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Padua MB, Helm BM, Wells JR, Smith AM, Bellchambers HM, Sridhar A, Ware SM. Congenital heart defects caused by FOXJ1. Hum Mol Genet 2023; 32:2335-2346. [PMID: 37158461 PMCID: PMC10321388 DOI: 10.1093/hmg/ddad065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/25/2023] [Accepted: 04/13/2023] [Indexed: 05/10/2023] Open
Abstract
FOXJ1 is expressed in ciliated cells of the airways, testis, oviduct, central nervous system and the embryonic left-right organizer. Ablation or targeted mutation of Foxj1 in mice, zebrafish and frogs results in loss of ciliary motility and/or reduced length and number of motile cilia, affecting the establishment of the left-right axis. In humans, heterozygous pathogenic variants in FOXJ1 cause ciliopathy leading to situs inversus, obstructive hydrocephalus and chronic airway disease. Here, we report a novel truncating FOXJ1 variant (c.784_799dup; p.Glu267Glyfs*12) identified by clinical exome sequencing from a patient with isolated congenital heart defects (CHD) which included atrial and ventricular septal defects, double outlet right ventricle (DORV) and transposition of the great arteries. Functional experiments show that FOXJ1 c.784_799dup; p.Glu267Glyfs*12, unlike FOXJ1, fails to induce ectopic cilia in frog epidermis in vivo or to activate the ADGB promoter, a downstream target of FOXJ1 in cilia, in transactivation assays in vitro. Variant analysis of patients with heterotaxy or heterotaxy-related CHD indicates that pathogenic variants in FOXJ1 are an infrequent cause of heterotaxy. Finally, we characterize embryonic-stage CHD in Foxj1 loss-of-function mice, demonstrating randomized heart looping. Abnormal heart looping includes reversed looping (dextrocardia), ventral looping and no looping/single ventricle hearts. Complex CHDs revealed by histological analysis include atrioventricular septal defects, DORV, single ventricle defects as well as abnormal position of the great arteries. These results indicate that pathogenic variants in FOXJ1 can cause isolated CHD.
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Affiliation(s)
- Maria B Padua
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202, USA
| | - John R Wells
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amanda M Smith
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Helen M Bellchambers
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Arthi Sridhar
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Stephanie M Ware
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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2
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Yagi H, Cui C, Saydmohammed M, Gabriel G, Baker C, Devine W, Wu Y, Lin JH, Malek M, Bais A, Murray S, Aronow B, Tsang M, Kostka D, Lo CW. Spatial transcriptome profiling uncovers metabolic regulation of left-right patterning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537827. [PMID: 37131609 PMCID: PMC10153223 DOI: 10.1101/2023.04.21.537827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Left-right patterning disturbance can cause severe birth defects, but it remains least understood of the three body axes. We uncovered an unexpected role for metabolic regulation in left-right patterning. Analysis of the first spatial transcriptome profile of left-right patterning revealed global activation of glycolysis, accompanied by right-sided expression of Bmp7 and genes regulating insulin growth factor signaling. Cardiomyocyte differentiation was left-biased, which may underlie the specification of heart looping orientation. This is consistent with known Bmp7 stimulation of glycolysis and glycolysis suppression of cardiomyocyte differentiation. Liver/lung laterality may be specified via similar metabolic regulation of endoderm differentiation. Myo1d , found to be left-sided, was shown to regulate gut looping in mice, zebrafish, and human. Together these findings indicate metabolic regulation of left-right patterning. This could underlie high incidence of heterotaxy-related birth defects in maternal diabetes, and the association of PFKP, allosteric enzyme regulating glycolysis, with heterotaxy. This transcriptome dataset will be invaluable for interrogating birth defects involving laterality disturbance.
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Abas R, Masrudin SS, Harun AM, Omar NS, Omar NS. Gastrulation and Body Axes Formation: A Molecular Concept and Its Clinical Correlates. Malays J Med Sci 2022; 29:6-14. [PMID: 36818899 PMCID: PMC9910376 DOI: 10.21315/mjms2022.29.6.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/02/2021] [Indexed: 12/25/2022] Open
Abstract
During the third week of human pregnancy, an embryo transforms from two germinal disc layers of hypoblast and epiblast to three germinal layers of endoderm, mesoderm and ectoderm. Gastrulation is a complex process that includes cellular mobility, morphogenesis and cell signalling, as well as chemical morphogenic gradients, transcription factors and differential gene expression. During gastrulation, many signalling channels coordinate individual cell actions in precise time and location. These channels control cell proliferation, shape, fate and migration to the correct sites. Subsequently, the anteroposterior (AP), dorsoventral (DV) and left-right (LR) body axes are formed before and during gastrulation via these signalling regulation signals. Hence, the anomalies in gastrulation caused by insults to certain molecular pathways manifest as a wide range of body axes-related disorders. This article outlines the formation of body axes during gastrulation and the anomalies as well as the clinical implications.
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Affiliation(s)
- Razif Abas
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia,Department of Anatomy and Embryology, Faculty of Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - Siti Saleha Masrudin
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | | | - Noorkardiffa Syawalina Omar
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia,Department of Obstetrics and Gynaecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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4
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Hernandez-Moran BA, Papanastasiou AS, Parry D, Meynert A, Gautier P, Grimes G, Adams IR, Trejo-Reveles V, Bengani H, Keighren M, Jackson IJ, Adams DJ, FitzPatrick DR, Rainger J. Robust Genetic Analysis of the X-Linked Anophthalmic ( Ie) Mouse. Genes (Basel) 2022; 13:1797. [PMID: 36292683 PMCID: PMC9601528 DOI: 10.3390/genes13101797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Anophthalmia (missing eye) describes a failure of early embryonic ocular development. Mutations in a relatively small set of genes account for 75% of bilateral anophthalmia cases, yet 25% of families currently are left without a molecular diagnosis. Here, we report our experimental work that aimed to uncover the developmental and genetic basis of the anophthalmia characterising the X-linked Ie (eye-ear reduction) X-ray-induced allele in mouse that was first identified in 1947. Histological analysis of the embryonic phenotype showed failure of normal eye development after the optic vesicle stage with particularly severe malformation of the ventral retina. Linkage analysis mapped this mutation to a ~6 Mb region on the X chromosome. Short- and long-read whole-genome sequencing (WGS) of affected and unaffected male littermates confirmed the Ie linkage but identified no plausible causative variants or structural rearrangements. These analyses did reduce the critical candidate interval and revealed evidence of multiple variants within the ancestral DNA, although none were found that altered coding sequences or that were unique to Ie. To investigate early embryonic events at a genetic level, we then generated mouse ES cells derived from male Ie embryos and wild type littermates. RNA-seq and accessible chromatin sequencing (ATAC-seq) data generated from cultured optic vesicle organoids did not reveal any large differences in gene expression or accessibility of putative cis-regulatory elements between Ie and wild type. However, an unbiased TF-footprinting analysis of accessible chromatin regions did provide evidence of a genome-wide reduction in binding of transcription factors associated with ventral eye development in Ie, and evidence of an increase in binding of the Zic-family of transcription factors, including Zic3, which is located within the Ie-refined critical interval. We conclude that the refined Ie critical region at chrX: 56,145,000-58,385,000 contains multiple genetic variants that may be linked to altered cis regulation but does not contain a convincing causative mutation. Changes in the binding of key transcription factors to chromatin causing altered gene expression during development, possibly through a subtle mis-regulation of Zic3, presents a plausible cause for the anophthalmia phenotype observed in Ie, but further work is required to determine the precise causative allele and its genetic mechanism.
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Affiliation(s)
- Brianda A. Hernandez-Moran
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Andrew S. Papanastasiou
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - David Parry
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Ian R. Adams
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Violeta Trejo-Reveles
- The Division of Functional Genetics and Development, The Roslin Institute, Midlothian EH25 9RG, UK
| | - Hemant Bengani
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Margaret Keighren
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Ian J. Jackson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - David J. Adams
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK
| | - Joe Rainger
- The Division of Functional Genetics and Development, The Roslin Institute, Midlothian EH25 9RG, UK
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Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors. Nat Cell Biol 2022; 24:1114-1128. [PMID: 35817961 PMCID: PMC7613098 DOI: 10.1038/s41556-022-00947-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/25/2022] [Indexed: 01/13/2023]
Abstract
The mammalian heart arises from various populations of Mesp1-expressing cardiovascular progenitors (CPs) that are specified during the early stages of gastrulation. Mesp1 is a transcription factor that acts as a master regulator of CP specification and differentiation. However, how Mesp1 regulates the chromatin landscape of nascent mesodermal cells to define the temporal and spatial patterning of the distinct populations of CPs remains unknown. Here, by combining ChIP-seq, RNA-seq and ATAC-seq during mouse pluripotent stem cell differentiation, we defined the dynamic remodelling of the chromatin landscape mediated by Mesp1. We identified different enhancers that are temporally regulated to erase the pluripotent state and specify the pools of CPs that mediate heart development. We identified Zic2 and Zic3 as essential cofactors that act with Mesp1 to regulate its transcription-factor activity at key mesodermal enhancers, thereby regulating the chromatin remodelling and gene expression associated with the specification of the different populations of CPs in vivo. Our study identifies the dynamics of the chromatin landscape and enhancer remodelling associated with temporal patterning of early mesodermal cells into the distinct populations of CPs that mediate heart development.
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6
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Bellchambers HM, Ware SM. Loss of Zic3 impairs planar cell polarity leading to abnormal left-right signaling, heart defects and neural tube defects. Hum Mol Genet 2021; 30:2402-2415. [PMID: 34274973 DOI: 10.1093/hmg/ddab195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/18/2023] Open
Abstract
Loss of function of ZIC3 causes heterotaxy (OMIM #306955), a disorder characterized by organ laterality defects including complex heart defects. Studies using Zic3 mutant mice have demonstrated that loss of Zic3 causes heterotaxy due to defects in establishment of left-right (LR) signaling, but the mechanistic basis for these defects remains unknown. Here, we demonstrate Zic3 null mice undergo cilia positioning defects at the embryonic node consistent with impaired planar cell polarity (PCP). Cell-based assays demonstrate that ZIC3 must enter the nucleus to regulate PCP and identify multiple critical ZIC3 domains required for regulation of PCP signaling. Furthermore, we show that Zic3 displays a genetic interaction with the PCP membrane protein Vangl2 and the PCP effector genes Rac1 and Daam1 resulting in increased frequency and severity of neural tube and heart defects. Gene and protein expression analyses indicate that Zic3 null embryos display disrupted expression of PCP components and reduced phosphorylation of the core PCP protein DVL2 at the time of LR axis determination. These results demonstrate that ZIC3 interacts with PCP signaling during early development, identifying a novel role for this transcription factor, and adding additional evidence about the importance of PCP function for normal LR patterning and subsequent heart development.
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Affiliation(s)
| | - Stephanie M Ware
- Herman B Wells Center for Pediatric Research, Departments of Pediatrics.,Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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7
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ZIC3 Controls the Transition from Naive to Primed Pluripotency. Cell Rep 2020; 27:3215-3227.e6. [PMID: 31189106 PMCID: PMC6581693 DOI: 10.1016/j.celrep.2019.05.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/14/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023] Open
Abstract
Embryonic stem cells (ESCs) must transition through a series of intermediate cell states before becoming terminally differentiated. Here, we investigated the early events in this transition by determining the changes in the open chromatin landscape as naive mouse ESCs transition to epiblast-like cells (EpiLCs). Motif enrichment analysis of the newly opening regions coupled with expression analysis identified ZIC3 as a potential regulator of this cell fate transition. Chromatin binding and genome-wide transcriptional profiling following Zic3 depletion confirmed ZIC3 as an important regulatory transcription factor, and among its targets are genes encoding a number of transcription factors. Among these is GRHL2, which acts through enhancer switching to maintain the expression of a subset of genes from the ESC state. Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation. Transcription factor ZIC3 regulates gene expression during the ESC to EpiLC transition Extensive changes occur in the open chromatin landscape as ESCs progress to EpiLCs ZIC3 activates the expression of a network of transcription factors ZIC3-activated genes in EpiLCs are upregulated in the post-implantation epiblast
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8
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Sibbritt T, Ip CK, Khoo P, Wilkie E, Jones V, Sun JQJ, Shen JX, Peng G, Han JJ, Jing N, Osteil P, Ramialison M, Tam PPL, Fossat N. A gene regulatory network anchored by LIM homeobox 1 for embryonic head development. Genesis 2018; 56:e23246. [DOI: 10.1002/dvg.23246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Tennille Sibbritt
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
- School of Medical Sciences, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Chi K. Ip
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
| | - Poh‐Lynn Khoo
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
| | - Emilie Wilkie
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
- Bioinformatics Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
| | - Vanessa Jones
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
| | - Jane Q. J. Sun
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
| | - Joanne X. Shen
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
| | - Guangdun Peng
- State Key Laboratory of Cell Biology Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai China
| | - Jing‐Dong J. Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences‐Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
| | - Naihe Jing
- State Key Laboratory of Cell Biology Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai China
- School of Life Science and Technology ShanghaiTech University Shanghai China
| | - Pierre Osteil
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
- School of Medical Sciences, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute Monash University Melbourne Victoria Australia
| | - Patrick P. L. Tam
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
- School of Medical Sciences, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Nicolas Fossat
- Embryology Unit, Children's Medical Research Institute The University of Sydney Sydney New South Wales Australia
- School of Medical Sciences, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
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9
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Transcriptome variations among human embryonic stem cell lines are associated with their differentiation propensity. PLoS One 2018; 13:e0192625. [PMID: 29444173 PMCID: PMC5812638 DOI: 10.1371/journal.pone.0192625] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/26/2018] [Indexed: 12/20/2022] Open
Abstract
Human embryonic stem cells (hESCs) have the potential to form any cell type in the body, making them attractive cell sources in drug screening, regenerative medicine, disease and developmental processes modeling. However, not all hESC lines have the equal potency to generate desired cell types in vitro. Significant variations have been observed for the differentiation efficiency of various human ESC lines. The precise underpinning molecular mechanisms are still unclear. In this work, we compared transcriptome variations of four hESC lines H7, HUES1, HUES8 and HUES9. We found that hESC lines have different gene expression profiles, and these differentially expressed genes (DEGs) are significantly enriched in developmental processes, such as ectodermal, mesodermal and endodermal development. The enrichment difference between hESC lines was consistent with its lineage bias. Among these DEGs, some pluripotency factors and genes involved in signaling transduction showed great variations as well. The pleiotropic functions of these genes in controlling hESC identity and early lineage specification, implicated that different hESC lines may utilize distinct balance mechanisms to maintain pluripotent state. When the balance is broken in a certain environment, gene expression variation between them could impact on their different lineage specification behavior.
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10
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Zebrafish Zic Genes Mediate Developmental Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:157-177. [PMID: 29442322 DOI: 10.1007/978-981-10-7311-3_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The introduction of genomics into the field of developmental biology led to a vast expansion of knowledge about developmental genes and signaling mechanisms they are involved in. Unlike mammals, the zebrafish features seven Zic genes. This provides an interesting insight into Zic gene evolution. In addition, an unprecedented bioimaging capability of semitransparent zebrafish embryos turns to be a crucial factor in medium- to large-scale analysis of the activity of potential regulatory elements. The Zic family of zinc finger proteins plays an important, relatively well-established, role in the regulation of stem cells and neural development and, in particular, during neural fate commitment and determination. At the same time, some Zic genes are expressed in mesodermal lineages, and their deficiency causes a number of developmental defects in axis formation, establishing body symmetry and cardiac morphogenesis. In stem cells, Zic genes are required to maintain pluripotency by binding to the proximal promoters of pluripotency genes (Oct4, Nanog, Sox2, etc.). During embryogenesis, the dynamic nature of Zic transcriptional regulation is manifested by the interaction of these factors with distal enhancers and other regulatory elements associated with the control of gene transcription and, in particular, with the Nodal and Wnt signaling pathways that play a role in establishing basic organization of the vertebrate body. Zic transcription factors may regulate development through acting alone as well as in combination with other transcription factors. This is achieved due to Zic binding to sites adjacent to the binding sites of other transcription factors, including Gli. This probably leads to the formation of multi-transcription factor complexes associated with enhancers.
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11
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Roles of ZIC2 in Regulation of Pluripotent Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:339-351. [PMID: 29442330 DOI: 10.1007/978-981-10-7311-3_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pioneered by the classical mouse embryonic stem cells (ESCs), various stem cell lines representing the peri- and postimplantation stages of embryogenesis have been established. To gain insight into the gene regulatory network operating in these cells, we first investigated epiblast stem cells (EpiSCs), performing ChIP-seq analysis for five major transcription factors (TFs) involved in epiblast regulation. The analysis indicated that SOX2-POU5F1 TF pairs highlighted in mouse ESCs are not the major players in other stem cells. The major acting transcription factors shift from SOX2/POU5F1 in mouse ESCs to ZIC2/OTX2 in EpiSCs, and this shift is primed in ESCs by binding of ZIC2 at relevant genomic positions that later function as enhancers.
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12
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Bellchambers HM, Ware SM. ZIC3 in Heterotaxy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:301-327. [PMID: 29442328 DOI: 10.1007/978-981-10-7311-3_15] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mutation of ZIC3 causes X-linked heterotaxy, a syndrome in which the laterality of internal organs is disrupted. Analysis of model organisms and gene expression during early development suggests ZIC3-related heterotaxy occurs due to defects at the earliest stage of left-right axis formation. Although there are data to support abnormalities of the node and cilia as underlying causes, it is unclear at the molecular level why loss of ZIC3 function causes such these defects. ZIC3 has putative roles in a number of developmental signalling pathways that have distinct roles in establishing the left-right axis. This complicates the understanding of the mechanistic basis of Zic3 in early development and left-right patterning. Here we summarise our current understanding of ZIC3 function and describe the potential role ZIC3 plays in important signalling pathways and their links to heterotaxy.
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Affiliation(s)
- Helen M Bellchambers
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephanie M Ware
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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13
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Paulussen ADC, Steyls A, Vanoevelen J, van Tienen FHJ, Krapels IPC, Claes GRF, Chocron S, Velter C, Tan-Sindhunata GM, Lundin C, Valenzuela I, Nagy B, Bache I, Maroun LL, Avela K, Brunner HG, Smeets HJM, Bakkers J, van den Wijngaard A. Rare novel variants in the ZIC3 gene cause X-linked heterotaxy. Eur J Hum Genet 2016; 24:1783-1791. [PMID: 27406248 PMCID: PMC5117940 DOI: 10.1038/ejhg.2016.91] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/25/2016] [Accepted: 05/20/2016] [Indexed: 02/08/2023] Open
Abstract
Variants in the ZIC3 gene are rare, but have demonstrated their profound clinical significance in X-linked heterotaxy, affecting in particular male patients with abnormal arrangement of thoracic and visceral organs. Several reports have shown relevance of ZIC3 gene variants in both familial and sporadic cases and with a predominance of mutations detected in zinc-finger domains. No studies so far have assessed the functional consequences of ZIC3 variants in an in vivo model organism. A study population of 348 patients collected over more than 10 years with a large variety of congenital heart disease including heterotaxy was screened for variants in the ZIC3 gene. Functional effects of three variants were assessed both in vitro and in vivo in the zebrafish. We identified six novel pathogenic variants (1,7%), all in either male patients with heterotaxy (n=5) or a female patient with multiple male deaths due to heterotaxy in the family (n=1). All variants were located within the zinc-finger domains or leading to a truncation before these domains. Truncating variants showed abnormal trafficking of mutated ZIC3 proteins, whereas the missense variant showed normal trafficking. Overexpression of wild-type and mutated ZIC protein in zebrafish showed full non-functionality of the two frame-shift variants and partial activity of the missense variant compared with wild-type, further underscoring the pathogenic character of these variants. Concluding, we greatly expanded the number of causative variants in ZIC3 and delineated the functional effects of three variants using in vitro and in vivo model systems.
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Affiliation(s)
- Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Anja Steyls
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jo Vanoevelen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Florence HJ van Tienen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Godelieve RF Claes
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sonja Chocron
- Cardiac Development and Genetics, Hubrecht Institute-KNAW and University Medical Centre Utrecht, The Netherlands
| | - Crool Velter
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Gita M Tan-Sindhunata
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Catarina Lundin
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Irene Valenzuela
- Department of Clinical Genetics and Cytogenetics, Hospital Vall d'Hebron, Barcelona, Spain
| | - Balint Nagy
- Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - Iben Bache
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lisa Leth Maroun
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hubert J M Smeets
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jeroen Bakkers
- Cardiac Development and Genetics, Hubrecht Institute-KNAW and University Medical Centre Utrecht, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
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14
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Winata CL, Kondrychyn I, Korzh V. Changing Faces of Transcriptional Regulation Reflected by Zic3. Curr Genomics 2015; 16:117-27. [PMID: 26085810 PMCID: PMC4467302 DOI: 10.2174/1389202916666150205124519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 02/07/2023] Open
Abstract
The advent of genomics in the study of developmental mechanisms has brought a trove of information
on gene datasets and regulation during development, where the Zic family of zinc-finger proteins
plays an important role. Genomic analysis of the modes of action of Zic3 in pluripotent cells demonstrated its
requirement for maintenance of stem cells pluripotency upon binding to the proximal regulatory regions
(promoters) of genes associated with cell pluripotency (Nanog, Sox2, Oct4, etc.) as well as cell cycle, proliferation, oncogenesis
and early embryogenesis. In contrast, during gastrulation and neurulation Zic3 acts by binding the distal regulatory
regions (enhancers, etc) associated with control of gene transcription in the Nodal and Wnt signaling pathways, including
genes that act to break body symmetry. This illustrates a general role of Zic3 as a transcriptional regulator that
acts not only alone, but in many instances in conjunction with other transcription factors. The latter is done by binding to
adjacent sites in the context of multi-transcription factor complexes associated with regulatory elements.
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Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
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15
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Cowan J, Tariq M, Ware SM. Genetic and functional analyses of ZIC3 variants in congenital heart disease. Hum Mutat 2014; 35:66-75. [PMID: 24123890 DOI: 10.1002/humu.22457] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 09/06/2013] [Accepted: 09/23/2013] [Indexed: 12/13/2022]
Abstract
Mutations in zinc-finger in cerebellum 3 (ZIC3) result in heterotaxy or isolated congenital heart disease (CHD). The majority of reported mutations cluster in zinc-finger domains. We previously demonstrated that many of these lead to aberrant ZIC3 subcellular trafficking. A relative paucity of N- and C-terminal mutations has, however, prevented similar analyses in these regions. Notably, an N-terminal polyalanine expansion was recently identified in a patient with VACTERL, suggesting a potentially distinct function for this domain. Here we report ZIC3 sequencing results from 440 unrelated patients with heterotaxy and CHD, the largest cohort yet examined. Variants were identified in 5.2% of sporadic male cases. This rate exceeds previous estimates of 1% and has important clinical implications for genetic testing and risk-based counseling. Eight of 11 were novel, including 5 N-terminal variants. Subsequent functional analyses included four additional reported but untested variants. Aberrant cytoplasmic localization and decreased luciferase transactivation were observed for all zinc-finger variants, but not for downstream or in-frame upstream variants, including both analyzed polyalanine expansions. Collectively, these results expand the ZIC3 mutational spectrum, support a higher than expected prevalence in sporadic cases, and suggest alternative functions for terminal mutations, highlighting a need for further study of these domains.
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16
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Haaning AM, Quinn ME, Ware SM. Heterotaxy-spectrum heart defects in Zic3 hypomorphic mice. Pediatr Res 2013; 74:494-502. [PMID: 23999067 PMCID: PMC4176930 DOI: 10.1038/pr.2013.147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/08/2013] [Indexed: 01/01/2023]
Abstract
BACKGROUND Mutations in Zinc Finger Protein of the Cerebellum 3 (ZIC3) cause X-linked heterotaxy and isolated cardiovascular malformations. Recent data suggest a potential cell-autonomous role for Zic3 in myocardium via regulation of Nppa and Tbx5. We sought to develop a hypomorphic Zic3 mouse to model human heterotaxy and investigate developmental mechanisms underlying variability in cardiac phenotypes. METHODS Zic3 hypomorphic mice were created by targeted insertion of a neomycin cassette and investigated by gross, histologic, and molecular methods. RESULTS Low-level Zic3 expression is sufficient for partial rescue of viability as compared with Zic3 null mice. Concordance of early left-right molecular marker abnormalities and later anatomic abnormalities suggests that the primary effect of Zic3 in heart development occurs during left-right patterning. Cardiac-specific gene expression of Nppa (atrial natriuretic factor) and Tbx5 marked the proper morphological locations in the heart regardless of looping abnormalities. CONCLUSION Zic3 hypomorphic mice are useful models to investigate the variable cardiac defects resulting from a single genetic defect. Low-level Zic3 expression rescues the left pulmonary isomerism identified in Zic3 null embryos. Our data do not support a direct role for Zic3 in the myocardium via regulation of Nppa and Tbx5 and suggest that the primary effect of Zic3 on cardiac development occurs during left-right patterning.
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Affiliation(s)
- Allison M. Haaning
- Cincinnati Children’s Hospital Medical Center, Division of Molecular Cardiovascular Biology, Cincinnati, OH
| | - Malgorzata E. Quinn
- Cincinnati Children’s Hospital Medical Center, Division of Molecular Cardiovascular Biology, Cincinnati, OH
| | - Stephanie M. Ware
- Cincinnati Children’s Hospital Medical Center, Division of Molecular Cardiovascular Biology, Cincinnati, OH
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17
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Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. PLoS Genet 2013; 9:e1003852. [PMID: 24204288 PMCID: PMC3814314 DOI: 10.1371/journal.pgen.1003852] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 08/19/2013] [Indexed: 02/06/2023] Open
Abstract
Zic3 regulates early embryonic patterning in vertebrates. Loss of Zic3 function is known to disrupt gastrulation, left-right patterning, and neurogenesis. However, molecular events downstream of this transcription factor are poorly characterized. Here we use the zebrafish as a model to study the developmental role of Zic3 in vivo, by applying a combination of two powerful genomics approaches – ChIP-seq and microarray. Besides confirming direct regulation of previously implicated Zic3 targets of the Nodal and canonical Wnt pathways, analysis of gastrula stage embryos uncovered a number of novel candidate target genes, among which were members of the non-canonical Wnt pathway and the neural pre-pattern genes. A similar analysis in zic3-expressing cells obtained by FACS at segmentation stage revealed a dramatic shift in Zic3 binding site locations and identified an entirely distinct set of target genes associated with later developmental functions such as neural development. We demonstrate cis-regulation of several of these target genes by Zic3 using in vivo enhancer assay. Analysis of Zic3 binding sites revealed a distribution biased towards distal intergenic regions, indicative of a long distance regulatory mechanism; some of these binding sites are highly conserved during evolution and act as functional enhancers. This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape. The Zic3 transcription factor regulates early embryonic patterning, and the loss of its function leads to defects in left-right body asymmetry. Previous studies have only identified a small number of Zic3 targets, which renders the molecular mechanism underlying its activity insufficiently understood. Utilizing two genomics technologies, next generation sequencing and microarray, we profile the genome-wide binding sites of Zic3 and identified its target genes in the developing zebrafish embryo. Our results show that Zic3 regulates its target genes predominantly through regulatory elements located far from promoters. Among the targets of Zic3 are the Nodal and Wnt pathways known to regulate gastrulation and left-right body asymmetry, as well as neural pre-pattern genes regulating proliferation of neural progenitors. Using enhancer activity assay, we further show that genomic regions bound by Zic3 function as enhancers. Our study provides a genome-wide view of the regulatory landscape of Zic3 and its changes during vertebrate development.
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18
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Houtmeyers R, Souopgui J, Tejpar S, Arkell R. The ZIC gene family encodes multi-functional proteins essential for patterning and morphogenesis. Cell Mol Life Sci 2013; 70:3791-811. [PMID: 23443491 PMCID: PMC11113920 DOI: 10.1007/s00018-013-1285-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 01/16/2013] [Accepted: 01/28/2013] [Indexed: 12/18/2022]
Abstract
The zinc finger of the cerebellum gene (ZIC) discovered in Drosophila melanogaster (odd-paired) has five homologs in Xenopus, chicken, mice, and humans, and seven in zebrafish. This pattern of gene copy expansion is accompanied by a divergence in gene and protein structure, suggesting that Zic family members share some, but not all, functions. ZIC genes are implicated in neuroectodermal development and neural crest cell induction. All share conserved regions encoding zinc finger domains, however their heterogeneity and specification remain unexplained. In this review, the evolution, structure, and expression patterns of the ZIC homologs are described; specific functions attributable to individual family members are supported. A review of data from functional studies in Xenopus and murine models suggest that ZIC genes encode multifunctional proteins operating in a context-specific manner to drive critical events during embryogenesis. The identification of ZIC mutations in congenital syndromes highlights the relevance of these genes in human development.
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Affiliation(s)
- Rob Houtmeyers
- Department of Oncology, Katholieke Universiteit Leuven, O&N1, 3000, Leuven, Belgium,
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19
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Ahmed JN, Ali RG, Warr N, Wilson HM, Bellchambers HM, Barratt KS, Thompson AJ, Arkell RM. A murine Zic3 transcript with a premature termination codon evades nonsense-mediated decay during axis formation. Dis Model Mech 2013; 6:755-67. [PMID: 23471918 PMCID: PMC3634658 DOI: 10.1242/dmm.011668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The ZIC transcription factors are key mediators of embryonic development and ZIC3 is the gene most commonly associated with situs defects (heterotaxy) in humans. Half of patient ZIC3 mutations introduce a premature termination codon (PTC). In vivo, PTC-containing transcripts might be targeted for nonsense-mediated decay (NMD). NMD efficiency is known to vary greatly between transcripts, tissues and individuals and it is possible that differences in survival of PTC-containing transcripts partially explain the striking phenotypic variability that characterizes ZIC3-associated congenital defects. For example, the PTC-containing transcripts might encode a C-terminally truncated protein that retains partial function or that dominantly interferes with other ZIC family members. Here we describe the katun (Ka) mouse mutant, which harbours a mutation in the Zic3 gene that results in a PTC. At the time of axis formation there is no discernible decrease in this PTC-containing transcript in vivo, indicating that the mammalian Zic3 transcript is relatively insensitive to NMD, prompting the need to re-examine the molecular function of the truncated proteins predicted from human studies and to determine whether the N-terminal portion of ZIC3 possesses dominant-negative capabilities. A combination of in vitro studies and analysis of the Ka phenotype indicate that it is a null allele of Zic3 and that the N-terminal portion of ZIC3 does not encode a dominant-negative molecule. Heterotaxy in patients with PTC-containing ZIC3 transcripts probably arises due to loss of ZIC3 function alone.
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Affiliation(s)
- Jehangir N Ahmed
- Early Mammalian Development Laboratory, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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20
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D'Alessandro LCA, Latney BC, Paluru PC, Goldmuntz E. The phenotypic spectrum of ZIC3 mutations includes isolated d-transposition of the great arteries and double outlet right ventricle. Am J Med Genet A 2013; 161A:792-802. [PMID: 23427188 DOI: 10.1002/ajmg.a.35849] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 12/13/2012] [Indexed: 12/22/2022]
Abstract
Disease causing mutations for heterotaxy syndrome were first identified in the X-linked laterality gene, ZIC3. Mutations typically result in males with situs ambiguus and complex congenital heart disease; however affected females and one male with isolated d-transposition of the great arteries (d-TGA) have been reported. We hypothesized that a subset of patients with heart defects common to heterotaxy but without laterality defects would have ZIC3 mutations. We also sought to estimate the prevalence of ZIC3 mutations in sporadic heterotaxy. Patients with TGA (n = 169), double outlet right ventricle (DORV; n = 89), common atrioventricular canal (CAVC; n = 41), and heterotaxy (n = 54) underwent sequencing of ZIC3 exons. We tested 90 patients with tetralogy of Fallot (TOF) to correlate genotype with phenotype. Three potentially disease-related missense mutations were detected: c.49G > T (Gly17Cys) in a female with isolated DORV, c.98C > T (Ala33Val) in a male with isolated d-TGA, and c.841C > T (His281Tyr) in a female with sporadic heterotaxy. We also identified a novel insertion (CPFP333ins) in a family with heterotaxy. All were absent in 200 control patients and the 1000 Genomes Project (n = 629). No significant mutations were found in patients with TOF. Functional studies demonstrated reduced transcriptional activity of the ZIC3 His281Tyr mutant protein. ZIC3 mutations were rarely identified in isolated DORV and d-TGA suggesting that a subset of DORV and d-TGA may fall within the spectrum of laterality defects. ZIC3 mutations were found in 3.7% of patients with sporadic heterotaxy; therefore testing should be considered in patients with heterotaxy.
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Affiliation(s)
- Lisa C A D'Alessandro
- Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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21
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Sutherland MJ, Wang S, Quinn ME, Haaning A, Ware SM. Zic3 is required in the migrating primitive streak for node morphogenesis and left-right patterning. Hum Mol Genet 2013; 22:1913-23. [PMID: 23303524 DOI: 10.1093/hmg/ddt001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In humans, loss-of-function mutations in ZIC3 cause isolated cardiovascular malformations and X-linked heterotaxy, a disorder with abnormal left-right asymmetry of organs. Zic3 null mice recapitulate the human heterotaxy phenotype but also have early gastrulation defects, axial patterning defects and neural tube defects complicating an assessment of the role of Zic3 in cardiac development. Zic3 is expressed ubiquitously during critical stages of left-right patterning but its later expression in the developing heart remains controversial and the molecular mechanism(s) by which it causes heterotaxy are unknown. To define the temporal and spatial requirements, for Zic3 in left-right patterning, we generated conditional Zic3 mice and Zic3-LacZ-BAC reporter mice. The latter provide compelling evidence that Zic3 is expressed in the mouse node and absent in the heart. Conditional deletion using T-Cre identifies a requirement for Zic3 in the primitive streak and migrating mesoderm for proper left-right patterning and cardiac development. In contrast, Zic3 is not required in heart progenitors or the cardiac compartment. In addition, the data demonstrate abnormal node morphogenesis in Zic3 null mice and identify similar node dysplasia when Zic3 was specifically deleted from the migrating mesoderm and primitive streak. These results define the temporal and spatial requirements for Zic3 in node morphogenesis, left-right patterning and cardiac development and suggest the possibility that a requirement for Zic3 in node ultrastructure underlies its role in heterotaxy and laterality disorders.
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Affiliation(s)
- Mardi J Sutherland
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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22
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Jiang Z, Zhu L, Hu L, Slesnick TC, Pautler RG, Justice MJ, Belmont JW. Zic3 is required in the extra-cardiac perinodal region of the lateral plate mesoderm for left-right patterning and heart development. Hum Mol Genet 2012. [PMID: 23184148 DOI: 10.1093/hmg/dds494] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations in ZIC3 cause human X-linked heterotaxy and isolated cardiovascular malformations. A mouse model with targeted deletion of Zic3 demonstrates an early role for Zic3 in gastrulation, CNS, cardiac and left-right axial development. The observation of multiple malformations in Zic3(null) mice and the relatively broad expression pattern of Zic3 suggest its important roles in multiple developmental processes. Here, we report that Zic3 is primarily required in epiblast derivatives to affect left-right patterning and its expression in epiblast is necessary for proper transcriptional control of embryonic cardiac development. However, cardiac malformations in Zic3 deficiency occur not because Zic3 is intrinsically required in the heart but rather because it functions early in the establishment of left-right body axis. In addition, we provide evidence supporting a role for Zic3 specifically in the perinodal region of the posterior lateral plate mesoderm for the establishment of laterality. These data delineate the spatial requirement of Zic3 during left-right patterning in the mammalian embryo, and provide basis for further understanding the molecular mechanisms underlying the complex interaction of Zic3 with signaling pathways involved in the early establishment of laterality.
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Affiliation(s)
- Zhengxin Jiang
- Department of Molecular and Human Genetics, Texas Children’s Hospital, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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23
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Iwafuchi-Doi M, Matsuda K, Murakami K, Niwa H, Tesar PJ, Aruga J, Matsuo I, Kondoh H. Transcriptional regulatory networks in epiblast cells and during anterior neural plate development as modeled in epiblast stem cells. Development 2012; 139:3926-37. [DOI: 10.1242/dev.085936] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Somatic development initiates from the epiblast in post-implantation mammalian embryos. Recent establishment of epiblast stem cell (EpiSC) lines has opened up new avenues of investigation of the mechanisms that regulate the epiblast state and initiate lineage-specific somatic development. Here, we investigated the role of cell-intrinsic core transcriptional regulation in the epiblast and during derivation of the anterior neural plate (ANP) using a mouse EpiSC model. Cells that developed from EpiSCs in one day in the absence of extrinsic signals were found to represent the ANP of ~E7.5 embryos. We focused on transcription factors that are uniformly expressed in the E6.5 epiblast but in a localized fashion within or external to the ANP at E7.5, as these are likely to regulate the epiblast state and ANP development depending on their balance. Analyses of the effects of knockdown and overexpression of these factors in EpiSCs on the levels of downstream transcription factors identified the following regulatory functions: cross-regulation among Zic, Otx2, Sox2 and Pou factors stabilizes the epiblastic state; Zic, Otx2 and Pou factors in combination repress mesodermal development; Zic and Sox2 factors repress endodermal development; and Otx2 represses posterior neural plate development. All of these factors variably activate genes responsible for neural plate development. The direct interaction of these factors with enhancers of Otx2, Hesx1 and Sox2 genes was demonstrated. Thus, a combination of regulatory processes that suppresses non-ANP lineages and promotes neural plate development determines the ANP.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazunari Matsuda
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuhiro Murakami
- RIKEN Center for Developmental Biology (CDB), Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hitoshi Niwa
- RIKEN Center for Developmental Biology (CDB), Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Paul J. Tesar
- Department of Genetics and Center for Stem Cell and Regenerative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jun Aruga
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Isao Matsuo
- Osaka Medical Center and Research Institute for Maternal and Child Health, Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Hisato Kondoh
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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24
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Bogdanović O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, van Heeringen SJ, Veenstra GJC, Gómez-Skarmeta JL. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res 2012; 22:2043-53. [PMID: 22593555 PMCID: PMC3460198 DOI: 10.1101/gr.134833.111] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 05/07/2012] [Indexed: 12/21/2022]
Abstract
The generation of distinctive cell types that form different tissues and organs requires precise, temporal and spatial control of gene expression. This depends on specific cis-regulatory elements distributed in the noncoding DNA surrounding their target genes. Studies performed on mammalian embryonic stem cells and Drosophila embryos suggest that active enhancers form part of a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac). Nevertheless, little is known about the dynamics and the potential roles of these marks during vertebrate embryogenesis. Here, we provide genomic maps of H3K4me1/me3 and H3K27ac at four developmental time-points of zebrafish embryogenesis and analyze embryonic enhancer activity. We find that (1) changes in H3K27ac enrichment at enhancers accompany the shift from pluripotency to tissue-specific gene expression, (2) in early embryos, the peaks of H3K27ac enrichment are bound by pluripotent factors such as Nanog, and (3) the degree of evolutionary conservation is higher for enhancers that become marked by H3K27ac at the end of gastrulation, suggesting their implication in the establishment of the most conserved (phylotypic) transcriptome that is known to occur later at the pharyngula stage.
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Affiliation(s)
- Ozren Bogdanović
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, 41013 Sevilla, Spain
| | - Ana Fernandez-Miñán
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, 41013 Sevilla, Spain
| | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, 41013 Sevilla, Spain
| | | | - Carmen Hidalgo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, 41013 Sevilla, Spain
| | - Ila van Kruysbergen
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, 41013 Sevilla, Spain
| | - Simon J. van Heeringen
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
| | - Gert Jan C. Veenstra
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
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25
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Abstract
The ciliopathies are a category of diseases caused by disruption of the physiological functions of cilia. Ciliary dysfunction results in a broad range of phenotypes, including renal, hepatic, and pancreatic cyst formation; situs abnormalities; retinal degeneration; anosmia; cerebellar or other brain anomalies; postaxial polydactyly; bronchiectasis; and infertility. The specific clinical features are dictated by the subtype, structure, distribution, and function of the affected cilia. This review highlights the clinical variability caused by dysfunction of motile and nonmotile primary cilia and emphasizes the genetic heterogeneity and phenotypic overlap that are characteristics of these disorders. There is a need for additional research to understand the shared and unique functions of motile and nonmotile cilia and the pathophysiology resulting from mutations in cilia, basal bodies, or centrosomes. Increased understanding of ciliary biology will improve the diagnosis and management of primary ciliary dyskinesia, syndromic ciliopathies, and cilia-related cystic diseases.
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26
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Cast AE, Gao C, Amack JD, Ware SM. An essential and highly conserved role for Zic3 in left-right patterning, gastrulation and convergent extension morphogenesis. Dev Biol 2012; 364:22-31. [PMID: 22285814 DOI: 10.1016/j.ydbio.2012.01.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 11/28/2022]
Abstract
Mutations in ZIC3 result in X-linked heterotaxy in humans, a syndrome consisting of left-right (L-R) patterning defects, midline abnormalities, and cardiac malformations. Similarly, loss of function of Zic3 in mouse results in abnormal L-R patterning and cardiac development. However, Zic3 null mice also exhibit defects in gastrulation, neural tube closure, and axial patterning, suggesting the hypothesis that Zic3 is necessary for proper convergent extension (C-E) morphogenesis. To further investigate the role of Zic3 in early embryonic development, we utilized two model systems, Xenopus laevis and zebrafish, and performed loss of function analysis using antisense morpholino-mediated gene knockdown. Both Xenopus and zebrafish demonstrated significant impairment of C-E in Zic3 morphants. L-R patterning was also disrupted, indicating that the role of Zic3 in L-R axis development is conserved across species. Correlation of L-R patterning and C-E defects in Xenopus suggests that early C-E defects may underlie L-R patterning defects at later stages, since Zic3 morphants with moderate to severe C-E defects exhibited an increase in laterality defects. Taken together, these results demonstrate a functional conservation of Zic3 in L-R patterning and uncover a previously unrecognized role for Zic3 in C-E morphogenesis during early vertebrate development.
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Affiliation(s)
- Ashley E Cast
- Division of Molecular Cardiovascular Biology, the Heart Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, MLC 7020, Cincinnati, OH 45229-3039, USA
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27
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Quinn ME, Haaning A, Ware SM. Preaxial polydactyly caused by Gli3 haploinsufficiency is rescued by Zic3 loss of function in mice. Hum Mol Genet 2012; 21:1888-96. [PMID: 22234993 DOI: 10.1093/hmg/dds002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Limb anomalies are important birth defects that are incompletely understood genetically and mechanistically. GLI3, a mediator of hedgehog signaling, is a genetic cause of limb malformations including pre- and postaxial polydactyly, Pallister-Hall syndrome and Greig cephalopolysyndactyly. A closely related Gli (glioma-associated oncogene homolog)-superfamily member, ZIC3, causes X-linked heterotaxy syndrome in humans but has not been investigated in limb development. During limb development, post-translational processing of Gli3 from activator to repressor antagonizes and posteriorly restricts Sonic hedgehog (Shh). We demonstrate that Zic3 and Gli3 expression overlap in developing limbs and that Zic3 converts Gli3 from repressor to activator in vitro. In Gli3 mutant mice, Zic3 loss of function abrogates ectopic Shh expression in anterior limb buds, limits overexpression in the zone of polarizing activity and normalizes aberrant Gli3 repressor/Gli3 activator ratios observed in Gli3+/- embryos. Zic3 null;Gli3+/- neonates show rescue of the polydactylous phenotype seen in Gli3+/- animals. These studies identify a previously unrecognized role for Zic3 in regulating limb digit number via its modifying effect on Gli3 and Shh expression levels. Together, these results indicate that two Gli superfamily members that cause disparate human congenital malformation syndromes interact genetically and demonstrate the importance of Zic3 in regulating Shh pathway in developing limbs.
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Affiliation(s)
- Malgorzata E Quinn
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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28
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Bedard JEJ, Haaning AM, Ware SM. Identification of a novel ZIC3 isoform and mutation screening in patients with heterotaxy and congenital heart disease. PLoS One 2011; 6:e23755. [PMID: 21858219 PMCID: PMC3157443 DOI: 10.1371/journal.pone.0023755] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 07/24/2011] [Indexed: 12/24/2022] Open
Abstract
Patients with heterotaxy have characteristic cardiovascular malformations, abnormal arrangement of their visceral organs, and midline patterning defects that result from abnormal left-right patterning during embryogenesis. Loss of function of the transcription factor ZIC3 causes X-linked heterotaxy and isolated congenital heart malformations and represents one of the few known monogenic causes of congenital heart disease. The birth incidence of heterotaxy-spectrum malformations is significantly higher in males, but our previous work indicated that mutations within ZIC3 did not account for the male over-representation. Therefore, cross species comparative sequence alignment was used to identify a putative novel fourth exon, and the existence of a novel alternatively spliced transcript was confirmed by amplification from murine embryonic RNA and subsequent sequencing. This transcript, termed Zic3-B, encompasses exons 1, 2, and 4 whereas Zic3-A encompasses exons 1, 2, and 3. The resulting protein isoforms are 466 and 456 amino acid residues respectively, sharing the first 407 residues. Importantly, the last two amino acids in the fifth zinc finger DNA binding domain are altered in the Zic3-B isoform, indicating a potential functional difference that was further evaluated by expression, subcellular localization, and transactivation analyses. The temporo-spatial expression pattern of Zic3-B overlaps with Zic3-A in vivo, and both isoforms are localized to the nucleus in vitro. Both isoforms can transcriptionally activate a Gli binding site reporter, but only ZIC3-A synergistically activates upon co-transfection with Gli3, suggesting that the isoforms are functionally distinct. Screening 109 familial and sporadic male heterotaxy cases did not identify pathogenic mutations in the newly identified fourth exon and larger studies are necessary to establish the importance of the novel isoform in human disease.
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Affiliation(s)
- James E. J. Bedard
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Allison M. Haaning
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Stephanie M. Ware
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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Chung B, Shaffer LG, Keating S, Johnson J, Casey B, Chitayat D. From VACTERL-H to heterotaxy: Variable expressivity of ZIC3-related disorders. Am J Med Genet A 2011; 155A:1123-8. [DOI: 10.1002/ajmg.a.33859] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/22/2010] [Indexed: 11/08/2022]
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30
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Lim LS, Hong FH, Kunarso G, Stanton LW. The pluripotency regulator Zic3 is a direct activator of the Nanog promoter in ESCs. Stem Cells 2011; 28:1961-9. [PMID: 20872845 DOI: 10.1002/stem.527] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The transcription factor Zic3 is required for maintenance of ESC pluripotency. By genome-wide chromatin immunoprecipitation (ChIP-chip) in ESCs, we have identified 379 direct Zic3 targets, many of which are functionally associated with pluripotency, cell cycle, proliferation, oncogenesis, and early embryogenesis. Through a computational analysis of Zic3 target sequences, we have identified a novel Zic3 consensus binding motif (5'-CC(C)/(T) GCTGGG-3'). ChIP results and in vitro DNA binding assays revealed that Zic3 binds with high affinity and specificity on the Nanog promoter. Here, we demonstrate that Zic3 functions as a transcriptional activator of the Nanog promoter in three ways: (a) Nanog transcript levels are sustained with Zic3 overexpression in differentiating ESCs, (b) Zic3 depletion in ESCs downregulates Nanog promoter activity, and (c) Zic3 overexpression leads to increased Nanog promoter activity. Furthermore, the activity of a mutant Nanog promoter with ablated Oct4/Sox2 binding is rescued by Zic3 overexpression to nearly wild-type levels. This indicates that Nanog is a positive transcriptional target of Zic3 in a mechanism that is independent of Oct4/Sox2 binding. Hence, we demonstrate an important pathway for regulation of Nanog expression in pluripotent ESCs through direct activation by Zic3.
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Affiliation(s)
- Linda Shushan Lim
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Singapore
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31
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Vandenberg LN, Levin M. Far from solved: a perspective on what we know about early mechanisms of left-right asymmetry. Dev Dyn 2010; 239:3131-46. [PMID: 21031419 PMCID: PMC10468760 DOI: 10.1002/dvdy.22450] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
Consistent laterality is a crucial aspect of embryonic development, physiology, and behavior. While strides have been made in understanding unilaterally expressed genes and the asymmetries of organogenesis, early mechanisms are still poorly understood. One popular model centers on the structure and function of motile cilia and subsequent chiral extracellular fluid flow during gastrulation. Alternative models focus on intracellular roles of the cytoskeleton in driving asymmetries of physiological signals or asymmetric chromatid segregation, at much earlier stages. All three models trace the origin of asymmetry back to the chirality of cytoskeletal organizing centers, but significant controversy exists about how this intracellular chirality is amplified onto cell fields. Analysis of specific predictions of each model and crucial recent data on new mutants suggest that ciliary function may not be a broadly conserved, initiating event in left-right patterning. Many questions about embryonic left-right asymmetry remain open, offering fascinating avenues for further research in cell, developmental, and evolutionary biology.
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Affiliation(s)
- Laura N. Vandenberg
- Biology Department, and Tufts Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts
| | - Michael Levin
- Biology Department, and Tufts Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts
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32
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Abstract
Duplication or absence of parts of the specialized cardiac conduction system in patients with heterotaxy syndrome causes significant clinical disease, but the mechanistic basis by which embryonic disruption of left-right patterning alters conduction system patterning in these patients is not well understood. We sought to determine whether a mouse model of X-linked human heterotaxy recapitulates conduction system abnormalities identified in patients with heterotaxy. Cardiac structure and conduction system patterning were evaluated in Zic3 null embryos from e9.5 to e16.5 using genetic and molecular methods. Severe structural abnormalities involving atrial, ventricular, and conotruncal development were associated with a spectrum of disorganized and ambiguous arrangements throughout the conduction system, including the appearance of duplicated structures. The severity and location of conduction system abnormalities correlated with the severity and location of associated structural heart disease and were identifiable at the earliest stages examined. The Zic3 mouse model provides a novel tool to dissect the mechanistic underpinnings of conduction system patterning and dysfunction and its relationship to cardiovascular malformations, making it a promising model to improve understanding and risk assessment in the clinical arena.
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Affiliation(s)
- Richard J Czosek
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
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33
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Wang S, Ware SM. Use of FOXJ1CreER2T mice for inducible deletion of embryonic node gene expression. Genesis 2009; 47:132-6. [PMID: 19165828 DOI: 10.1002/dvg.20467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The ciliated cells of the node of the mouse embryo contribute to the establishment of left-right patterning via generation of leftward laminar fluid flow and initiation of a left-sided morphogen gradient. Here, we identify FOXJ1CreER(2T) mice in which expression of Cre recombinase is directed to ciliated node cells. The data demonstrate that foxj1 is expressed specifically in the node throughout the developmental window critical for left-right patterning. In transgenic embryos, Cre expression is detected by immunohistochemistry in ciliated cells of the node. Rosa26R reporter mice, in which expression of lacZ is activated only after Cre-mediated recombination, demonstrate strong and uniform labeling at the node when crossed with FOXJ1CreER(2T) mice. Cell labeling occurred as early as 0- to 2-somite stages, specifically within cells of the node, and recombination was highly efficient in response to tamoxifen. FOXJ1CreER(2T) transgenic mice represent a new genetic tool for the analysis of node-specific gene expression and will also be valuable in the study of node cell lineage and temporal cell fate mapping.
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Affiliation(s)
- Shuyun Wang
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
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Chandler KJ, Chandler RL, Mortlock DP. Identification of an ancient Bmp4 mesoderm enhancer located 46 kb from the promoter. Dev Biol 2009; 327:590-602. [PMID: 19159624 DOI: 10.1016/j.ydbio.2008.12.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 12/19/2008] [Accepted: 12/22/2008] [Indexed: 01/19/2023]
Abstract
Bone morphogenetic protein 4 (Bmp4) is a multi-functional, developmentally regulated gene that is essential for mouse development, as most Bmp4-null mouse embryos die at the onset of gastrulation and fail to develop mesoderm. Little is known about the transcriptional regulation of Bmp4. To identify potential long-range cis-regulatory elements that direct its complex spatiotemporal expression patterns, we surveyed the mouse Bmp4 locus using two overlapping bacterial artificial chromosome (BAC) reporter transgenes. Our findings indicate that tissue-specific cis-regulatory elements reside greater than 28 kb 5' or 3' to the mouse Bmp4 transcription unit. In addition, comparative analyses identified three noncoding evolutionarily conserved regions (ECRs), spaced around the gene and conserved from mammals to fish, that are maintained in a syntenic group across vertebrates. Deletion of one of these conserved sequences (ECR2) from a BAC transgene revealed a tissue-specific requirement for ECR2 in driving Bmp4 expression in extraembryonic and embryonic mesoderm. Furthermore, a 467 bp mouse sequence containing ECR2 reproducibly directed lacZ minigene expression in mesoderm. Taken together, this shows that an ancient, mesoderm-specific cis-regulatory element resides nearly 50 kb 5' to mouse Bmp4.
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Affiliation(s)
- Kelly J Chandler
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University School of Medicine, 1175 MRBIV, 2215 Garland Avenue, Nashville, TN 37232, USA
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MicroRNA-155 is an Epstein-Barr virus-induced gene that modulates Epstein-Barr virus-regulated gene expression pathways. J Virol 2008; 82:5295-306. [PMID: 18367535 DOI: 10.1128/jvi.02380-07] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The cellular microRNA miR-155 has been shown to be involved in lymphocyte activation and is expressed in Epstein-Barr virus (EBV)-infected cells displaying type III latency gene expression but not type I latency gene expression. We show here that the elevated levels of miR-155 in type III latency cells is due to EBV gene expression and not epigenetic differences in cell lines tested, and we show that expression in EBV-infected cells requires a conserved AP-1 element in the miR-155 promoter. Gene expression analysis was carried out in a type I latency cell line transduced with an miR-155-expressing retrovirus. This analysis identified both miR-155-suppressed and -induced cellular mRNAs and suggested that in addition to direct targeting of 3' untranslated regions (UTRs), miR-155 alters gene expression in part through the alteration of signal transduction pathways. 3' UTR reporter analysis of predicted miR-155 target genes identified the transcriptional regulatory genes encoding BACH1, ZIC3, HIVEP2, CEBPB, ZNF652, ARID2, and SMAD5 as miR-155 targets. Western blot analysis of the most highly suppressed of these, BACH1, showed lower expression in cells transduced with a miR-155 retrovirus. Inspection of the promoters from genes regulated in EBV-infected cells and in cells infected with an miR-155 retrovirus identified potential binding sequences for BACH1 and ZIC3. Together, these experiments suggest that the induction of miR-155 by EBV contributes to EBV-mediated signaling in part through the modulation of transcriptional regulatory factors.
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36
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Ware SM, Harutyunyan KG, Belmont JW. Heart defects in X-linked heterotaxy: evidence for a genetic interaction of Zic3 with the nodal signaling pathway. Dev Dyn 2007; 235:1631-7. [PMID: 16496285 DOI: 10.1002/dvdy.20719] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The complex cardiac defects that occur in heterotaxy result from abnormal left-right patterning. Mutations in the zinc finger transcription factor ZIC3 cause X-linked heterotaxy, HTX1. We previously have generated a targeted deletion of the murine Zic3 locus and demonstrated that these knockout mice correctly model HTX1. Fifty percent of Zic3 null embryos have cardiac looping anomalies at embryonic day 10.5 to 14.5, with ventral looping and sinistral looping as the predominant phenotypes. The penetrance of these phenotypes is increased in mice that are also haploinsufficient for Nodal. Zic3(+/-); Nodal (+/-) compound heterozygous mice are born in significantly reduced numbers (P=0.0001), indicating a genetic interaction between the loci. Furthermore, an upstream Nodal enhancer is responsive to Zic3 in both Xenopus and mouse. These studies provide evidence that Zic3 interacts genetically with Nodal in left-right patterning and subsequent cardiac development and delineate a critical Zic3-responsive enhancer required for mediating Nodal expression at the node.
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Affiliation(s)
- Stephanie M Ware
- Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Department of Pediatrics, Cincinnati, Ohio, USA
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37
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Stanton LW, Bakre MM. Genomic and proteomic characterization of embryonic stem cells. Curr Opin Chem Biol 2007; 11:399-404. [PMID: 17646122 DOI: 10.1016/j.cbpa.2007.05.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 05/24/2007] [Indexed: 11/28/2022]
Abstract
Stem cell biology, like all areas of cell biology, has been significantly affected by the arrival of the genomics era. The rendering of the human and mouse genome sequences and the development of attendant technologies have made it possible to comprehensively explore embryonic stem cell biology at the molecular level. Recently, there has been emphasis on global characterization of the transcriptome, epigenome, and proteome of embryonic stem cells. These omic evaluations of embryonic stem cells are leading to improved methods for cell-based therapies and are advancing our basic understanding of early embryonic development.
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Affiliation(s)
- Lawrence W Stanton
- Stem Cell and Developmental Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
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38
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Chhin B, Hatayama M, Bozon D, Ogawa M, Schön P, Tohmonda T, Sassolas F, Aruga J, Valard AG, Chen SC, Bouvagnet P. Elucidation of penetrance variability of aZIC3mutation in a family with complex heart defects and functional analysis ofZIC3mutations in the first zinc finger domain. Hum Mutat 2007; 28:563-70. [PMID: 17295247 DOI: 10.1002/humu.20480] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We studied a series of 42 cases of transposition of the great arteries (TGA), a complex heart defect (CHD) that is two times more prevalent in males than in females. A mutation in the X chromosome at the ZIC3 gene was found in two affected siblings (one male, one female) and their unaffected mother. A second factor, skewed X-inactivation pattern explained the discrepancy between the daughter/mother phenotype. In this family, the missense mutation (p.W255G) was found in the first zinc finger of ZIC3, a domain that is relatively specific to each of the five human ZIC genes. It was tested further along with two other mutations of this domain (p.C253S and p.H286R). In transfected 3T3 cells, mutants p.W255G and p.H286R expressed lower protein levels, and an increased protein degradation (p.W255G only). Moreover, mutants p.C253S and p.W255G had a decreased transcription activation of the TK-luciferase reporter gene. Nuclear translocation of the three ZIC3 mutants varied considerably depending on the experimental models. Finally, p.W255G and p.H286R showed diminished activities for both left-right axis disturbance and neural crest induction in Xenopus embryos. These results suggest that mutations in the first zinc finger of ZIC3 mildly affect several functions of the protein.
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Affiliation(s)
- Brigitte Chhin
- INSERM, Equipe de Recherche Methodologique (ERM) 0107, Bron, France
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39
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Zhu L, Harutyunyan KG, Peng JL, Wang J, Schwartz RJ, Belmont JW. Identification of a novel role of ZIC3 in regulating cardiac development. Hum Mol Genet 2007; 16:1649-60. [PMID: 17468179 DOI: 10.1093/hmg/ddm106] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutations in ZIC3 cause X-linked heterotaxy, a disorder characterized by abnormal lateralization of normally asymmetric thoracic and abdominal organs. Animal models demonstrate an early role for ZIC3 in embryonic left-right (LR) patterning. ZIC3 mutations have also been described in patients with isolated cardiovascular malformations. We wished to address the hypothesis that ZIC3 has plieotropic effects in development and may regulate cardiac development independent of its role in LR patterning. We observed significantly reduced expression of several markers of cardiac lineage commitment in Zic3(null/y) embryonic stem cells including atrial natriuretic factor (ANF), Nkx2.5 and Tbx5. Likewise, ANF expression-a molecular marker of trabecular myocardium and a direct target of multiple cardiac-specific transcription factors-was severely reduced in E9.5 Zic3 null hearts. Trabecular myocardium was reduced in these embryos. This finding was similar to that observed in embryos with cardiac-specific ablation of serum response factor (SRF), a direct transcriptional regulator of ANF expression. While ZIC3 by itself had no effect on the ANF promoter, it could bind to and inhibit a cardiac alpha-actin promoter through its zinc finger domains. We observed that ZIC3 could function as a coactivator of SRF on both cardiac alpha-actin and ANF promoters. The zinc fingers of ZIC3 and the mcm1, agamous deficiens SRF (MADS) box motif of SRF were found to mediate their physical and functional interactions. These findings reveal a novel role of ZIC3 in regulating cardiac gene expression and may explain, in part, the association of ZIC3 mutation with cardiovascular malformations.
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Affiliation(s)
- Lirong Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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40
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Inoue T, Ota M, Mikoshiba K, Aruga J. Zic2 and Zic3 synergistically control neurulation and segmentation of paraxial mesoderm in mouse embryo. Dev Biol 2007; 306:669-84. [PMID: 17490632 DOI: 10.1016/j.ydbio.2007.04.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 04/04/2007] [Accepted: 04/05/2007] [Indexed: 01/10/2023]
Abstract
Zic family zinc-finger proteins play various roles in animal development. In mice, five Zic genes (Zic1-5) have been reported. Despite the partly overlapping expression profiles of these genes, mouse mutants for each Zic show distinct phenotypes. To uncover possible redundant roles, we characterized Zic2/Zic3 compound mutant mice. Zic2 and Zic3 are both expressed in presomitic mesoderm, forming and newly generated somites with differential spatiotemporal accentuation. Mice heterozygous for the hypomorphic Zic2 allele together with null Zic3 allele generally showed severe malformations of the axial skeleton, including asymmetric or rostro-caudally bridged vertebrae, and reduction of the number of caudal vertebral bones, that are not obvious in single mutants. These defects were preceded by perturbed somitic marker expression, and reduced paraxial mesoderm progenitors in the primitive streak. These results suggest that Zic2 and Zic3 cooperatively control the segmentation of paraxial mesoderm at multiple stages. In addition to the segmentation abnormality, the compound mutant also showed neural tube defects that ran the entire rostro-caudal extent (craniorachischisis), suggesting that neurulation is another developmental process where Zic2 and Zic3 have redundant functions.
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Affiliation(s)
- Takashi Inoue
- Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan
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41
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Lim LS, Loh YH, Zhang W, Li Y, Chen X, Wang Y, Bakre M, Ng HH, Stanton LW. Zic3 is required for maintenance of pluripotency in embryonic stem cells. Mol Biol Cell 2007; 18:1348-58. [PMID: 17267691 PMCID: PMC1838990 DOI: 10.1091/mbc.e06-07-0624] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Embryonic stem (ES) cell pluripotency is dependent upon sustained expression of the key transcriptional regulators Oct4, Nanog, and Sox2. Dissection of the regulatory networks downstream of these transcription factors has provided critical insight into the molecular mechanisms that regulate ES cell pluripotency and early differentiation. Here we describe a role for Zic3, a member of the Gli family of zinc finger transcription factors, in the maintenance of pluripotency in ES cells. We show that Zic3 is expressed in ES cells and that this expression is repressed upon differentiation. The expression of Zic3 in pluripotent ES cells is also directly regulated by Oct4, Sox2, and Nanog. Targeted repression of Zic3 in human and mouse ES cells by RNA interference-induced expression of several markers of the endodermal lineage. Notably, the expression of Nanog, a key pluripotency regulator and repressor of extraembryonic endoderm specification in ES cells, was significantly reduced in Zic3 knockdown cells. This suggests that Zic3 may prevent endodermal marker expression through Nanog-regulated pathways. Thus our results extend the ES cell transcriptional network beyond Oct4, Nanog, and Sox2, and further establish that Zic3 plays an important role in the maintenance of pluripotency by preventing endodermal lineage specification in embryonic stem cells.
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Affiliation(s)
| | | | - Weiwei Zhang
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Yixun Li
- Information and Mathematical Sciences Group, Genome Institute of Singapore, Singapore 138672; and
| | - Xi Chen
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Yinan Wang
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | | | - Huck-Hui Ng
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Lawrence W. Stanton
- *Stem Cell and Developmental Biology Group
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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Bedard JEJ, Purnell JD, Ware SM. Nuclear import and export signals are essential for proper cellular trafficking and function of ZIC3. Hum Mol Genet 2006; 16:187-98. [PMID: 17185387 DOI: 10.1093/hmg/ddl461] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Missense, frameshift and nonsense mutations in the zinc finger transcription factor ZIC3 cause heterotaxy as well as isolated congenital heart disease. Previously, we developed transactivation and subcellular localization assays to test the function of ZIC3 point mutations. Aberrant cytoplasmic localization suggested that the pathogenesis of ZIC3 mutations results, at least in part, from failure of appropriate cellular trafficking. To further investigate this hypothesis, the nucleocytoplasmic shuttling properties of ZIC3 have been examined. Subcellular localization assays designed to span the entire open-reading frame of wild-type and mutant ZIC3 proteins identified the presence of nucleocytoplasmic transport signals. ZIC3 domain mapping indicates that a relatively large region containing the zinc finger binding sites and a known GLI interacting domain is required for transport to the nucleus. Site-directed mutagenesis of critical residues within two putative nuclear localization signals (NLSs) leads to loss of nuclear localization. No further decrease was observed when both NLS sites were mutated, suggesting that mutation of either NLS site is sufficient for loss of importin-mediated nuclear localization. Additionally, we identify a cryptic CRM-1-dependent nuclear export signal (NES) within ZIC3, and identify a mutation within this region in a patient with heterotaxy. These results provide the first evidence that control of cellular trafficking of ZIC3 is critical for function and suggest a possible mechanism for transcriptional control during left-right patterning. Identification of mutations in mapped NLS or NES domains in heterotaxy patients demonstrates the functional importance of these domains in cardiac morphogenesis and allows for integration of structural analysis with developmental function.
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Affiliation(s)
- James E J Bedard
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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