGI and highlight recent enhancements to the resource with a focus on new data and functionality for MGD and GXD.
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Affiliation(s)
| | | | | | | | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
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3
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Kondoh H, Takemoto T. The Origin and Regulation of Neuromesodermal Progenitors (NMPs) in Embryos. Cells 2024; 13:549. [PMID: 38534393 DOI: 10.3390/cells13060549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Neuromesodermal progenitors (NMPs), serving as the common origin of neural and paraxial mesodermal development in a large part of the trunk, have recently gained significant attention because of their critical importance in the understanding of embryonic organogenesis and the design of in vitro models of organogenesis. However, the nature of NMPs at many essential points remains only vaguely understood or even incorrectly assumed. Here, we discuss the nature of NMPs, focusing on their dynamic migratory behavior during embryogenesis and the mechanisms underlying their neural vs. mesodermal fate choice. The discussion points include the following: (1) How the sinus rhomboidals is organized; the tissue where the neural or mesodermal fate choice of NMPs occurs. (2) NMPs originating from the broad posterior epiblast are associated with Sox2 N1 enhancer activity. (3) Tbx6-dependent Sox2 repression occurs during NMP-derived paraxial mesoderm development. (4) The nephric mesenchyme, a component of the intermediate mesoderm, was newly identified as an NMP derivative. (5) The transition of embryonic tissue development from tissue-specific progenitors in the anterior part to that from NMPs occurs at the forelimb bud axial level. (6) The coexpression of Sox2 and Bra in NMPs is conditional and is not a hallmark of NMPs. (7) The ability of the NMP pool to sustain axial embryo growth depends on Wnt3a signaling in the NMP population. Current in vitro models of NMPs are also critically reviewed.
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Affiliation(s)
- Hisato Kondoh
- Biohistory Research Hall, Takatsuki 569-1125, Japan
- Osaka University, Suita 565-0871, Japan
| | - Tatsuya Takemoto
- Laboratory for Embryology, Institute for Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
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4
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Suzuki K, Kwon SJ, Saito D, Atsuta Y. LIN28 is essential for the maintenance of chicken primordial germ cells. Cells Dev 2023; 176:203874. [PMID: 37453484 DOI: 10.1016/j.cdev.2023.203874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Understanding the mechanism of stem cell maintenance underlies the establishment of long-term and mass culture methods for stem cells that are fundamental for clinical and agricultural applications. In this study, we use chicken primordial germ cell (PGC) as a model to elucidate the molecular mechanisms underlying stem cell maintenance. The PGC is a useful experimental model because it is readily gene-manipulatable and easy to test gene function in vivo using transplantation. Previous studies to establish a long-term culture system have shown that secreted factors such as FGF2 are required to maintain the self-renewal capability of PGC. On the other hand, we know little about intracellular regulators responsible for PGC maintenance. Among representative stem cell factors, we focus on RNA-binding factors LIN28A and LIN28B as possible central regulators for the gene regulatory network essential to PGC maintenance. By taking advantage of the CRISPR/Cas9-mediated gene editing and a clonal culture technique, we find that both LIN28A and LIN28B regulate the proliferation of PGC in vitro. We further showed that colonization efficiency of grafted PGC at the genital ridges, rudiments for the gonads, of chicken embryos were significantly decreased by knockout (KO) of LIN28A or LIN28B. Of note, overexpression of human LIN28 in LIN28-KO PGC was sufficient to restore the low colonization rates, suggesting that LIN28 plays a key role in PGC colonization at the gonads. Transcriptomic analyses of LIN28-KO PGC reveal that several genes related to mesenchymal traits are upregulated, including EGR1, a transcription factor that promotes the differentiation of mesodermal tissues. Finally, we show that the forced expression of human EGR1 deteriorates replication activity and colonization efficiency of PGCs. Taken together, this work demonstrates that LIN28 maintains self-renewal of PGC by suppressing the expression of differentiation genes including EGR1.
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Affiliation(s)
- Katsuya Suzuki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Seung June Kwon
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Daisuke Saito
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Atsuta
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan.
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5
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Kasemeier-Kulesa JC, Morrison JA, McKinney S, Li H, Gogol M, Hall K, Chen S, Wang Y, Perera A, McLennan R, Kulesa PM. Cell-type profiling of the sympathetic nervous system using spatial transcriptomics and spatial mapping of mRNA. Dev Dyn 2023. [PMID: 36840366 DOI: 10.1002/dvdy.577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/03/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The molecular identification of neural progenitor cell populations that connect to establish the sympathetic nervous system (SNS) remains unclear. This is due to technical limitations in the acquisition and spatial mapping of molecular information to tissue architecture. RESULTS To address this, we applied Slide-seq spatial transcriptomics to intact fresh frozen chick trunk tissue transversely cryo-sectioned at the developmental stage prior to SNS formation. In parallel, we performed age- and location-matched single cell (sc) RNA-seq and 10× Genomics Visium to inform our analysis. Downstream bioinformatic analyses led to the unique molecular identification of neural progenitor cells within the peripheral sympathetic ganglia (SG) and spinal cord preganglionic neurons (PGNs). We then successfully applied the HiPlex RNAscope fluorescence in situ hybridization and multispectral confocal microscopy to visualize 12 gene targets in stage-, age- and location-matched chick trunk tissue sections. CONCLUSIONS Together, these data demonstrate a robust strategy to acquire and integrate single cell and spatial transcriptomic information, resulting in improved resolution of molecular heterogeneities in complex neural tissue architectures. Successful application of this strategy to the developing SNS provides a roadmap for functional studies of neural connectivity and platform to address complex questions in neural development and regeneration.
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Affiliation(s)
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Kate Hall
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Paul M Kulesa
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, Kansas, USA
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6
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The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111893. [PMID: 36431028 PMCID: PMC9695872 DOI: 10.3390/life12111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
For more than a decade, next-generation sequencing (NGS) has been emerging as the mainstay of agrigenomics research. High-throughput technologies have made it feasible to facilitate research at the scale and cost required for using this data in livestock research. Scale frameworks of sequencing for agricultural and livestock improvement, management, and conservation are partly attributable to innovative informatics methodologies and advancements in sequencing practices. Genome-wide sequence-based investigations are often conducted worldwide, and several databases have been created to discover the connections between worldwide scientific accomplishments. Such studies are beginning to provide revolutionary insights into a new era of genomic prediction and selection capabilities of various domesticated livestock species. In this concise review, we provide selected examples of the current state of sequencing methods, many of which are already being used in animal genomic studies, and summarize the state of the positive attributes of genome-based research for cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa domesticus), horses (Equus caballus), chickens (Gallus gallus domesticus), and ducks (Anas platyrhyncos). This review also emphasizes the advantageous features of sequencing technologies in monitoring and detecting infectious zoonotic diseases. In the coming years, the continued advancement of sequencing technologies in livestock agrigenomics will significantly influence the sustained momentum toward regulatory approaches that encourage innovation to ensure continued access to a safe, abundant, and affordable food supplies for future generations.
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7
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Fu W, Wang R, Xu N, Wang J, Li R, Asadollahpour Nanaei H, Nie Q, Zhao X, Han J, Yang N, Jiang Y. Galbase: a comprehensive repository for integrating chicken multi-omics data. BMC Genomics 2022; 23:364. [PMID: 35549894 PMCID: PMC9097087 DOI: 10.1186/s12864-022-08598-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background Multi-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including chickens, these resources are poorly integrated and reused, greatly limiting genetic research and breeding processes of the species. Results Here, we constructed Galbase, an easily accessible repository that integrates public chicken multi-omics data from 928 re-sequenced genomes, 429 transcriptomes, 379 epigenomes, 15,275 QTL entries, and 7,526 associations. A total of 21.67 million SNPs, 2.71 million InDels, and 488,583 cis-regulatory elements were included. Galbase allows users to retrieve genomic variations in geographical maps, gene expression profiling in heatmaps, and epigenomic signals in peak patterns. It also provides modules for batch annotation of genes, regions, and loci based on multi-layered omics data. Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features. Conclusion Galbase grants new opportunities to research communities to undertake in-depth functional genomic studies on chicken. All features of Galbase make it a useful resource to identify genetic variations responsible for chicken complex traits. Galbase is publicly available at http://animal.nwsuaf.edu.cn/ChickenVar. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08598-2.
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Affiliation(s)
- Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Rui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Naiyi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jinxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, Québec, Canada
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China. .,Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, China.
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8
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Kim DW, Place E, Chinnaiya K, Manning E, Sun C, Dai W, Groves I, Ohyama K, Burbridge S, Placzek M, Blackshaw S. Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors. Cell Rep 2022; 38:110251. [PMID: 35045288 PMCID: PMC8918062 DOI: 10.1016/j.celrep.2021.110251] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/13/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023] Open
Affiliation(s)
- Dong Won Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elsie Place
- School of Biosciences, University of Sheffield, Sheffield, UK; Bateson Centre, University of Sheffield, Sheffield, UK; Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Kavitha Chinnaiya
- School of Biosciences, University of Sheffield, Sheffield, UK; Bateson Centre, University of Sheffield, Sheffield, UK; Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Elizabeth Manning
- School of Biosciences, University of Sheffield, Sheffield, UK; Bateson Centre, University of Sheffield, Sheffield, UK; Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Changyu Sun
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Weina Dai
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ian Groves
- School of Mathematics and Statistics, University of Sheffield, Sheffield, UK
| | - Kyoji Ohyama
- School of Biosciences, University of Sheffield, Sheffield, UK; Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, Japan
| | - Sarah Burbridge
- School of Biosciences, University of Sheffield, Sheffield, UK; Bateson Centre, University of Sheffield, Sheffield, UK; Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Marysia Placzek
- School of Biosciences, University of Sheffield, Sheffield, UK; Bateson Centre, University of Sheffield, Sheffield, UK; Neuroscience Institute, University of Sheffield, Sheffield, UK.
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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9
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Major AT, Estermann MA, Roly ZY, Smith CA. An evo-devo perspective of the female reproductive tract. Biol Reprod 2021; 106:9-23. [PMID: 34494091 DOI: 10.1093/biolre/ioab166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/22/2023] Open
Abstract
The vertebrate female reproductive tract has undergone considerable diversification over evolution, having become physiologically adapted to different reproductive strategies. This review considers the female reproductive tract from the perspective of evolutionary developmental biology (evo-devo). Very little is known about how the evolution of this organ system has been driven at the molecular level. In most vertebrates, the female reproductive tract develops from paired embryonic tubes, the Müllerian ducts. We propose that formation of the Müllerian duct is a conserved process that has involved co-option of genes and molecular pathways involved in tubulogenesis in the adjacent mesonephric kidney and Wolffian duct. Downstream of this conservation, genetic regulatory divergence has occurred, generating diversity in duct structure. Plasticity of the Hox gene code and wnt signaling, in particular, may underlie morphological variation of the uterus in mammals, and evolution of the vagina. This developmental plasticity in Hox and Wnt activity may also apply to other vertebrates, generating the morphological diversity of female reproductive tracts evident today.
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Affiliation(s)
- Andrew T Major
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800. Australia
| | - Martin A Estermann
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800. Australia
| | - Zahida Y Roly
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800. Australia
| | - Craig A Smith
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800. Australia
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10
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Melendez J, Sieiro D, Salgado D, Morin V, Dejardin MJ, Zhou C, Mullen AC, Marcelle C. TGFβ signalling acts as a molecular brake of myoblast fusion. Nat Commun 2021; 12:749. [PMID: 33531476 PMCID: PMC7854724 DOI: 10.1038/s41467-020-20290-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/21/2020] [Indexed: 01/30/2023] Open
Abstract
Fusion of nascent myoblasts to pre-existing myofibres is critical for skeletal muscle growth and repair. The vast majority of molecules known to regulate myoblast fusion are necessary in this process. Here, we uncover, through high-throughput in vitro assays and in vivo studies in the chicken embryo, that TGFβ (SMAD2/3-dependent) signalling acts specifically and uniquely as a molecular brake on muscle fusion. While constitutive activation of the pathway arrests fusion, its inhibition leads to a striking over-fusion phenotype. This dynamic control of TGFβ signalling in the embryonic muscle relies on a receptor complementation mechanism, prompted by the merging of myoblasts with myofibres, each carrying one component of the heterodimer receptor complex. The competence of myofibres to fuse is likely restored through endocytic degradation of activated receptors. Altogether, this study shows that muscle fusion relies on TGFβ signalling to regulate its pace.
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Affiliation(s)
- Julie Melendez
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Daniel Sieiro
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, VIC, Australia
- Plexus Ventures LLC, Boston, MA, USA
| | - David Salgado
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, VIC, Australia
- Marseille Medical Genetics (MMG), Aix Marseille University, INSERM U1251, Marseille, France
| | - Valérie Morin
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Marie-Julie Dejardin
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France
| | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Alan C Mullen
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christophe Marcelle
- Institut NeuroMyoGène (INMG), University Claude Bernard Lyon1, CNRS UMR 5310, INSERM U1217, Lyon, France.
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, VIC, Australia.
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11
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Baldarelli RM, Smith CM, Finger JH, Hayamizu TF, McCright IJ, Xu J, Shaw DR, Beal JS, Blodgett O, Campbell J, Corbani LE, Frost PJ, Giannatto SC, Miers DB, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2021 update. Nucleic Acids Res 2021; 49:D924-D931. [PMID: 33104772 PMCID: PMC7778941 DOI: 10.1093/nar/gkaa914] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 01/05/2023] Open
Abstract
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD’s enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment.
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Affiliation(s)
| | | | | | - Terry F Hayamizu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jingxia Xu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - David R Shaw
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jonathan S Beal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Olin Blodgett
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jeffrey Campbell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Lori E Corbani
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Pete J Frost
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Dave B Miers
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Martin Ringwald
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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12
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Abstract
For more than 2000 years, the avian embryo has helped scientists understand questions of developmental and cell biology. As early as 350 BC Aristotle described embryonic development inside a chicken egg (Aristotle, Generation of animals. Loeb Classical Library (translated), vol. 8, 1943). In the seventeenth century, Marcello Malpighi, referred to as the father of embryology, first diagramed the microscopic morphogenesis of the chick embryo, including extensive characterization of the cardiovascular system (Pearce Eur Neurol 58(4):253-255, 2007; West, Am J Physiol Lung Cell Mol Physiol 304(6):L383-L390, 2016). The ease of accessibility to the embryo and similarity to mammalian development have made avians a powerful system among model organisms. Currently, a unique combination of classical and modern techniques is employed for investigation of the vascular system in the avian embryo. Here, we will introduce the essential techniques of embryonic manipulation for experimental study in vascular biology.
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Affiliation(s)
- Rieko Asai
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Michael Bressan
- Department of Cell Biology and Physiology, McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takashi Mikawa
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
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13
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Malatesta M, Mori G, Acquotti D, Campanini B, Peracchi A, Antin PB, Percudani R. Birth of a pathway for sulfur metabolism in early amniote evolution. Nat Ecol Evol 2020; 4:1239-1246. [PMID: 32601391 PMCID: PMC8364350 DOI: 10.1038/s41559-020-1232-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/22/2020] [Indexed: 11/09/2022]
Abstract
Among amniotes, reptiles and mammals are differently adapted to terrestrial life. It is generally appreciated that terrestrialization required adaptive changes of vertebrate metabolism, particularly in the mode of nitrogen excretion. However, the current paradigm is that metabolic adaptation to life on land did not involve synthesis of enzymatic pathways de novo, but rather repurposing of existing ones. Here, by comparing the inventory of pyridoxal 5'-phosphate-dependent enzymes in different amniotes, we identify in silico a pathway for sulfur metabolism present in chick embryos but not in mammals. Cysteine lyase contains haem and pyridoxal 5'-phosphate co-factors and converts cysteine and sulfite into cysteic acid and hydrogen sulfide, respectively. A specific cysteic acid decarboxylase produces taurine, while hydrogen sulfide is recycled into cysteine by cystathionine beta-synthase. This reaction sequence enables the formation of sulfonated amino acids during embryo development in the egg at no cost of reduced sulfur. The pathway originated around 300 million years ago in a proto-reptile by cystathionine beta-synthase duplication, cysteine lyase neofunctionalization and cysteic acid decarboxylase co-option. Our findings indicate that adaptation to terrestrial life involved innovations in metabolic pathways, and reveal the molecular mechanisms by which such innovations arose in amniote evolution.
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Affiliation(s)
- Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Domenico Acquotti
- Centro Interdipartimentale Misure 'Giuseppe Casnati', University of Parma, Parma, Italy
| | | | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Parker B Antin
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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14
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Serralbo O, Salgado D, Véron N, Cooper C, Dejardin MJ, Doran T, Gros J, Marcelle C. Transgenesis and web resources in quail. eLife 2020; 9:56312. [PMID: 32459172 PMCID: PMC7286689 DOI: 10.7554/elife.56312] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022] Open
Abstract
Due to its amenability to manipulations, to live observation and its striking similarities to mammals, the chicken embryo has been one of the major animal models in biomedical research. Although it is technically possible to genome-edit the chicken, its long generation time (6 months to sexual maturity) makes it an impractical lab model and has prevented it widespread use in research. The Japanese quail (Coturnix coturnix japonica) is an attractive alternative, very similar to the chicken, but with the decisive asset of a much shorter generation time (1.5 months). In recent years, transgenic quail lines have been described. Most of them were generated using replication-deficient lentiviruses, a technique that presents diverse limitations. Here, we introduce a novel technology to perform transgenesis in quail, based on the in vivo transfection of plasmids in circulating Primordial Germ Cells (PGCs). This technique is simple, efficient and allows using the infinite variety of genome engineering approaches developed in other models. Furthermore, we present a website centralizing quail genomic and technological information to facilitate the design of genome-editing strategies, showcase the past and future transgenic quail lines and foster collaborative work within the avian community.
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Affiliation(s)
- Olivier Serralbo
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Australia
| | - David Salgado
- Marseille Medical Genetics (GMGF), Aix Marseille University, Marseille, France
| | - Nadège Véron
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Australia
| | - Caitlin Cooper
- CSIRO Health & Biosecurity, Australian Animal Health Laboratory, Geelong, Australia
| | | | - Timothy Doran
- CSIRO Health & Biosecurity, Australian Animal Health Laboratory, Geelong, Australia
| | - Jérome Gros
- Department of Developmental and Stem Cell Biology, Pasteur Institute, Paris, France
| | - Christophe Marcelle
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Australia.,Institut NeuroMyoGène (INMG), University Claude Bernard Lyon 1, Lyon, France
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15
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Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD. Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res 2019; 46:D861-D868. [PMID: 29059324 PMCID: PMC5753396 DOI: 10.1093/nar/gkx936] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023] Open
Abstract
Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems. Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses. Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing. These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated ChIP-Seq mapping, GO terms, protein interaction data, ORFeome support, and improved connectivity to other biomedical and bioinformatic resources.
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Affiliation(s)
- Kamran Karimi
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Joshua D Fortriede
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Vaneet S Lotay
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Kevin A Burns
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Dong Zhou Wang
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Malcom E Fisher
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Troy J Pells
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Christina James-Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Ying Wang
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - V G Ponferrada
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Stanley Chu
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Praneet Chaturvedi
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Peter D Vize
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
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16
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Somorjai IML, Martí-Solans J, Diaz-Gracia M, Nishida H, Imai KS, Escrivà H, Cañestro C, Albalat R. Wnt evolution and function shuffling in liberal and conservative chordate genomes. Genome Biol 2018; 19:98. [PMID: 30045756 PMCID: PMC6060547 DOI: 10.1186/s13059-018-1468-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/22/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of genome evolution and EvoDevo. To investigate these problems, we have analyzed the evolution of the Wnt ligand repertoire in the chordate phylum as a case study. RESULTS We conduct an exhaustive survey of Wnt genes in genomic databases, identifying 156 Wnt genes in 13 non-vertebrate chordates. This represents the most complete Wnt gene catalog of the chordate subphyla and has allowed us to resolve previous ambiguities about the orthology of many Wnt genes, including the identification of WntA for the first time in chordates. Moreover, we create the first complete expression atlas for the Wnt family during amphioxus development, providing a useful resource to investigate the evolution of Wnt expression throughout the radiation of chordates. CONCLUSIONS Our data underscore extraordinary genomic stasis in cephalochordates, which contrasts with the liberal and dynamic evolutionary patterns of gene loss and duplication in urochordate genomes. Our analysis has allowed us to infer ancestral Wnt functions shared among all chordates, several cases of function shuffling among Wnt paralogs, as well as unique expression domains for Wnt genes that likely reflect functional innovations in each chordate lineage. Finally, we propose a potential relationship between the evolution of WntA and the evolution of the mouth in chordates.
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Affiliation(s)
- Ildikó M L Somorjai
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
- Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, KY16 8LB, Scotland, UK.
| | - Josep Martí-Solans
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Miriam Diaz-Gracia
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hector Escrivà
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Cristian Cañestro
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
| | - Ricard Albalat
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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17
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Vermillion KL, Bacher R, Tannenbaum AP, Swanson S, Jiang P, Chu LF, Stewart R, Thomson JA, Vereide DT. Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Dev Biol 2018; 439:30-41. [PMID: 29678445 DOI: 10.1016/j.ydbio.2018.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 01/07/2023]
Abstract
During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos. The single-cell transcriptomes were then ordered by the statistical method Wave-Crest to deduce both the relative position along the AP axis and the prospective lineage of single cells. The ordered transcriptomes reveal intricate patterns of gene expression along the primitive streak.
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Affiliation(s)
| | - Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA
| | | | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell&Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Molecular, Cellular,&Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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18
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Allalou A, Wu Y, Ghannad-Rezaie M, Eimon PM, Yanik MF. Automated deep-phenotyping of the vertebrate brain. eLife 2017; 6:e23379. [PMID: 28406399 PMCID: PMC5441873 DOI: 10.7554/elife.23379] [Citation(s) in RCA: 14] [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: 12/28/2016] [Accepted: 04/07/2017] [Indexed: 11/13/2022] Open
Abstract
Here, we describe an automated platform suitable for large-scale deep-phenotyping of zebrafish mutant lines, which uses optical projection tomography to rapidly image brain-specific gene expression patterns in 3D at cellular resolution. Registration algorithms and correlation analysis are then used to compare 3D expression patterns, to automatically detect all statistically significant alterations in mutants, and to map them onto a brain atlas. Automated deep-phenotyping of a mutation in the master transcriptional regulator fezf2 not only detects all known phenotypes but also uncovers important novel neural deficits that were overlooked in previous studies. In the telencephalon, we show for the first time that fezf2 mutant zebrafish have significant patterning deficits, particularly in glutamatergic populations. Our findings reveal unexpected parallels between fezf2 function in zebrafish and mice, where mutations cause deficits in glutamatergic neurons of the telencephalon-derived neocortex.
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Affiliation(s)
- Amin Allalou
- Massachusetts Institute of Technology, Cambridge, United States
- Uppsala University, Uppsala, Sweden
| | - Yuelong Wu
- Massachusetts Institute of Technology, Cambridge, United States
| | - Mostafa Ghannad-Rezaie
- Massachusetts Institute of Technology, Cambridge, United States
- ETH Zürich, Zürich, Switzerland
| | - Peter M Eimon
- Massachusetts Institute of Technology, Cambridge, United States
| | - Mehmet Fatih Yanik
- Massachusetts Institute of Technology, Cambridge, United States
- ETH Zürich, Zürich, Switzerland
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19
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Finger JH, Smith CM, Hayamizu TF, McCright IJ, Xu J, Law M, Shaw DR, Baldarelli RM, Beal JS, Blodgett O, Campbell JW, Corbani LE, Lewis JR, Forthofer KL, Frost PJ, Giannatto SC, Hutchins LN, Miers DB, Motenko H, Stone KR, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2017 update. Nucleic Acids Res 2016; 45:D730-D736. [PMID: 27899677 PMCID: PMC5210556 DOI: 10.1093/nar/gkw1073] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/21/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. At present, GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata. Since our last report in 2014, we have added a large amount of data, we have enhanced data and database infrastructure, and we have implemented many new search and display features. Interface enhancements include: a new Mouse Developmental Anatomy Browser; interactive tissue-by-developmental stage and tissue-by-gene matrix views; capabilities to filter and sort expression data summaries; a batch search utility; gene-based expression overviews; and links to expression data from other species.
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Affiliation(s)
| | | | - Terry F Hayamizu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jingxia Xu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Meiyee Law
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - David R Shaw
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jon S Beal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Olin Blodgett
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jeff W Campbell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Lori E Corbani
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jill R Lewis
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Kim L Forthofer
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Pete J Frost
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Lucie N Hutchins
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Dave B Miers
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Howie Motenko
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Kevin R Stone
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Martin Ringwald
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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20
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Atsuta Y, Takahashi Y. Early formation of the Müllerian duct is regulated by sequential actions of BMP/Pax2 and FGF/Lim1 signaling. Development 2016; 143:3549-3559. [PMID: 27578782 DOI: 10.1242/dev.137067] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/04/2016] [Indexed: 12/13/2022]
Abstract
The Müllerian duct (MD) and Wolffian duct (WD) are embryonic tubular tissues giving rise to female and male reproductive tracts, respectively. In amniote embryos, both MD and WD emerge in both sexes, but subsequently degenerate in the males and females, respectively. Here, by using MD-specific gene manipulations in chicken embryos, we identify the molecular and cellular mechanisms that link early MD specification to tubular invagination. Early (pre-)specification of MD precursors in the coelomic epithelium requires BMP signaling and its downstream target Pax2 in a WD-independent process. Subsequently, the BMP/Pax2 axis induces Lim1 expression, a hallmark of MD specification, for which FGF/ERK and WD-derived signals are also required. Finally, the sequential actions of the BMP/Pax2 and FGF/Lim1 axes culminate in epithelial invagination to form a tubular structure driven by an apical constriction, where apical accumulation of phospho-myosin light chain is positively regulated by FGF/ERK signaling. Our study delineates mechanisms governing the early formation of the MD, and also serves as a model of how an epithelial cell sheet is transformed to a tubular structure, a process seen in a variety of developmental contexts.
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Affiliation(s)
- Yuji Atsuta
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoshiko Takahashi
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan AMED Core Research for Evolutional Science and Technology (AMED-CREST), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo 100-0004, Japan
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21
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Clarkson MD. Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. BMC DEVELOPMENTAL BIOLOGY 2016; 16:18. [PMID: 27206491 PMCID: PMC4875762 DOI: 10.1186/s12861-016-0116-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable. RESULTS I first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures. CONCLUSIONS This collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.
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Affiliation(s)
- Melissa D Clarkson
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA, USA.
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22
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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23
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Atsuta Y, Takahashi Y. FGF8 coordinates tissue elongation and cell epithelialization during early kidney tubulogenesis. Development 2015; 142:2329-37. [PMID: 26130757 PMCID: PMC4510593 DOI: 10.1242/dev.122408] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
When a tubular structure forms during early embryogenesis, tubular elongation and lumen formation (epithelialization) proceed simultaneously in a spatiotemporally coordinated manner. We here demonstrate, using the Wolffian duct (WD) of early chicken embryos, that this coordination is regulated by the expression of FGF8, which shifts posteriorly during body axis elongation. FGF8 acts as a chemoattractant on the leader cells of the elongating WD and prevents them from epithelialization, whereas static (‘rear’) cells that receive progressively less FGF8 undergo epithelialization to form a lumen. Thus, FGF8 acts as a binary switch that distinguishes tubular elongation from lumen formation. The posteriorly shifting FGF8 is also known to regulate somite segmentation, suggesting that multiple types of tissue morphogenesis are coordinately regulated by macroscopic changes in body growth. Highlighted article: Body axis elongation is regulated by posterior FGF8 signals . In chicken, nephric duct extension also requires this FGF8 signal, while low FGF8 anteriorly triggers duct lumen formation.
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Affiliation(s)
- Yuji Atsuta
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoshiko Takahashi
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
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Abstract
For more than 2,000 years, philosophers and scientists have turned to the avian embryo with questions of how life begins (Aristotle and Peck Generations of Animals. Loeb Classics, vol. XIII. Harvard University Press, Cambridge, 1943; Needham, A history of embryology. Abelard-Schuman, New York, 1959). Then, as now, the unique accessibility of the embryo both in terms of acquisition of eggs from domesticated fowl and ease at which the embryo can be visualized by simply opening the shell has made avians an appealing and powerful model system for the study of development. Thus, as the field of embryology has evolved through observational, comparative, and experimental embryology into its current iteration as the cellular and molecular biology of development, avians have remained a useful and practical system of study.
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Affiliation(s)
- Michael Bressan
- Cardiovascular Research Institute, University of California, San Francisco, 555 Mission Bay Blvd South, MC3120, San Francisco, CA, 94143-3120, USA,
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Attia L, Schneider J, Yelin R, Schultheiss TM. Collective cell migration of the nephric duct requires FGF signaling. Dev Dyn 2014; 244:157-67. [PMID: 25516335 DOI: 10.1002/dvdy.24241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND During the course of development, the vertebrate nephric duct (ND) extends and migrates from the place of its initial formation, adjacent to the anterior somites, until it inserts into the bladder or cloaca in the posterior region of the embryo. The molecular mechanisms that guide ND migration are poorly understood. RESULTS A novel Gata3-enhancer-Gfp-based chick embryo live imaging system was developed that permits documentation of ND migration at the individual cell level for the first time. FGF Receptors and FGF response genes are expressed in the ND, and FGF ligands are expressed in surrounding tissues. FGF receptor inhibition blocked nephric duct migration. Individual inhibitors of the Erk, p38, or Jnk pathways did not affect duct migration, but inhibition of all three pathways together did inhibit migration of the duct. A localized source of FGF8 placed adjacent to the nephric duct did not affect the duct migration path. CONCLUSIONS FGF signaling acts as a "motor" that is required for duct migration, but other signals are needed to determine the directionality of the duct migration pathway. Developmental Dynamics 244:157-167, 2015. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Lital Attia
- Department of Anatomy and Cell Biology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol 2014; 32:23-8. [PMID: 25415961 PMCID: PMC4271537 DOI: 10.1093/molbev/msu309] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements and 100% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.
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Affiliation(s)
- Craig B Lowe
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA
| | - Julia A Clarke
- Department of Geological Sciences, University of Texas at Austin, Austin TX
| | - Allan J Baker
- Department of Natural History, Royal Ontario Museum, Toronto, and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada (Deceased)
| | - David Haussler
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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Smith CM, Finger JH, Kadin JA, Richardson JE, Ringwald M. The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. Dev Dyn 2014; 243:1176-86. [PMID: 24958384 DOI: 10.1002/dvdy.24155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/16/2014] [Accepted: 06/17/2014] [Indexed: 12/15/2022] Open
Abstract
Because molecular mechanisms of development are extraordinarily complex, the understanding of these processes requires the integration of pertinent research data. Using the Gene Expression Database for Mouse Development (GXD) as an example, we illustrate the progress made toward this goal, and discuss relevant issues that apply to developmental databases and developmental research in general. Since its first release in 1998, GXD has served the scientific community by integrating multiple types of expression data from publications and electronic submissions and by making these data freely and widely available. Focusing on endogenous gene expression in wild-type and mutant mice and covering data from RNA in situ hybridization, in situ reporter (knock-in), immunohistochemistry, reverse transcriptase-polymerase chain reaction, Northern blot, and Western blot experiments, the database has grown tremendously over the years in terms of data content and search utilities. Currently, GXD includes over 1.4 million annotated expression results and over 260,000 images. All these data and images are readily accessible to many types of database searches. Here we describe the data and search tools of GXD; explain how to use the database most effectively; discuss how we acquire, curate, and integrate developmental expression information; and describe how the research community can help in this process.
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