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Catela C, Assimacopoulos S, Chen Y, Tsioras K, Feng W, Kratsios P. The Iroquois ( Iro/Irx) homeobox genes are conserved Hox targets involved in motor neuron development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596714. [PMID: 38853975 PMCID: PMC11160718 DOI: 10.1101/2024.05.30.596714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Iroquois (Iro/Irx) homeobox genes encode transcription factors with fundamental roles in animal development. Despite their link to various congenital conditions in humans, our understanding of Iro/Irx gene expression, function, and regulation remains incomplete. Here, we conducted a systematic expression analysis of all six mouse Irx genes in the embryonic spinal cord. We found five Irx genes (Irx1, Irx2, Irx3, Irx5, and Irx6) to be confined mostly to ventral spinal domains, offering new molecular markers for specific groups of post-mitotic motor neurons (MNs). Further, we engineered Irx2, Irx5, and Irx6 mouse mutants and uncovered essential but distinct roles for Irx2 and Irx6 in MN development. Last, we found that the highly conserved regulators of MN development across species, the HOX proteins, directly control Irx gene expression both in mouse and C. elegans MNs, critically expanding the repertoire of HOX target genes in the developing nervous system. Altogether, our study provides important insights into Iro/Irx expression and function in the developing spinal cord, and uncovers an ancient gene regulatory relationship between HOX and Iro/Irx genes.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Stavroula Assimacopoulos
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Konstantinos Tsioras
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
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2
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Williamson I, Boyle S, Grimes GR, Friman ET, Bickmore WA. Dispersal of PRC1 condensates disrupts polycomb chromatin domains and loops. Life Sci Alliance 2023; 6:e202302101. [PMID: 37487640 PMCID: PMC10366532 DOI: 10.26508/lsa.202302101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) strongly influences 3D genome organization, mediating local chromatin compaction and clustering of target loci. Several PRC1 subunits have the capacity to form biomolecular condensates through liquid-liquid phase separation in vitro and when tagged and over-expressed in cells. Here, we use 1,6-hexanediol, which can disrupt liquid-like condensates, to examine the role of endogenous PRC1 biomolecular condensates on local and chromosome-wide clustering of PRC1-bound loci. Using imaging and chromatin immunoprecipitation, we show that PRC1-mediated chromatin compaction and clustering of targeted genomic loci-at different length scales-can be reversibly disrupted by the addition and subsequent removal of 1,6-hexanediol to mouse embryonic stem cells. Decompaction and dispersal of polycomb domains and clusters cannot be solely attributable to reduced PRC1 occupancy detected by chromatin immunoprecipitation following 1,6-hexanediol treatment as the addition of 2,5-hexanediol has similar effects on binding despite this alcohol not perturbing PRC1-mediated 3D clustering, at least at the sub-megabase and megabase scales. These results suggest that weak hydrophobic interactions between PRC1 molecules may have a role in polycomb-mediated genome organization.
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Affiliation(s)
- Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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3
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Iyer VJ, Osman MA. The Antipsychotic Drug Haldol Modulates IQGAP1-Signaling and Inhibits Cell Proliferation in Triple Negative Breast Cancer Cell Lines. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000823. [PMID: 37215640 PMCID: PMC10199339 DOI: 10.17912/micropub.biology.000823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023]
Abstract
The signaling scaffold oncoprotein IQGAP1 was identified as a classification and therapeutic biomarker in triple negative breast cancer (TNBC) cell lines. Here, we report that the antipsychotic drug Haldol induces novel protein-protein interactions with IQGAP1 and inhibits cell proliferation in TNBC cell lines. The identified proteins share known functions of IQGAP1 in secretion, transcription and apoptosis and provide further classification tools and potential precision therapeutic targets for Haldol in TNBC.
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Affiliation(s)
- Varun J. Iyer
- Department of Medicine, Division of Oncology, University of Toledo Medical Center, Toledo, Ohio, 43614 United States
| | - Mahasin A. Osman
- Department of Medicine, Division of Oncology, University of Toledo Medical Center, Toledo, Ohio, 43614 United States
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Narwidina A, Miyazaki A, Iwata K, Kurogoushi R, Sugimoto A, Kudo Y, Kawarabayashi K, Yamakawa Y, Akazawa Y, Kitamura T, Nakagawa H, Yamaguchi-Ueda K, Hasegawa T, Yoshizaki K, Fukumoto S, Yamamoto A, Ishimaru N, Iwasaki T, Iwamoto T. Iroquois homeobox 3 regulates odontoblast proliferation and differentiation mediated by Wnt5a expression. Biochem Biophys Res Commun 2023; 650:47-54. [PMID: 36773339 DOI: 10.1016/j.bbrc.2023.02.004] [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: 12/21/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Iroquois homeobox (Irx) genes are TALE-class homeobox genes that are evolutionarily conserved across species and have multiple critical cellular functions in fundamental tissue development processes. Previous studies have shown that Irxs genes are expressed during tooth development. However, the precise roles of genes in teeth remain unclear. Here, we demonstrated for the first time that Irx3 is an essential molecule for the proliferation and differentiation of odontoblasts. Using cDNA synthesized from postnatal day 1 (P1) tooth germs, we examined the expression of all Irx genes (Irx1-Irx6) by RT-PCR and found that all genes except Irx4 were expressed in the tooth tissue. Irx1-Irx3 a were expressed in the dental epithelial cell line M3H1 cells, while Irx3 and Irx5 were expressed in the dental mesenchymal cell line mDP cells. Only Irx3 was expressed in both undifferentiated cell lines. Immunostaining also revealed the presence of IRX3 in the dental epithelial cells and mesenchymal condensation. Inhibition of endogenous Irx3 by siRNA blocks the proliferation and differentiation of mDP cells. Wnt3a, Wnt5a, and Bmp4 are factors involved in odontoblast differentiation and were highly expressed in mDP cells by quantitative PCR analysis. Interestingly, the expression of Wnt5a (but not Wnt3a or Bmp4) was suppressed by Irx3 siRNA. These results suggest that Irx3 plays an essential role in part through the regulation of Wnt5a expression during odontoblast proliferation and differentiation.
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Affiliation(s)
- Anrizandy Narwidina
- Department of Pediatric Dentistry, Graduate School of Oral Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan; Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Aya Miyazaki
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Kokoro Iwata
- Department of Pediatric Dentistry / Special Needs Dentistry, Division of Oral Health Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8549, Japan
| | - Rika Kurogoushi
- Department of Pediatric Dentistry / Special Needs Dentistry, Division of Oral Health Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8549, Japan
| | - Asuna Sugimoto
- Department of Pediatric Dentistry / Special Needs Dentistry, Division of Oral Health Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8549, Japan
| | - Yasusei Kudo
- Department of Oral Bioscience, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Keita Kawarabayashi
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Yoshihito Yamakawa
- Department of Pediatric Dentistry, Graduate School of Oral Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan; Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Yuki Akazawa
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Takamasa Kitamura
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Hiroshi Nakagawa
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Kimiko Yamaguchi-Ueda
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Tomokazu Hasegawa
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Keigo Yoshizaki
- Orthodontics and Dentofacial Orthopedics Section, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, 812-8582, Japan
| | - Satoshi Fukumoto
- Pediatric Dentistry Section, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, 812-8582, Japan
| | - Akihito Yamamoto
- Department of Tissue Regeneration, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Naozumi Ishimaru
- Department of Oral Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Tomonori Iwasaki
- Department of Pediatric Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8504, Japan
| | - Tsutomu Iwamoto
- Department of Pediatric Dentistry / Special Needs Dentistry, Division of Oral Health Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8549, Japan.
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Iroquois Family Genes in Gastric Carcinogenesis: A Comprehensive Review. Genes (Basel) 2023; 14:genes14030621. [PMID: 36980893 PMCID: PMC10048635 DOI: 10.3390/genes14030621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Gastric cancer (GC) is the fifth leading cause of cancer-associated death worldwide, accounting for 768,793 related deaths and 1,089,103 new cases in 2020. Despite diagnostic advances, GC is often detected in late stages. Through a systematic literature search, this study focuses on the associations between the Iroquois gene family and GC. Accumulating evidence indicates that Iroquois genes are involved in the regulation of various physiological and pathological processes, including cancer. To date, information about Iroquois genes in GC is very limited. In recent years, the expression and function of Iroquois genes examined in different models have suggested that they play important roles in cell and cancer biology, since they were identified to be related to important signaling pathways, such as wingless, hedgehog, mitogen-activated proteins, fibroblast growth factor, TGFβ, and the PI3K/Akt and NF-kB pathways. In cancer, depending on the tumor, Iroquois genes can act as oncogenes or tumor suppressor genes. However, in GC, they seem to mostly act as tumor suppressor genes and can be regulated by several mechanisms, including methylation, microRNAs and important GC-related pathogens. In this review, we provide an up-to-date review of the current knowledge regarding Iroquois family genes in GC.
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Brown RM, Wang L, Fu A, Kannan A, Mussar M, Bagchi IC, Jorgensen JS. Irx3 promotes gap junction communication between uterine stromal cells to regulate vascularization during embryo implantation†. Biol Reprod 2022; 106:1000-1010. [PMID: 35138358 PMCID: PMC9113487 DOI: 10.1093/biolre/ioac015] [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: 05/10/2021] [Revised: 11/16/2021] [Accepted: 02/07/2022] [Indexed: 11/14/2022] Open
Abstract
Appropriate embryo-uterine interactions are essential for implantation. Besides oocyte abnormalities, implantation failure is a major contributor to early pregnancy loss. Previously, we demonstrated that two members of the Iroquois homeobox transcription factor family, IRX3 and IRX5, exhibited distinct and dynamic expression profiles in the developing ovary to promote oocyte and follicle survival. Elimination of each gene independently caused subfertility, but with different breeding pattern outcomes. Irx3 KO (Irx3LacZ/LacZ) females produced fewer pups throughout their reproductive lifespan which could only be partially explained by poor oocyte quality. Thus, we hypothesized that IRX3 is also expressed in the uterus where it acts to support pregnancy. To test this hypothesis, we harvested pregnant uteri from control and Irx3 KO females to evaluate IRX3 expression profiles and the integrity of embryo implantation sites. Our results indicate that IRX3 is expressed in the endometrial stromal cells at day 4 of pregnancy (D4) with peak expression at D5-D6, and then greatly diminishes by D7. Further, studies showed that while embryos were able to attach to the uterus, implantation sites in Irx3 KO pregnant mice exhibited impaired vascularization and abnormal expression of decidualization markers. Finally, we also observed an impaired response of the Irx3 KO uteri to an artificial deciduogenic stimulus, indicating a critical role of this factor in regulating the decidualization program. Together, these data established that IRX3 promotes female fertility via at least two different mechanisms: (1) promoting competent oocytes and (2) facilitating functional embryo-uterine interactions during implantation.
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Affiliation(s)
- Ryan M Brown
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Linda Wang
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Anqi Fu
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Athilakshmi Kannan
- Department of Comparative Biosciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Michael Mussar
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Indrani C Bagchi
- Department of Comparative Biosciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Joan S Jorgensen
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
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7
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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Kim KH, Oh Y, Liu J, Dababneh S, Xia Y, Kim RY, Kim DK, Ban K, Husain M, Hui CC, Backx PH. Irx5 and transient outward K + currents contribute to transmural contractile heterogeneities in the mouse ventricle. Am J Physiol Heart Circ Physiol 2022; 322:H725-H741. [PMID: 35245131 DOI: 10.1152/ajpheart.00572.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous studies have established that fast transmural gradients of transient outward K+ current (Ito,f) correlate with regional differences in action potential (AP) profile and excitation-contraction coupling (ECC) with high Ito,f expression in the epimyocardium (EPI) being associated with short APs and low contractility and vice versa. Herein, we investigated the effects of disrupted Ito,f gradient on contractile properties using mouse models of Irx5 knockout (Irx5-KO) for selective Ito,f elevation in the endomyocardium (ENDO) of the left ventricle (LV) and Kcnd2 ablation (KV4.2-KO) for selective Ito,freduction in the EPI. Irx5-KO mice exhibited decreased global LV contractility in association with reductions in cell shortening and Ca2+ transient amplitudes in isolated ENDO but not EPI cardiomyocytes. Moreover, transcriptional profiling revealed that the primary effect of Irx5 ablation on ECC-related genes was to increase Ito,f gene expression (i.e. Kcnd2 and Kcnip2) in the ENDO, but not the EPI. Indeed, KV4.2-KO mice showed selective increases in cell shortening and Ca2+ transients in isolated EPI cardiomyocytes, leading to enhanced ventricular contractility and mice lacking both Irx5 and Kcnd2 displayed elevated ventricular contractility comparable to KV4.2-KO mice. Our findings demonstrate that the transmural electromechanical heterogeneities in the healthy ventricles depend on the Irx5-dependent Ito,f gradients. These observations provide a useful framework for assessing the molecular mechanisms underlying the alterations in contractile heterogeneity seen in the diseased heart.
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Affiliation(s)
- Kyoung-Han Kim
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Yena Oh
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jie Liu
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Saif Dababneh
- University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - Ying Xia
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ri Youn Kim
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Dae-Kyum Kim
- University of Ottawa Heart Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kiwon Ban
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Mansoor Husain
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter H Backx
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Biology, Faculty of Science, York University, Toronto, ON, Canada.,Toronto General Research Institute, University Health Network, Toronto, ON, Canada
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Dou Z, Son JE, Hui CC. Irx3 and Irx5 - Novel Regulatory Factors of Postnatal Hypothalamic Neurogenesis. Front Neurosci 2021; 15:763856. [PMID: 34795556 PMCID: PMC8593166 DOI: 10.3389/fnins.2021.763856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022] Open
Abstract
The hypothalamus is a brain region that exhibits highly conserved anatomy across vertebrate species and functions as a central regulatory hub for many physiological processes such as energy homeostasis and circadian rhythm. Neurons in the arcuate nucleus of the hypothalamus are largely responsible for sensing of peripheral signals such as leptin and insulin, and are critical for the regulation of food intake and energy expenditure. While these neurons are mainly born during embryogenesis, accumulating evidence have demonstrated that neurogenesis also occurs in postnatal-adult mouse hypothalamus, particularly in the first two postnatal weeks. This second wave of active neurogenesis contributes to the remodeling of hypothalamic neuronal populations and regulation of energy homeostasis including hypothalamic leptin sensing. Radial glia cell types, such as tanycytes, are known to act as neuronal progenitors in the postnatal mouse hypothalamus. Our recent study unveiled a previously unreported radial glia-like neural stem cell (RGL-NSC) population that actively contributes to neurogenesis in the postnatal mouse hypothalamus. We also identified Irx3 and Irx5, which encode Iroquois homeodomain-containing transcription factors, as genetic determinants regulating the neurogenic property of these RGL-NSCs. These findings are significant as IRX3 and IRX5 have been implicated in FTO-associated obesity in humans, illustrating the importance of postnatal hypothalamic neurogenesis in energy homeostasis and obesity. In this review, we summarize current knowledge regarding postnatal-adult hypothalamic neurogenesis and highlight recent findings on the radial glia-like cells that contribute to the remodeling of postnatal mouse hypothalamus. We will discuss characteristics of the RGL-NSCs and potential actions of Irx3 and Irx5 in the regulation of neural stem cells in the postnatal-adult mouse brain. Understanding the behavior and regulation of neural stem cells in the postnatal-adult hypothalamus will provide novel mechanistic insights in the control of hypothalamic remodeling and energy homeostasis.
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Affiliation(s)
- Zhengchao Dou
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Joe Eun Son
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chi-chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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10
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Al Sayed ZR, Canac R, Cimarosti B, Bonnard C, Gourraud JB, Hamamy H, Kayserili H, Girardeau A, Jouni M, Jacob N, Gaignerie A, Chariau C, David L, Forest V, Marionneau C, Charpentier F, Loussouarn G, Lamirault G, Reversade B, Zibara K, Lemarchand P, Gaborit N. Human model of IRX5 mutations reveals key role for this transcription factor in ventricular conduction. Cardiovasc Res 2021; 117:2092-2107. [PMID: 32898233 DOI: 10.1093/cvr/cvaa259] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/15/2020] [Accepted: 08/28/2020] [Indexed: 01/02/2023] Open
Abstract
AIMS Several inherited arrhythmic diseases have been linked to single gene mutations in cardiac ion channels and interacting proteins. However, the mechanisms underlying most arrhythmias, are thought to involve altered regulation of the expression of multiple effectors. In this study, we aimed to examine the role of a transcription factor (TF) belonging to the Iroquois homeobox family, IRX5, in cardiac electrical function. METHODS AND RESULTS Using human cardiac tissues, transcriptomic correlative analyses between IRX5 and genes involved in cardiac electrical activity showed that in human ventricular compartment, IRX5 expression strongly correlated to the expression of major actors of cardiac conduction, including the sodium channel, Nav1.5, and Connexin 40 (Cx40). We then generated human-induced pluripotent stem cells (hiPSCs) derived from two Hamamy syndrome-affected patients carrying distinct homozygous loss-of-function mutations in IRX5 gene. Cardiomyocytes derived from these hiPSCs showed impaired cardiac gene expression programme, including misregulation in the control of Nav1.5 and Cx40 expression. In accordance with the prolonged QRS interval observed in Hamamy syndrome patients, a slower ventricular action potential depolarization due to sodium current reduction was observed on electrophysiological analyses performed on patient-derived cardiomyocytes, confirming the functional role of IRX5 in electrical conduction. Finally, a cardiac TF complex was newly identified, composed by IRX5 and GATA4, in which IRX5 potentiated GATA4-induction of SCN5A expression. CONCLUSION Altogether, this work unveils a key role for IRX5 in the regulation of human ventricular depolarization and cardiac electrical conduction, providing therefore new insights into our understanding of cardiac diseases.
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Affiliation(s)
- Zeina R Al Sayed
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Robin Canac
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Bastien Cimarosti
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Carine Bonnard
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Jean-Baptiste Gourraud
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, Geneva University, 1 rue Michel-Servet, Geneva 1211, Switzerland
| | - Hulya Kayserili
- Medical Genetics Department, Koç University School of Medicine(KUSOM), Rumelifeneri Yolu 34450, Istanbul, Turkey
| | - Aurore Girardeau
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Mariam Jouni
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Nicolas Jacob
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Anne Gaignerie
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, 8 Quai Moncousu, F-44000 Nantes, France
| | - Caroline Chariau
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, 8 Quai Moncousu, F-44000 Nantes, France
| | - Laurent David
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, 8 Quai Moncousu, F-44000 Nantes, France
- Université de Nantes, INSERM, CRTI, 30 Bd Jean Monnet, F-44093 Nantes, France
- ITUN, CHU Nantes, 30 Bd Jean Monnet, F-44093 Nantes, France
| | - Virginie Forest
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Céline Marionneau
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Flavien Charpentier
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Gildas Loussouarn
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Guillaume Lamirault
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Bruno Reversade
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Singapore 138648, Singapore
- Medical Genetics Department, Koç University School of Medicine(KUSOM), Rumelifeneri Yolu 34450, Istanbul, Turkey
- Department of Paediatrics, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore
- Institute of Molecular and Cellular Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
- Reproductive Biology Laboratory, Amsterdam UMC, Meibergdreef 9 1105, Amsterdam-Zuidoost, Netherlands
| | - Kazem Zibara
- ER045, Laboratory of stem cells, DSST, Biology department, Faculty of Sciences, Lebanese University, Rafic Hariri Campus - Hadath, Beirut 1700, Lebanon
| | - Patricia Lemarchand
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
| | - Nathalie Gaborit
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 8 quai Moncousu, F-44000 Nantes, France
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11
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Kohl S, Llavona P, Sauer A, Reuter P, Weisschuh N, Kempf M, Dehmelt FA, Arrenberg AB, Sliesoraityte I, Zrenner E, van Schooneveld MJ, Rudolph G, Kühlewein L, Wissinger B. A duplication on chromosome 16q12 affecting the IRXB gene cluster is associated with autosomal dominant cone dystrophy with early tritanopic color vision defect. Hum Mol Genet 2021; 30:1218-1229. [PMID: 33891002 PMCID: PMC8212766 DOI: 10.1093/hmg/ddab117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
Cone dystrophies are a rare subgroup of inherited retinal dystrophies and hallmarked by color vision defects, low or decreasing visual acuity and central vision loss, nystagmus and photophobia. Applying genome-wide linkage analysis and array comparative genome hybridization, we identified a locus for autosomal dominant cone dystrophy on chromosome 16q12 in four independent multigeneration families. The locus is defined by duplications of variable size with a smallest region of overlap of 608 kb affecting the IRXB gene cluster and encompasses the genes IRX5 and IRX6. IRX5 and IRX6 belong to the Iroquois (Iro) protein family of homeodomain-containing transcription factors involved in patterning and regionalization of embryonic tissue in vertebrates, including the eye and the retina. All patients presented with a unique progressive cone dystrophy phenotype hallmarked by early tritanopic color vision defects. We propose that the disease underlies a misregulation of the IRXB gene cluster on chromosome 16q12 and demonstrate that overexpression of Irx5a and Irx6a, the two orthologous genes in zebrafish, results in visual impairment in 5-day-old zebrafish larvae.
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Affiliation(s)
- Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany
| | - Pablo Llavona
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany
| | - Alexandra Sauer
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany
| | - Peggy Reuter
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany
| | - Nicole Weisschuh
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany
| | - Melanie Kempf
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Universitätsklinikum Tübingen, Tübingen 72076, Germany.,Center for Rare Eye Diseases, University of Tübingen, Tübingen 72076, Germany
| | - Florian Alexander Dehmelt
- Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, University of Tübingen, Tübingen 72076, Germany
| | - Aristides B Arrenberg
- Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, University of Tübingen, Tübingen 72076, Germany
| | - Ieva Sliesoraityte
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany
| | - Eberhart Zrenner
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany.,Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, University of Tübingen, Tübingen 72076, Germany
| | - Mary J van Schooneveld
- Department of Ophthalmology, Amsterdam University Medical Centre, Amsterdam 1100 DD, The Netherlands.,Bartiméus Diagnostic Department, Zeist, The Netherlands
| | - Günther Rudolph
- Department of Ophthalmology, University Hospital, LMU Munich, München 80336, Germany
| | - Laura Kühlewein
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany.,University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Universitätsklinikum Tübingen, Tübingen 72076, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen 72076, Germany
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12
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Reichlmeir M, Elias L, Schulte D. Posttranslational Modifications in Conserved Transcription Factors: A Survey of the TALE-Homeodomain Superclass in Human and Mouse. Front Cell Dev Biol 2021; 9:648765. [PMID: 33768097 PMCID: PMC7985065 DOI: 10.3389/fcell.2021.648765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022] Open
Abstract
Transcription factors (TFs) guide effector proteins like chromatin-modifying or -remodeling enzymes to distinct sites in the genome and thereby fulfill important early steps in translating the genome’s sequence information into the production of proteins or functional RNAs. TFs of the same family are often highly conserved in evolution, raising the question of how proteins with seemingly similar structure and DNA-binding properties can exert physiologically distinct functions or respond to context-specific extracellular cues. A good example is the TALE superclass of homeodomain-containing proteins. All TALE-homeodomain proteins share a characteristic, 63-amino acid long homeodomain and bind to similar sequence motifs. Yet, they frequently fulfill non-redundant functions even in domains of co-expression and are subject to regulation by different signaling pathways. Here we provide an overview of posttranslational modifications that are associated with murine and human TALE-homeodomain proteins and discuss their possible importance for the biology of these TFs.
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Affiliation(s)
- Marina Reichlmeir
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Lena Elias
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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13
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Fu A, Koth ML, Brown RM, Shaw SA, Wang L, Krentz KJ, Zhang X, Hui CC, Jorgensen JS. IRX3 and IRX5 collaborate during ovary development and follicle formation to establish responsive granulosa cells in the adult mouse†. Biol Reprod 2020; 103:620-629. [PMID: 32507881 PMCID: PMC7822710 DOI: 10.1093/biolre/ioaa100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
Healthy development of ovarian follicles depends on appropriate interactions and function between oocytes and their surrounding granulosa cells. Previously, we showed that double knockout of Irx3 and Irx5 (Irx3/5 DKO) in mice resulted in abnormal follicle morphology and follicle death. Further, female mouse models of individual Irx3 or Irx5 knockouts were both subfertile but with distinct defects. Notably, the expression profile of each gene suggests independent roles for each; first, they are colocalized in pre-granulosa cells during development that then progresses to include oocyte expression during germline nest breakdown and primordial follicle formation. Thereafter, their expression patterns diverge between oocytes and granulosa cells coinciding with the formulation and maturation of intimate oocyte-granulosa cell interactions. The objective of this study was to investigate the contributions of Irx5 and somatic cell-specific expression of Irx3 during ovarian development. Our results show that Irx3 and Irx5 contribute to female fertility through different mechanisms and that Irx3 expression in somatic cells is important for oocyte quality and survival. Based on evaluation of a series of genetically modified mouse models, we conclude that IRX3 and IRX5 collaborate in the same cells and then in neighboring cells to foster a healthy and responsive follicle. Long after these two factors have extinguished, their legacy enables these intercellular connections to mature and respond to extracellular signals to promote follicle maturation and ovulation.
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Affiliation(s)
- Anqi Fu
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Megan L Koth
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Ryan M Brown
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Sarah A Shaw
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Linda Wang
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Kathleen J Krentz
- Genome Editing and Animal Models Core, Biotechnology Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Xiaoyun Zhang
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chi-chung Hui
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Joan S Jorgensen
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI, USA
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14
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Koth ML, Garcia-Moreno SA, Novak A, Holthusen KA, Kothandapani A, Jiang K, Taketo MM, Nicol B, Yao HHC, Futtner CR, Maatouk DM, Jorgensen JS. Canonical Wnt/β-catenin activity and differential epigenetic marks direct sexually dimorphic regulation of Irx3 and Irx5 in developing mouse gonads. Development 2020; 147:dev183814. [PMID: 32108023 PMCID: PMC7132837 DOI: 10.1242/dev.183814] [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: 08/10/2019] [Accepted: 02/14/2020] [Indexed: 11/20/2022]
Abstract
Members of the Iroquois B (IrxB) homeodomain cluster genes, specifically Irx3 and Irx5, are crucial for heart, limb and bone development. Recently, we reported their importance for oocyte and follicle survival within the developing ovary. Irx3 and Irx5 expression begins after sex determination in the ovary but remains absent in the fetal testis. Mutually antagonistic molecular signals ensure ovary versus testis differentiation with canonical Wnt/β-catenin signals paramount for promoting the ovary pathway. Notably, few direct downstream targets have been identified. We report that Wnt/β-catenin signaling directly stimulates Irx3 and Irx5 transcription in the developing ovary. Using in silico analysis of ATAC- and ChIP-Seq databases in conjunction with mouse gonad explant transfection assays, we identified TCF/LEF-binding sequences within two distal enhancers of the IrxB locus that promote β-catenin-responsive ovary expression. Meanwhile, Irx3 and Irx5 transcription is suppressed within the developing testis by the presence of H3K27me3 on these same sites. Thus, we resolved sexually dimorphic regulation of Irx3 and Irx5 via epigenetic and β-catenin transcriptional control where their ovarian presence promotes oocyte and follicle survival vital for future ovarian health.
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Affiliation(s)
- Megan L Koth
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | | | - Annie Novak
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Kirsten A Holthusen
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Anbarasi Kothandapani
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Keer Jiang
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Makoto Mark Taketo
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Barbara Nicol
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Humphrey H-C Yao
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Christopher R Futtner
- Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL 60611, USA
| | - Danielle M Maatouk
- Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL 60611, USA
| | - Joan S Jorgensen
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
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15
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Jung IH, Jung DE, Chung YY, Kim KS, Park SW. Iroquois Homeobox 1 Acts as a True Tumor Suppressor in Multiple Organs by Regulating Cell Cycle Progression. Neoplasia 2019; 21:1003-1014. [PMID: 31450023 PMCID: PMC6715957 DOI: 10.1016/j.neo.2019.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/16/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Iroquois homeobox 1 (IRX1) belongs to the Iroquois homeobox family known to play an important role during embryonic development. Interestingly, however, recent studies have suggested that IRX1 also acts as a tumor suppressor. Here, we use homozygous knockout mutants of zebrafish to demonstrate that the IRX1 gene is a true tumor suppressor gene and mechanism of the tumor suppression is mediated by repressing cell cycle progression. In this study, we found that knockout of zebrafish Irx1 gene induced hyperplasia and tumorigenesis in the multiple organs where the gene was expressed. On the other hands, overexpression of the IRX1 gene in human tumor cell lines showed delayed cell proliferation of the tumor cells. These results suggest that the IRX1 gene is truly involved in tumor suppression. In an attempt to identify the genes regulated by the transcription factor IRX1, we performed microarray assay using the cRNA obtained from the knockout mutants. Our result indicated that the highest fold change of the differential genes fell into the gene category of cell cycle regulation, suggesting that the significant canonical pathway of IRX1 in antitumorigenesis is done by regulating cell cycle. Experiment with cell cycle blockers treated to IRX1 overexpressing tumor cells showed that the IRX1 overexpression actually delayed the cell cycle. Furthermore, Western blot analysis with cyclin antibodies showed that IRX1 overexpression induced decrease of cyclin production in the cancer cells. In conclusion, our in vivo and in vitro studies revealed that IRX1 gene functionally acts as a true tumor suppressor, inhibiting tumor cell growth by regulating cell cycle.
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Affiliation(s)
- In Hye Jung
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Dawoon E Jung
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Yong-Yoon Chung
- Research Institute of SMT Bio, SMT Bio Co., Ltd., Seoul, Republic of Korea.
| | - Kyung-Sik Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Seung Woo Park
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.
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16
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Zhu Q, Wu Y, Yang M, Wang Z, Zhang H, Jiang X, Chen M, Jin T, Wang T. IRX5 promotes colorectal cancer metastasis by negatively regulating the core components of the RHOA pathway. Mol Carcinog 2019; 58:2065-2076. [PMID: 31432570 DOI: 10.1002/mc.23098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 01/20/2023]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors worldwide. As tumor metastasis is the leading cause of death in patients with CRC, it is important to elucidate the molecular mechanisms that drive CRC metastasis. Studies have shown a close relationship between Iroquois homeobox (IRX) family genes and multiple cancers, while the mechanism by which IRX5 promotes CRC metastasis is unclear. Therefore, we focused on the involvement of IRX5 in CRC metastasis. In this study, analyses of clinical data indicated that the expression of IRX5 was coincided with metastatic colorectal tumors tissues and was negatively correlated with the overall survival of patients with CRC. Functional analysis showed that IRX5 promoted the migration and invasion of CRC cells, accompanied by a large number of cellular protrusions. IRX5-overexpressing cells were more likely to form metastatic tumors in nude mice. Further analysis demonstrated that the core components of the RHOA/ROCK1/LIMK1 pathway were significantly inhibited in IRX5-overexpressing cells. Overexpression of LIMK1 effectively reversed the enhanced cellular motility caused by IRX5 overexpression. Moreover, we found that high levels of IRX5 in intestinal tissues were correlated with the inflammatory response. IRX5 was significantly increased in azoxymethane/dextran sodium sulfate intestinal tissue of mice and IRX5-overexpressing may also enhance chemokines CXCL1 and CXCL8. In summary, our findings suggested that IRX5 promoted CRC metastasis by inhibiting the RHOA-ROCK1-LIMK1 axis, which correlates with a poor prognosis.
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Affiliation(s)
- Qiangqiang Zhu
- Department of Cell Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yiqi Wu
- Department of Cell Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mengli Yang
- Department of Cell Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhen Wang
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hailing Zhang
- Department of Cell Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinying Jiang
- Department of Cell Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Meng Chen
- Department of Molecular, Cellular and Biomedical Sciences, Medical Laboratory Science Program, College of Life Sciences and Agriculture, The University of New Hampshire, Durham, New Hampshire
| | - Tianyu Jin
- Department of Clinic School, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ting Wang
- Department of Cell Biology, Nanjing Medical University, Nanjing, Jiangsu, China
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17
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Onimaru K, Kuraku S. Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications. Brief Funct Genomics 2019; 17:352-361. [PMID: 29566222 PMCID: PMC6158797 DOI: 10.1093/bfgp/ely008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as ‘chronological reconstruction of ohnolog functions (CHROF)’. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.
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Affiliation(s)
- Koh Onimaru
- RIKEN Center for Life Science Technologies, Kobe, Hyogo Japan.,Department of biological science, Tokyo Institute of Technology, Tokyo, Japan
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18
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Fu A, Oberholtzer SM, Bagheri-Fam S, Rastetter RH, Holdreith C, Caceres VL, John SV, Shaw SA, Krentz KJ, Zhang X, Hui CC, Wilhelm D, Jorgensen JS. Dynamic expression patterns of Irx3 and Irx5 during germline nest breakdown and primordial follicle formation promote follicle survival in mouse ovaries. PLoS Genet 2018; 14:e1007488. [PMID: 30071018 PMCID: PMC6071956 DOI: 10.1371/journal.pgen.1007488] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/13/2018] [Indexed: 01/12/2023] Open
Abstract
Women and other mammalian females are born with a finite supply of oocytes that determine their reproductive lifespan. During fetal development, individual oocytes are enclosed by a protective layer of granulosa cells to form primordial follicles that will grow, mature, and eventually release the oocyte for potential fertilization. Despite the knowledge that follicles are dysfunctional and will die without granulosa cell-oocyte interactions, the mechanisms by which these cells establish communication is unknown. We previously identified that two members of the Iroquois homeobox transcription factor gene family, Irx3 and Irx5, are expressed within developing ovaries but not testes. Deletion of both factors (Irx3-Irx5EGFP/Irx3-Irx5EGFP) disrupted granulosa cell-oocyte contact during early follicle development leading to oocyte death. Thus, we hypothesized that Irx3 and Irx5 are required to develop cell-cell communication networks to maintain follicle integrity and female fertility. A series of Irx3 and Irx5 mutant mouse models were generated to assess roles for each factor. While both Irx3 and Irx5 single mutant females were subfertile, their breeding outcomes and ovary histology indicated distinct causes. Careful analysis of Irx3- and Irx5-reporter mice linked the cause of this disparity to dynamic spatio-temporal changes in their expression patterns. Both factors marked the progenitor pre-granulosa cell population in fetal ovaries. At the critical phase of germline nest breakdown and primordial follicle formation however, Irx3 and Irx5 transitioned to oocyte- and granulosa cell-specific expression respectively. Further investigation into the cause of follicle death in Irx3-Irx5EGFP/Irx3-Irx5EGFP ovaries uncovered specific defects in both granulosa cells and oocytes. Granulosa cell defects included poor contributions to basement membrane deposition and mis-localization of gap junction proteins. Granulosa cells and oocytes both presented fewer cell projections resulting in compromised cell-cell communication. Altogether, we conclude that Irx3 and Irx5 first work together to define the pregranulosa cell population of germline nests. During primordial follicle formation, they transition to oocyte- and granulosa cell-specific expression patterns where they cooperate in neighboring cells to build the foundation for follicle integrity. This foundation is left as their legacy of the essential oocyte-granulosa cell communication network that ensures and ultimately optimizes the integrity of the ovarian reserve and therefore, the female reproductive lifespan.
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Affiliation(s)
- Anqi Fu
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Sydney M. Oberholtzer
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Stefan Bagheri-Fam
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Victoria, Australia
| | - Raphael H. Rastetter
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Claire Holdreith
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Valeria L. Caceres
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Steven V. John
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Sarah A. Shaw
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Kathleen J. Krentz
- Genome Editing and Animal Models Core, Biotechnology Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Xiaoyun Zhang
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chi-chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dagmar Wilhelm
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Victoria, Australia
| | - Joan S. Jorgensen
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
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19
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Man J, Barnett P, Christoffels VM. Structure and function of the Nppa-Nppb cluster locus during heart development and disease. Cell Mol Life Sci 2018; 75:1435-1444. [PMID: 29302701 PMCID: PMC5852170 DOI: 10.1007/s00018-017-2737-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/07/2017] [Accepted: 12/20/2017] [Indexed: 01/20/2023]
Abstract
Atrial natriuretic factor and brain natriuretic peptide are two important biomarkers in clinical cardiology. These two natriuretic peptide hormones are encoded by the paralogous genes Nppa and Nppb, which are evolutionary conserved. Both genes are predominantly expressed by the heart muscle during the embryonic and fetal stages, and in particular Nppa expression is strongly reduced in the ventricles after birth. Upon cardiac stress, Nppa and Nppb are strongly upregulated in the ventricular myocardium. Much is known about the molecular and physiological ques inducing Nppa and Nppb expression; however, the transcriptional regulatory mechanisms of the Nppa-Nppb cluster in vivo has proven to be quite complex and is not well understood. In this review, we will provide recent insights into the dynamic and complex regulation of Nppa and Nppb during heart development and hypertrophy, and the association of this gene cluster with the cardiomyocyte-intrinsic program of heart regeneration.
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Affiliation(s)
- Joyce Man
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Phil Barnett
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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Hu W, Xin Y, Zhang L, Hu J, Sun Y, Zhao Y. Iroquois Homeodomain transcription factors in ventricular conduction system and arrhythmia. Int J Med Sci 2018; 15:808-815. [PMID: 30008591 PMCID: PMC6036080 DOI: 10.7150/ijms.25140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/29/2018] [Indexed: 02/05/2023] Open
Abstract
Iroquois homeobox genes, Irx, encode cardiac transcription factors, Irx1-6 in most mammals. These six transcription factors are expressed in different patterns mainly in the ventricular part of the heart. Existing researches show that Irx genes play key roles in the differentiation and development of ventricular conduction system and the establishment and maintenance of gradient expression of potassium channels, Kv4.2. Our main focus of this review is on the recent advances in the discovery of above-mentioned genes and the function of the encoding products, how Irx genes establish ventricular conduction system and regulate ventricular repolarization, how the individual and complementary functions can be verified to complement our cognition and leads to novel therapeutic approaches.
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Affiliation(s)
- Wenyu Hu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yanguo Xin
- Department of Cardiology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Zhang
- Department of Cardiology, Jinqiu Hosipital Of Liaoning Province, Shenyang, Liaoning110001, China
| | - Jian Hu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yingxian Sun
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yinan Zhao
- Department of Neurology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
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21
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Yokoyama S, Furukawa S, Kitada S, Mori M, Saito T, Kawakami K, Belmonte JCI, Kawakami Y, Ito Y, Sato T, Asahara H. Analysis of transcription factors expressed at the anterior mouse limb bud. PLoS One 2017; 12:e0175673. [PMID: 28467430 PMCID: PMC5415108 DOI: 10.1371/journal.pone.0175673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/29/2017] [Indexed: 12/21/2022] Open
Abstract
Limb bud patterning, outgrowth, and differentiation are precisely regulated in a spatio-temporal manner through integrated networks of transcription factors, signaling molecules, and downstream genes. However, the exact mechanisms that orchestrate morphogenesis of the limb remain to be elucidated. Previously, we have established EMBRYS, a whole-mount in situ hybridization database of transcription factors. Based on the findings from EMBRYS, we focused our expression pattern analysis on a selection of transcription factor genes that exhibit spatially localized and temporally dynamic expression patterns with respect to the anterior-posterior axis in the E9.5–E11.5 limb bud. Among these genes, Irx3 showed a posteriorly expanded expression domain in Shh-/- limb buds and an anteriorly reduced expression domain in Gli3-/- limb buds, suggesting their importance in anterior-posterior patterning. To assess the stepwise EMBRYS-based screening system for anterior regulators, we generated Irx3 transgenic mice in which Irx3 was expressed in the entire limb mesenchyme under the Prrx1 regulatory element. The Irx3 gain-of-function model displayed complex phenotypes in the autopods, including digit loss, radial flexion, and fusion of the metacarpal bones, suggesting that Irx3 may contribute to the regulation of limb patterning, especially in the autopods. Our results demonstrate that gene expression analysis based on EMBRYS could contribute to the identification of genes that play a role in patterning of the limb mesenchyme.
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Affiliation(s)
- Shigetoshi Yokoyama
- Department of Systems Biomedicine, National Institute of Child Health and Development, Setagaya, Tokyo, Japan
| | - Soichi Furukawa
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Shoya Kitada
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Masaki Mori
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Takeshi Saito
- Department of Systems Biomedicine, National Institute of Child Health and Development, Setagaya, Tokyo, Japan
| | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Yasuhiko Kawakami
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Yoshiaki Ito
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Tempei Sato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Hiroshi Asahara
- Department of Systems Biomedicine, National Institute of Child Health and Development, Setagaya, Tokyo, Japan
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- Department of Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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22
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Cardeña-Núñez S, Sánchez-Guardado LÓ, Corral-San-Miguel R, Rodríguez-Gallardo L, Marín F, Puelles L, Aroca P, Hidalgo-Sánchez M. Expression patterns of Irx genes in the developing chick inner ear. Brain Struct Funct 2016; 222:2071-2092. [PMID: 27783221 DOI: 10.1007/s00429-016-1326-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
The vertebrate inner ear is a complex three-dimensional sensorial structure with auditory and vestibular functions. The molecular patterning of the developing otic epithelium creates various positional identities, consequently leading to the stereotyped specification of each neurosensory and non-sensory element of the membranous labyrinth. The Iroquois (Iro/Irx) genes, clustered in two groups (A: Irx1, Irx2, and Irx4; and B: Irx3, Irx5, and Irx6), encode for transcriptional factors involved directly in numerous patterning processes of embryonic tissues in many phyla. This work presents a detailed study of the expression patterns of these six Irx genes during chick inner ear development, paying particular attention to the axial specification of the otic anlagen. The Irx genes seem to play different roles at different embryonic periods. At the otic vesicle stage (HH18), all the genes of each cluster are expressed identically. Both clusters A and B seem involved in the specification of the lateral and posterior portions of the otic anlagen. Cluster B seems to regulate a larger area than cluster A, including the presumptive territory of the endolymphatic apparatus. Both clusters seem also to be involved in neurogenic events. At stages HH24/25-HH27, combinations of IrxA and IrxB genes participate in the specification of most sensory patches and some non-sensory components of the otic epithelium. At stage HH34, the six Irx genes show divergent patterns of expression, leading to the final specification of the membranous labyrinth, as well as to cell differentiation.
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Affiliation(s)
- Sheila Cardeña-Núñez
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain
| | - Luis Óscar Sánchez-Guardado
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain
| | - Rubén Corral-San-Miguel
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Lucía Rodríguez-Gallardo
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain
| | - Faustino Marín
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Pilar Aroca
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Instituto Murciano de Investigación Biosanitaria-Virgen de La Arrixaca (IMIB-Arrixaca), E30100, Murcia, Spain
| | - Matías Hidalgo-Sánchez
- Department of Cell Biology, School of Science, University of Extremadura, Avda de Elvas s/n, E06071, Badajoz, Spain.
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Sena E, Feistel K, Durand BC. An Evolutionarily Conserved Network Mediates Development of the zona limitans intrathalamica, a Sonic Hedgehog-Secreting Caudal Forebrain Signaling Center. J Dev Biol 2016; 4:jdb4040031. [PMID: 29615594 PMCID: PMC5831802 DOI: 10.3390/jdb4040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 09/29/2016] [Accepted: 10/13/2016] [Indexed: 12/16/2022] Open
Abstract
Recent studies revealed new insights into the development of a unique caudal forebrain-signaling center: the zona limitans intrathalamica (zli). The zli is the last brain signaling center to form and the first forebrain compartment to be established. It is the only part of the dorsal neural tube expressing the morphogen Sonic Hedgehog (Shh) whose activity participates in the survival, growth and patterning of neuronal progenitor subpopulations within the thalamic complex. Here, we review the gene regulatory network of transcription factors and cis-regulatory elements that underlies formation of a shh-expressing delimitated domain in the anterior brain. We discuss evidence that this network predates the origin of chordates. We highlight the contribution of Shh, Wnt and Notch signaling to zli development and discuss implications for the fact that the morphogen Shh relies on primary cilia for signal transduction. The network that underlies zli development also contributes to thalamus induction, and to its patterning once the zli has been set up. We present an overview of the brain malformations possibly associated with developmental defects in this gene regulatory network (GRN).
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Affiliation(s)
- Elena Sena
- Institut Curie, Université Paris Sud, INSERM U1021, CNRS UMR3347, Centre Universitaire, Bâtiment 110, F-91405 Orsay Cedex, France.
| | - Kerstin Feistel
- Institute of Zoology, University of Hohenheim, Garbenstr. 30, 70593 Stuttgart, Germany.
| | - Béatrice C Durand
- Institut Curie, Université Paris Sud, INSERM U1021, CNRS UMR3347, Centre Universitaire, Bâtiment 110, F-91405 Orsay Cedex, France.
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24
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Liu D, Pattabiraman V, Bacanamwo M, Anderson LM. Iroquois homeobox transcription factor (Irx5) promotes G1/S-phase transition in vascular smooth muscle cells by CDK2-dependent activation. Am J Physiol Cell Physiol 2016; 311:C179-89. [PMID: 27170637 PMCID: PMC5129766 DOI: 10.1152/ajpcell.00293.2015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 05/06/2016] [Indexed: 12/30/2022]
Abstract
The Iroquois homeobox (Irx5) gene is essential in embryonic development and cardiac electrophysiology. Although recent studies have reported that IRX5 protein is involved in regulation of the cell cycle and apoptosis in prostate cancer cells, little is known about the role of IRX5 in the adult vasculature. Here we report novel observations on the role of IRX5 in adult vascular smooth muscle cells (VSMCs) during proliferation in vitro and in vivo. Comparative studies using primary human endothelial cells, VSMCs, and intact carotid arteries to determine relative expression of Irx5 in the peripheral vasculature demonstrate significantly higher expression in VSMCs. Sprague-Dawley rat carotid arteries were subjected to balloon catherization, and the presence of IRX5 was examined by immunohistochemistry after 2 wk. Results indicate markedly elevated IRX5 signal at 14 days compared with uninjured controls. Total RNA was isolated from injured and uninjured arteries, and Irx5 expression was measured by RT-PCR. Results demonstrate a significant increase in Irx5 expression at 3-14 days postinjury compared with controls. Irx5 genetic gain- and loss-of-function studies using thymidine and 5-bromo-2'-deoxyuridine incorporation assays resulted in modulation of DNA synthesis in primary rat aortic VSMCs. Quantitative RT-PCR results revealed modulation of cyclin-dependent kinase inhibitor 1B (p27(kip1)), E2F transcription factor 1 (E2f1), and proliferating cell nuclear antigen (Pcna) expression in Irx5-transduced VSMCs compared with controls. Subsequently, apoptosis was observed and confirmed by morphological observation, caspase-3 cleavage, and enzymatic activation compared with control conditions. Taken together, these results indicate that Irx5 plays an important role in VSMC G1/S-phase cell cycle checkpoint control and apoptosis.
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Affiliation(s)
- Dong Liu
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia; Department of Physiology, Morehouse School of Medicine, Atlanta, Georgia; and
| | - Vaishnavi Pattabiraman
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia; Department of Medicine, Morehouse School of Medicine, Atlanta, Georgia
| | - Methode Bacanamwo
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia; Department of Physiology, Morehouse School of Medicine, Atlanta, Georgia; and
| | - Leonard M Anderson
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia; Department of Physiology, Morehouse School of Medicine, Atlanta, Georgia; and
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25
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Evaluation of IRX Genes and Conserved Noncoding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis. G3-GENES GENOMES GENETICS 2016; 6:1707-12. [PMID: 27172222 PMCID: PMC4889666 DOI: 10.1534/g3.116.029975] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because of genetic heterogeneity present in idiopathic scoliosis, we previously defined clinical subsets (a priori) from a sample of families with idiopathic scoliosis to find genes involved with spinal curvature. Previous genome-wide linkage analysis of seven families with at least two individuals with kyphoscoliosis found linkage (P-value = 0.002) in a 3.5-Mb region on 5p13.3 containing only three known genes, IRX1, IRX2, and IRX4. In this study, the exons of IRX1, IRX2, and IRX4, the conserved noncoding elements in the region, and the exons of a nonprotein coding RNA, LOC285577, were sequenced. No functional sequence variants were identified. An intrafamilial test of association found several associated noncoding single nucleotide variants. The strongest association was with rs12517904 (P = 0.00004), located 6.5 kb downstream from IRX1. In one family, the genotypes of nine variants differed from the reference allele in all individuals with kyphoscoliosis, and two of three individuals with scoliosis, but did not differ from the reference allele in all other genotyped individuals. One of these variants, rs117273909, was located in a conserved noncoding region that functions as an enhancer in mice. To test whether the variant allele at rs117273909 had an effect on enhancer activity, zebrafish transgenesis was performed with overlapping fragments of 198 and 687 bp containing either the wild type or the variant allele. Our data suggests that this region acts as a regulatory element; however, its size and target gene(s) need to be identified to determine its role in idiopathic scoliosis.
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26
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Hunt LE, Noyvert B, Bhaw-Rosun L, Sesay AK, Paternoster L, Nohr EA, Davey Smith G, Tommerup N, Sørensen TIA, Elgar G. Complete re-sequencing of a 2Mb topological domain encompassing the FTO/IRXB genes identifies a novel obesity-associated region upstream of IRX5. Genome Med 2015; 7:126. [PMID: 26642925 PMCID: PMC4671217 DOI: 10.1186/s13073-015-0250-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/17/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Association studies have identified a number of loci that contribute to an increased body mass index (BMI), the strongest of which is in the first intron of the FTO gene on human chromosome 16q12.2. However, this region is both non-coding and under strong linkage disequilibrium, making it recalcitrant to functional interpretation. Furthermore, the FTO gene is located within a complex cis-regulatory landscape defined by a topologically associated domain that includes the IRXB gene cluster, a trio of developmental regulators. Consequently, at least three genes in this interval have been implicated in the aetiology of obesity. METHODS Here, we sequence a 2 Mb region encompassing the FTO, RPGRIP1L and IRXB cluster genes in 284 individuals from a well-characterised study group of Danish men containing extremely overweight young adults and controls. We further replicate our findings both in an expanded male cohort and an independent female study group. Finally, we compare our variant data with a previous study describing IRX3 and FTO interactions in this region. RESULTS We obtain deep coverage across the entire region, allowing accurate and unequivocal determination of almost every single nucleotide polymorphism and short insertion/deletion. As well as confirming previous findings across the interval, we identify a further novel age-dependent association upstream of IRX5 that imposes a similar burden on BMI to the FTO locus. CONCLUSIONS Our findings are consistent with the hypothesis that chromatin architectures play a role in regulating gene expression levels across topological domains while our targeted sequence approach represents a widely applicable methodology for high-resolution analysis of regional variation across candidate genomic loci.
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Affiliation(s)
- Lilian E Hunt
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Boris Noyvert
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Leena Bhaw-Rosun
- Genomics Facility, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Abdul K Sesay
- Genomics Facility, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK
| | - Ellen A Nohr
- Research Unit for Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK
| | - Niels Tommerup
- Willhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, The Faculty of Health Sciences, The University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK.,The Novo Nordisk Foundation Centre for Basic Metabolic Research, Section on Metabolic genetics, The Faculty of Health and Medical Sciences, University of Copenhagen, DK2100, Copenhagen Ø, Denmark.,Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, The Capital Region, DK2000, Frederiksberg, Denmark
| | - Greg Elgar
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK.
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Rask-Andersen M, Almén MS, Schiöth HB. Scrutinizing the FTO locus: compelling evidence for a complex, long-range regulatory context. Hum Genet 2015; 134:1183-93. [DOI: 10.1007/s00439-015-1599-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/30/2015] [Indexed: 01/06/2023]
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28
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Mallika C, Guo Q, Li JYH. Gbx2 is essential for maintaining thalamic neuron identity and repressing habenular characters in the developing thalamus. Dev Biol 2015; 407:26-39. [PMID: 26297811 DOI: 10.1016/j.ydbio.2015.08.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 12/30/2022]
Abstract
The thalamus and habenula, two important nodes of the forebrain circuitry, are derived from a single developmental compartment, called prosomere 2, in the diencephalon. Habenular and thalamic neurons display distinct molecular identity, neurochemistry, and connectivity. Furthermore, their progenitors exhibit distinctive neurogenic patterns with a marked delay in the onset of neurogenesis in the thalamus. However, the progenitors in prosomere 2 express many common developmental regulators and the mechanism underlying the specification and differentiation of these two populations of neurons remains unknown. Gbx2, coding for a homeodomain transcription factor, is initially expressed in thalamic neuronal precursors that have just exited the cell cycle, and its expression is maintained in many mature thalamic neurons in adults. Deletion of Gbx2 severely disrupts histogenesis of the thalamus and abolishes thalamocortical projections in mice. Here, by using genome-wide transcriptional profiling, we show that Gbx2 promotes thalamic but inhibits habenular molecular characters. Remarkably, although Gbx2 is expressed in postmitotic neuronal precursors, deletion of Gbx2 changes gene expression and cell proliferation in dividing progenitors in the developing thalamus. These defects are partially rescued by the mosaic presence of wild-type cells, demonstrating a cell non-autonomous role of Gbx2 in regulating the development of thalamic progenitors. Our results suggest that Gbx2 is essential for the acquisition of the thalamic neuronal identity by repressing habenular identity through a feedback signaling from postmitotic neurons to progenitors.
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Affiliation(s)
- Chatterjee Mallika
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, Farmington, CT 06030-6403, United States
| | - Qiuxia Guo
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, Farmington, CT 06030-6403, United States
| | - James Y H Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, Farmington, CT 06030-6403, United States.
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29
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Zagozewski JL, Zhang Q, Pinto VI, Wigle JT, Eisenstat DD. The role of homeobox genes in retinal development and disease. Dev Biol 2014; 393:195-208. [PMID: 25035933 DOI: 10.1016/j.ydbio.2014.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/02/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022]
Abstract
Homeobox genes are an evolutionarily conserved class of transcription factors that are critical for development of many organ systems, including the brain and eye. During retinogenesis, homeodomain-containing transcription factors, which are encoded by homeobox genes, play essential roles in the regionalization and patterning of the optic neuroepithelium, specification of retinal progenitors and differentiation of all seven of the retinal cell classes that derive from a common progenitor. Homeodomain transcription factors control retinal cell fate by regulating the expression of target genes required for retinal progenitor cell fate decisions and for terminal differentiation of specific retinal cell types. The essential role of homeobox genes during retinal development is demonstrated by the number of human eye diseases, including colobomas and anophthalmia, which are attributed to homeobox gene mutations. In the following review, we highlight the role of homeodomain transcription factors during retinogenesis and regulation of their gene targets. Understanding the complexities of vertebrate retina development will enhance our ability to drive differentiation of specific retinal cell types towards novel cell-based replacement therapies for retinal degenerative diseases.
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Affiliation(s)
- Jamie L Zagozewski
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Qi Zhang
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB, Canada R3E 0J9
| | - Vanessa I Pinto
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9
| | - Jeffrey T Wigle
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9; Institute of Cardiovascular Sciences, St. Boniface Hospital Research Institute, Winnipeg, MB, Canada R2H 2A6
| | - David D Eisenstat
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2H7; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9; Department of Pediatrics, University of Alberta, Edmonton, AB, Canada T6G 1C9.
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30
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Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) affect 1/500 live births. CAKUT lead to end stage renal failure in children, and are associated with high morbidity rates. Understanding the mechanisms of kidney development, and that of other associated urogenital tissues, is crucial to the prevention and treatment of CAKUT. The kidney arises from self-renewing mesenchymal renal stem cells that produce nephrons, which are the principal functional units of the organ. To date, the genetic and cellular mechanisms that control nephrogenesis have remained poorly understood. In recent years, developmental studies using amphibians and zebrafish have revealed that their simple embryonic kidney, known as the pronephros, is a useful paradigm for comparative studies of nephron ontogeny. Here, we discuss the new found roles for Iroquois transcription factors in pronephric nephron patterning, and explore the relevance of these findings for kidney development in humans.
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Affiliation(s)
| | - Rebecca A. Wingert
- Corresponding author: Rebecca A. Wingert, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA, Tel: 574-631-0907; Fax: 574-631-7413;
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31
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Kim KH, Rosen A, Bruneau BG, Hui CC, Backx PH. Iroquois homeodomain transcription factors in heart development and function. Circ Res 2012; 110:1513-24. [PMID: 22628575 DOI: 10.1161/circresaha.112.265041] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Numerous cardiac transcription factors play overlapping roles in both the specification and proliferation of the cardiac tissues and chambers during heart development. It has become increasingly apparent that cardiac transcription factors also play critical roles in the regulation of expression of many functional genes in the prenatal and postnatal hearts. Accordingly, mutations of cardiac transcription factors cannot only result in congenital heart defects but also alter heart function thereby predisposing to heart disease and cardiac arrhythmias. In this review, we summarize the roles of Iroquois homeobox (Irx) family of transcription factors in heart development and function. In all, 6 Irx genes are expressed with distinct and overlapping patterns in the mammalian heart. Studies in several animal models demonstrate that Irx genes are important for the establishment of ventricular chamber properties, the ventricular conduction system, as well as heterogeneity of the ventricular repolarization. The molecular mechanisms by which Irx proteins regulate gene expression and the clinical relevance of Irx functions in the heart are discussed.
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Affiliation(s)
- Kyoung-Han Kim
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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Chatterjee M, Li JYH. Patterning and compartment formation in the diencephalon. Front Neurosci 2012; 6:66. [PMID: 22593732 PMCID: PMC3349951 DOI: 10.3389/fnins.2012.00066] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 04/17/2012] [Indexed: 01/03/2023] Open
Abstract
The diencephalon gives rise to structures that play an important role in connecting the anterior forebrain with the rest of the central nervous system. The thalamus is the major diencephalic derivative that functions as a relay station between the cortex and other lower order sensory systems. Almost two decades ago, neuromeric/prosomeric models were proposed describing the subdivision and potential segmentation of the diencephalon. Unlike the laminar structure of the cortex, the diencephalon is progressively divided into distinct functional compartments consisting principally of thalamus, epithalamus, pretectum, and hypothalamus. Neurons generated within these domains further aggregate to form clusters called nuclei, which form specific structural and functional units. We review the recent advances in understanding the genetic mechanisms that are involved in the patterning and compartment formation of the diencephalon.
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Affiliation(s)
- Mallika Chatterjee
- Department of Genetics and Developmental Biology, University of Connecticut Health Center Farmington, CT, USA
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Tena JJ, Alonso ME, de la Calle-Mustienes E, Splinter E, de Laat W, Manzanares M, Gómez-Skarmeta JL. An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nat Commun 2011; 2:310. [PMID: 21556064 DOI: 10.1038/ncomms1301] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 04/04/2011] [Indexed: 01/22/2023] Open
Abstract
Developmental gene clusters are paradigms for the study of gene regulation; however, the mechanisms that mediate phenomena such as coregulation and enhancer sharing remain largely elusive. Here we address this issue by analysing the vertebrate Irx clusters. We first present a deep enhancer screen of a 2-Mbp span covering the IrxA cluster. Using chromosome conformation capture, we show that enhancer sharing is widespread within the cluster, explaining its evolutionarily conserved organization. We also identify a three-dimensional architecture, probably formed through interactions with CCCTC-binding factor, which is present within both Irx clusters of mouse, Xenopus and zebrafish. This architecture brings the promoters of the first two genes together in the same chromatin landscape. We propose that this unique and evolutionarily conserved genomic architecture of the vertebrate Irx clusters is essential for the coregulation of the first two genes and simultaneously maintains the third gene in a partially independent regulatory landscape.
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Affiliation(s)
- Juan J Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013 Sevilla, Spain
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Kim B, Kim Y, Cooke PS, Rüther U, Jorgensen JS. The fused toes locus is essential for somatic-germ cell interactions that foster germ cell maturation in developing gonads in mice. Biol Reprod 2011; 84:1024-32. [PMID: 21293032 DOI: 10.1095/biolreprod.110.088559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ovarian development absolutely depends on communication between somatic and germ cell components. In contrast, it is not until after birth that interactions between somatic and germ cells play an important role in testicular maturation and spermatogenesis. Previously, we discovered that Irx3 expression was localized specifically to female gonads during embryonic development; therefore, we sought to determine the function of this genetic locus in developing gonads of both sexes. The fused toes (Ft) mutant mouse is missing 1.6 Mb of chromosome 8, which includes the entire IrxB cluster (Irx3, Irx5, Irx6), Ftm, Fts, and Fto genes. Homozygote Ft mutant embryos die around embryonic day 13.5 (E13.5); therefore, to assess later development, we harvested gonads at E11.5 and transplanted them into nude mouse hosts. Our results show defects in somatic and germ cell maturation in developing gonads of both sexes. Testis development was normal initially; however, by 3-wk posttransplantation, expression of Sertoli and peritubular myoid cell markers were decreased. In many cases, gonocytes failed to migrate to structurally impaired basement membranes of seminiferous cords. Developmental abnormalities of the ovary appeared earlier and were more severe. Over time, the Ft mutant ovary formed very few primordial or primary follicles, which contained oocytes that failed to grow and were surrounded by scarce granulosa cells that expressed low levels of FOXL2. By 3 wk after transplantation, it was difficult to identify ovarian tissue in Ft mutant ovary transplants. In summary, we conclude that the Ft locus contains genes essential for somatic-germ cell interactions, without which the germ cell niche fails to mature in both sexes.
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Affiliation(s)
- Bongki Kim
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
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Doi T, Lukošiūtė A, Ruttenstock E, Dingemann J, Puri P. Expression of Iroquois genes is up-regulated during early lung development in the nitrofen-induced pulmonary hypoplasia. J Pediatr Surg 2011; 46:62-6. [PMID: 21238641 DOI: 10.1016/j.jpedsurg.2010.09.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 09/30/2010] [Indexed: 11/17/2022]
Abstract
BACKGROUND/PURPOSE Iroquois homeobox (Irx) genes have been implicated in the early lung morphogenesis of vertebrates. Irx1-3 and Irx5 gene expression is seen in fetal lung in rodents up to day (D) 18.5 of gestation. Fetal lung in Irx knockdown mice shows loss of mesenchyme and dilated airspaces, whereas nitrofen-induced hypoplastic lung displays thickened mesenchyme and diminished airspaces. We hypothesized that the Irx genes are up-regulated during early lung morphogenesis in the nitrofen-induced hypoplastic lung. METHODS Pregnant rats were exposed either to olive oil or nitrofen on D9. Fetal lungs harvested on D15 were divided into control and nitrofen groups; and the lungs harvested on D18 were divided into control, nitrofen without congenital diaphragmatic hernia (CDH[-]), and nitrofen with CDH (CDH[+]). Irx gene expression levels were analyzed by reverse transcriptase polymerase chain reaction. Immunohistochemistry was performed to evaluate protein expression of Irx family. RESULTS Pulmonary Irx1-3 and Irx5 messenger RNA expression levels were significantly up-regulated in nitrofen group compared with controls at D15. On D15, Irx immunoreactivity was increased in nitrofen-induced hypoplastic lung compared with controls. CONCLUSION Overexpression of Irx genes in the early lung development may cause pulmonary hypoplasia in the nitrofen CDH model by inducing lung dysmorphogenesis with thickened mesenchyme and diminished airspaces.
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Affiliation(s)
- Takashi Doi
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
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Kim B, Kim Y, Sakuma R, Hui CC, Rüther U, Jorgensen JS. Primordial germ cell proliferation is impaired in Fused Toes mutant embryos. Dev Biol 2010; 349:417-26. [PMID: 20969841 DOI: 10.1016/j.ydbio.2010.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/06/2010] [Accepted: 10/13/2010] [Indexed: 11/30/2022]
Abstract
Over the first 4 days of their life, primordial germ cells invade the endoderm, migrate into and through the developing hindgut, and traverse to the genital ridge where they cluster and ultimately inhabit the nascent gonad. Specific signal-receptor combinations between primordial germ cells and their immediate environment establish successful migration and colonization. Here we demonstrate that disruption of a cluster of six genes on murine chromosome 8, as exemplified by the Fused Toes (Ft) mutant mouse model, results in severely decreased numbers of primordial germ cells within the early gonad. Primordial germ cell migration appeared normal within Ft mutant embryos; however, germ cell counts progressively decreased during this time. Although no difference in apoptosis was detected, we report a critical decrease in primordial germ cell proliferation by E12.5. The six genes within the Ft locus include the IrxB cluster (Irx3, -5, -6), Fts, Ftm, and Fto, of which only Ftm, Fto, and Fts are expressed in primordial germ cells of the early gonad. From these studies, we have discovered that the Ft locus on mouse chromosome 8 is associated with cell cycle deficits within the primordial germ cell population that initiates just before translocation into the genital ridge.
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Affiliation(s)
- Bongki Kim
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
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McDonald LA, Gerrelli D, Fok Y, Hurst LD, Tickle C. Comparison of Iroquois gene expression in limbs/fins of vertebrate embryos. J Anat 2010; 216:683-91. [PMID: 20408909 PMCID: PMC2952381 DOI: 10.1111/j.1469-7580.2010.01233.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2010] [Indexed: 11/30/2022] Open
Abstract
In Drosophila, Iroquois (Irx) genes have various functions including the specification of the identity of wing veins. Vertebrate Iroquois (Irx) genes have been reported to be expressed in the developing digits of mouse limbs. Here we carry out a phylogenetic analysis of vertebrate Irx genes and compare expression in developing limbs of mouse, chick and human embryos and in zebrafish pectoral fin buds. We confirm that the six Irx gene families in vertebrates are well defined and that Clusters A and B are duplicates; in contrast, Irx1 and 3, Irx2 and 5, and Irx4 and 6 are paralogs. All Irx genes in mouse and chick are expressed in developing limbs. Detailed comparison of the expression patterns in mouse and chick shows that expression patterns of genes in the same cluster are generally similar but paralogous genes have different expression patterns. Mouse and chick Irx1 are expressed in digit condensations, whereas mouse and chick Irx6 are expressed interdigitally. The timing of Irx1 expression in individual digits in mouse and chick is different. Irx1 is also expressed in digit condensations in developing human limbs, thus showing conservation of expression of this gene in higher vertebrates. In zebrafish, Irx genes of all but six of the families are expressed in early stage pectoral fin buds but not at later stages, suggesting that these genes are not involved in patterning distal structures in zebrafish fins.
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Affiliation(s)
- Laura A McDonald
- Department of Biology & Biochemistry, University of BathSomerset, UK
| | - Dianne Gerrelli
- Human Developmental Biology Resource, Neural Development Unit, UCL Institute of Child HealthLondon, UK
| | - Yvonne Fok
- Human Developmental Biology Resource, Neural Development Unit, UCL Institute of Child HealthLondon, UK
| | - Laurence D Hurst
- Department of Biology & Biochemistry, University of BathSomerset, UK
| | - Cheryll Tickle
- Department of Biology & Biochemistry, University of BathSomerset, UK
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Chuang HN, Cheng HY, Hsiao KM, Lin CW, Lin ML, Pan H. The zebrafish homeobox gene irxl1 is required for brain and pharyngeal arch morphogenesis. Dev Dyn 2009; 239:639-50. [DOI: 10.1002/dvdy.22187] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Developmental expression of the three iroquois genes of amphioxus (BfIrxA, BfIrxB, and BfIrxC) with special attention to the gastrula organizer and anteroposterior boundaries in the central nervous system. Gene Expr Patterns 2009; 9:329-34. [DOI: 10.1016/j.gep.2009.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 02/06/2009] [Accepted: 02/11/2009] [Indexed: 11/16/2022]
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Kerner P, Ikmi A, Coen D, Vervoort M. Evolutionary history of the iroquois/Irx genes in metazoans. BMC Evol Biol 2009; 9:74. [PMID: 19368711 PMCID: PMC2674049 DOI: 10.1186/1471-2148-9-74] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 04/15/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The iroquois (iro/Irx) genes encode transcriptional regulators that belong to the TALE superclass of homeodomain proteins and have key functions during development in both vertebrates and insects. The Irx genes occur in one or two genomic clusters containing three genes each within the Drosophila and several vertebrate genomes, respectively. The similar genomic organization in Drosophila and vertebrates is widely considered as a result of convergent evolution, due to independent tandem gene duplications. In this study, we investigate the evolutionary history of the Irx genes at the scale of the whole metazoan kingdom. RESULTS We identified in silico the putative full complement of Irx genes in the sequenced genomes of 36 different species representative of the main metazoan lineages, including non bilaterian species, several arthropods, non vertebrate chordates, and a basal vertebrate, the sea lamprey. We performed extensive phylogenetic analyses of the identified Irx genes and defined their genomic organizations. We found that, in most species, there are several Irx genes, these genes form two to four gene clusters, and the Irx genes are physically linked to a structurally and functionally unrelated gene known as CG10632 in Drosophila. CONCLUSION Three main conclusions can be drawn from our study. First, an Irx cluster composed of two genes, araucan/caupolican and mirror, is ancestral to the crustaceans+insects clade and has been strongly conserved in this clade. Second, three Irx genes were probably present in the last common ancestor of vertebrates and the duplication that has given rise to the six genes organized into two clusters found in most vertebrates, likely occurred in the gnathostome lineage after its separation from sea lampreys. Third, the clustered organization of the Irx genes in various evolutionary lineages may represent an exceptional case of convergent evolution or may point to the existence of an Irx gene cluster ancestral to bilaterians.
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Affiliation(s)
- Pierre Kerner
- Evolution et Développement des métazoaires, Centre de Génétique Moléculaire – FRE 3144 CNRS, 1, av. de la terrasse, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Diderot – Paris 7, 5 rue Marie-Andrée Lagroua Weill-Hallé, 75205 Paris Cedex 13, France
- Institut Jacques Monod, UMR 7592 CNRS/Université Paris Diderot – Paris 7, 15, rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Aissam Ikmi
- Développement, Morphogenèse et Évolution, CNRS UMR 8080, Université Paris-Sud, 91405 Orsay, France
- Present address: Stowers Institute for Medical Research, 1000 E 50th St Kansas City, Missouri 64110 USA
| | - Dario Coen
- Développement, Morphogenèse et Évolution, CNRS UMR 8080, Université Paris-Sud, 91405 Orsay, France
| | - Michel Vervoort
- Evolution et Développement des métazoaires, Centre de Génétique Moléculaire – FRE 3144 CNRS, 1, av. de la terrasse, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Diderot – Paris 7, 5 rue Marie-Andrée Lagroua Weill-Hallé, 75205 Paris Cedex 13, France
- Institut Jacques Monod, UMR 7592 CNRS/Université Paris Diderot – Paris 7, 15, rue Hélène Brion, 75205 Paris Cedex 13, France
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Rodríguez-Seguel E, Alarcón P, Gómez-Skarmeta JL. The Xenopus Irx genes are essential for neural patterning and define the border between prethalamus and thalamus through mutual antagonism with the anterior repressors Fezf and Arx. Dev Biol 2009; 329:258-68. [PMID: 19268445 DOI: 10.1016/j.ydbio.2009.02.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 02/20/2009] [Accepted: 02/24/2009] [Indexed: 12/17/2022]
Abstract
The Iroquois (Irx) genes encode homeoproteins conserved during evolution. Vertebrate genomes contain six Irx genes organized in two clusters, IrxA (which harbors Irx1, Irx2 and Irx4) and IrxB (which harbors Irx3, Irx5 and Irx6). To determine the precise role of these genes during development and their putative redundancies, we conducted a comparative expression analysis and a comprehensive loss-of-function study of all the early expressed Irx genes (Irx1-5) using specific morpholinos in Xenopus. We found that the five Irx genes display largely overlapping expression patterns and contribute to neural patterning. All Irx genes are required for proper formation of posterior forebrain, midbrain, hindbrain and, to a lesser an extent, spinal cord. Nevertheless, Irx1 and Irx3 seem to have a predominant role during regionalization of the neural plate. In addition, we find that the common anterior limit of Irx gene expression, which will correspond to the future border between the prethalamus and thalamus, is defined by mutual repression between Fezf and Irx proteins. This mutual repression is likely direct. Finally, we show that Arx, another anteriorly expressed repressor, also contribute to delineate the anterior border of Irx expression.
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Affiliation(s)
- Elisa Rodríguez-Seguel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013 Sevilla, Spain
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Feijóo CG, Saldias MP, De la Paz JF, Gómez-Skarmeta JL, Allende ML. Formation of posterior cranial placode derivatives requires the Iroquois transcription factor irx4a. Mol Cell Neurosci 2009; 40:328-37. [DOI: 10.1016/j.mcn.2008.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 09/02/2008] [Accepted: 11/17/2008] [Indexed: 01/29/2023] Open
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Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae. Dev Genes Evol 2008; 218:579-90. [DOI: 10.1007/s00427-008-0245-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 08/11/2008] [Indexed: 01/01/2023]
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Myrthue A, Rademacher BLS, Pittsenbarger J, Kutyba-Brooks B, Gantner M, Qian DZ, Beer TM. The iroquois homeobox gene 5 is regulated by 1,25-dihydroxyvitamin D3 in human prostate cancer and regulates apoptosis and the cell cycle in LNCaP prostate cancer cells. Clin Cancer Res 2008; 14:3562-70. [PMID: 18519790 DOI: 10.1158/1078-0432.ccr-07-4649] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
1,25-Dihydroxyvitamin D3 [1,25(OH)2D3], the most active metabolite of vitamin D3, has significant antitumor activity in a broad range of preclinical models of cancer. In this study, we show that the Iroquois homeobox gene 5 (Irx5) is down-regulated by 1,25(OH)2D3 in human prostate cancer samples from patients randomly assigned to receive weekly high-dose 1,25(OH)2D3 or placebo before radical prostatectomy. Down-regulation of Irx5 by 1,25(OH)2D3 was also shown in the human androgen-sensitive prostate cancer cell line LNCaP and in estrogen-sensitive MCF-7 breast cancer cells. Knockdown of Irx5 by RNA interference showed a significant reduction in LNCaP cell viability, which was accompanied by an increase in p21 protein expression, G2-M arrest, and an increase in apoptosis. The induced apoptosis was partially mediated by p53, and p53 protein expression was increased as a result of Irx5 knockdown. Cell survival was similarly reduced by Irx5 knockdown in the colon cancer cell line HCT 116 and in MCF-7 breast cancer cells, each being derived from clinical tumor types that seem to be inhibited by 1,25(OH)2D3. Overexpression of Irx5 led to a reduction of p21 and p53 expression. This is the first report that Irx5 is regulated by 1,25(OH)2D3 in humans and the first report to show that Irx5 is involved in the regulation of both the cell cycle and apoptosis in human prostate cancer cells. Irx5 may be a promising new therapeutic target in cancer treatment.
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Affiliation(s)
- Anne Myrthue
- Division of Hematology and Medical Oncology, Oregon Health and Science University, CH-14R, 3303 SW Bond Avenue, Portland, OR 97239, USA
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Irimia M, Maeso I, Garcia-Fernàndez J. Convergent evolution of clustering of Iroquois homeobox genes across metazoans. Mol Biol Evol 2008; 25:1521-5. [PMID: 18469332 DOI: 10.1093/molbev/msn109] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vertebrate and Drosophila Iroquois genes are organized in clusters of 3 genes sharing blocks of conserved regulatory sequences. Here, we report a 3-gene cluster in the basal, preduplicative chordate amphioxus. Surprisingly, however, the origin of the amphioxus cluster is independent of those in vertebrates and drosophilids. Investigation of genomic organization of Iroquois genes in other 17 metazoan genomes revealed a fourth independent 3-gene cluster organization in polychaetes, as well as additional 2- and 4-gene clusters in other clades, in one of the most striking examples of convergence in genomic organization described so far. The recurrent independent evolution of Iroquois clusters suggests a functional importance of this organization for these genes, perhaps related to the sharing of regulatory elements. Consistent with this, comparative analysis of genomic regions flanking the 3 amphioxus Irx genes revealed several blocks of sequences, conserved for at least 100 Myr. Finally, we discuss the possible causes and implications of the convergent evolution of this genomic and regulatory organization throughout metazoans.
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Affiliation(s)
| | | | - Ulrich Rüther
- *Prof. Dr. Ulrich Rüther, Institut für Entwicklungs- und Molekularbiologie der Tiere, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany, Tel. +49 211 811-1391, Fax -5113, E-mail
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Spitz F, Duboule D. Global control regions and regulatory landscapes in vertebrate development and evolution. ADVANCES IN GENETICS 2008; 61:175-205. [PMID: 18282506 DOI: 10.1016/s0065-2660(07)00006-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the course of evolution, many genes that control the development of metazoan body plans were co-opted to exert novel functions, along with the emergence or modification of structures. Gene amplification and/or changes in the cis-regulatory modules responsible for the transcriptional activity of these genes have certainly contributed in a major way to evolution of gene functions. In some cases, these processes led to the formation of groups of adjacent genes that appear to be controlled by both global and shared mechanisms.
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Affiliation(s)
- Francois Spitz
- Developmental Biology Unit, EMBL, 69117 Heidelberg, Germany
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Holland PWH, Booth HAF, Bruford EA. Classification and nomenclature of all human homeobox genes. BMC Biol 2007; 5:47. [PMID: 17963489 PMCID: PMC2211742 DOI: 10.1186/1741-7007-5-47] [Citation(s) in RCA: 285] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Accepted: 10/26/2007] [Indexed: 12/19/2022] Open
Abstract
Background The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described. Results We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'. Conclusion We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.
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Affiliation(s)
- Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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Reggiani L, Raciti D, Airik R, Kispert A, Brändli AW. The prepattern transcription factor Irx3 directs nephron segment identity. Genes Dev 2007; 21:2358-70. [PMID: 17875669 PMCID: PMC1973149 DOI: 10.1101/gad.450707] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nephron, the basic structural and functional unit of the vertebrate kidney, is organized into discrete segments, which are composed of distinct renal epithelial cell types. Each cell type carries out highly specific physiological functions to regulate fluid balance, osmolarity, and metabolic waste excretion. To date, the genetic basis of regionalization of the nephron has remained largely unknown. Here we show that Irx3, a member of the Iroquois (Irx) gene family, acts as a master regulator of intermediate tubule fate. Comparative studies in Xenopus and mouse have identified Irx1, Irx2, and Irx3 as an evolutionary conserved subset of Irx genes, whose expression represents the earliest manifestation of intermediate compartment patterning in the developing vertebrate nephron discovered to date. Intermediate tubule progenitors will give rise to epithelia of Henle's loop in mammals. Loss-of-function studies indicate that irx1 and irx2 are dispensable, whereas irx3 is necessary for intermediate tubule formation in Xenopus. Furthermore, we demonstrate that misexpression of irx3 is sufficient to direct ectopic development of intermediate tubules in the Xenopus mesoderm. Taken together, irx3 is the first gene known to be necessary and sufficient to specify nephron segment fate in vivo.
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Affiliation(s)
- Luca Reggiani
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniela Raciti
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Rannar Airik
- Institute of Molecular Biology, Hannover Medical School, D-30625 Hannover, Germany
| | - Andreas Kispert
- Institute of Molecular Biology, Hannover Medical School, D-30625 Hannover, Germany
| | - André W. Brändli
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, CH-8093 Zurich, Switzerland
- Corresponding author.E-MAIL ; FAX 41-44-633-1358
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Allende ML, Manzanares M, Tena JJ, Feijóo CG, Gómez-Skarmeta JL. Cracking the genome's second code: enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos. Methods 2006; 39:212-9. [PMID: 16806968 DOI: 10.1016/j.ymeth.2005.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Accepted: 12/17/2005] [Indexed: 02/05/2023] Open
Abstract
Genes involved in vertebrate development are unusually enriched for highly conserved non-coding sequence elements. These regions are readily detected in silico, by genome-wide sequence comparisons between different vertebrates, from mammals to fish (phylogenetic footprinting). It follows that sequence conservation must be the result of positive selection for an essential physiological role. An obvious possibility is that these conserved sequences possess regulatory or structural functions important for gene expression and, thus, an in vivo assay becomes necessary. We have developed a rapid testing system using zebrafish and Xenopus laevis embryos that allows us to assign transcriptional regulatory functions to conserved non-coding sequence elements. The sequences are cloned into a vector containing a minimal promoter and the GFP reporter, and are assayed for their putative cis-regulatory activity in zebrafish or Xenopus transgenic experiments. Vectors used include plasmid DNA and the Tol2 transposon system in fish and X. laevis. We have followed this logic to detect and analyze conserved elements in an intergenic region present in the Iroquois (Irx) gene clusters of zebrafish, Xenopus tropicalis, Fugu rubripes and mouse. We have assayed approximately 50 of these conserved elements and shown that the majority behave as modular positive regulatory elements (enhancers) that contribute to specific temporal and spatial domains that are part of the endogenous gene expression pattern. Moreover, comparison of the activity of cognate Irx enhancers from different organisms demonstrates that conservation of sequence is accompanied by in vivo functional conservation across species. Finally, for some of the most conserved elements, we have been able to identify a critical core sequence, essential for correct enhancer function.
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Affiliation(s)
- Miguel L Allende
- Millennium Nucleus in Developmental Biology, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.
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