1
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Perez CJ, Mecklenburg L, Fernandez A, Cantero M, de Souza TA, Lin K, Dent SYR, Montoliu L, Awgulewitsch A, Benavides F. Naked (N) mutant mice carry a nonsense mutation in the homeobox of Hoxc13. Exp Dermatol 2021; 31:330-340. [PMID: 34657330 DOI: 10.1111/exd.14469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/23/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022]
Abstract
Loss of function mutations in HOXC13 have been associated with Ectodermal Dysplasia-9, Hair/Nail Type (ECTD9) in consanguineous families, characterized by sparse to complete absence of hair and nail dystrophy. Here we characterize the spontaneous mouse mutation Naked (N) as a terminal truncation in the Hoxc13 (homeobox C13) gene. Similar to previous reports for homozygous Hoxc13 knock-out (KO) mice, homozygous N/N mice exhibit generalized alopecia with abnormal nails and a short lifespan. However, in contrast to Hoxc13 heterozygous KO mice, N/+ mice show generalized or partial alopecia, associated with loss of hair fibres, along with normal lifespan and fertility. Our data point to a lack of nonsense-mediated Hoxc13 transcript decay and the presence of the truncated mutant protein in N/N and N/+ hair follicles, thus suggesting a dominant-negative mutation. To our knowledge, this is the first report of a semi-dominant and potentially dominant-negative mutation affecting Hoxc13/HOXC13. Furthermore, recreating the N mutant allele in mice using CRISPR/Cas9-mediated genome editing resulted in the same spectrum of deficiencies as those associated with the spontaneous Naked mutation, thus confirming that N is indeed a Hoxc13 mutant allele. Considering the low viability of the Hoxc13 KO mice, the Naked mutation provides an attractive new model for studying ECTD9 disease mechanisms.
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Affiliation(s)
- Carlos J Perez
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | | | - Almudena Fernandez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Marta Cantero
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | | | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas, USA
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Alexander Awgulewitsch
- Department of Medicine and Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina (MUSC), Charleston, South Carolina, USA
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas, USA
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2
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Lan HC, Du TH, Yao YL, Yang WM. Ocular disease-associated mutations diminish the mitotic chromosome retention ability of PAX6. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194751. [PMID: 34500082 DOI: 10.1016/j.bbagrm.2021.194751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
Transcription factors play a key role in maintaining cell identity. One mechanism of such cell memory after multiple rounds of cell division cycles is through persistent mitotic chromosome binding, although how individual transcription factors achieve mitotic chromosome retention is not completely understood. Here we show that PAX6, a lineage-determining transcription factor, coats mitotic chromosomes. Using deletion and point mutants associated with human ocular diseases in live-cell imaging analysis, we identified two regions, MCR-D1 and MCR-D2, that were responsible for mitotic chromosome retention of PAX6. We also identified three nuclear localization signals (NLSs) that contributed to mitotic chromosome retention independent of their nuclear import functions. Full mitotic chromosome retention required the presence of DNA-binding domains as well as NLSs within MCR-Ds. Furthermore, disease-associated mutations and NLS mutations changed the distribution of intrinsically disordered regions (IDRs) in PAX6. Our findings not only identify PAX6 as a novel mitotic chromosome retention factor but also demonstrate that the mechanism of mitotic chromosome retention involves sequence-specific DNA binding, NLSs, and molecular conformation determined by IDRs. These findings link mitotic chromosome retention with PAX6-related pathogenesis and imply similar mechanisms for other lineage-determining factors in the PAX family.
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Affiliation(s)
- Hsin-Chi Lan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ting-Huei Du
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ya-Li Yao
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan.
| | - Wen-Ming Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
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3
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Lewin TD, Royall AH, Holland PWH. Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires. J Mol Evol 2021; 89:396-414. [PMID: 34097121 PMCID: PMC8208926 DOI: 10.1007/s00239-021-10012-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/11/2021] [Indexed: 11/21/2022]
Abstract
The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX, are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of a large tandem array of LEUTX loci in the genome of the European rabbit (Oryctolagus cuniculus). Despite extensive gene gain and loss, all sampled species possess at least two ETCHbox genes, suggesting their collective role is indispensable. We find evidence for positive selection and show that TPRX1 and TPRX2 have been the subject of repeated gene conversion across the Boreoeutheria, homogenising their sequences and preventing divergence, especially in the homeobox region. Together, these results are consistent with a model where mammalian ETCHbox genes are dynamic in evolution due to functional overlap, yet have collective indispensable roles.
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Affiliation(s)
- Thomas D Lewin
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Amy H Royall
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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4
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Williamson KA, Hall HN, Owen LJ, Livesey BJ, Hanson IM, Adams GGW, Bodek S, Calvas P, Castle B, Clarke M, Deng AT, Edery P, Fisher R, Gillessen-Kaesbach G, Heon E, Hurst J, Josifova D, Lorenz B, McKee S, Meire F, Moore AT, Parker M, Reiff CM, Self J, Tobias ES, Verheij JBGM, Willems M, Williams D, van Heyningen V, Marsh JA, FitzPatrick DR. Recurrent heterozygous PAX6 missense variants cause severe bilateral microphthalmia via predictable effects on DNA-protein interaction. Genet Med 2020; 22:598-609. [PMID: 31700164 PMCID: PMC7056646 DOI: 10.1038/s41436-019-0685-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Most classical aniridia is caused by PAX6 haploinsufficiency. PAX6 missense variants can be hypomorphic or mimic haploinsufficiency. We hypothesized that missense variants also cause previously undescribed disease by altering the affinity and/or specificity of PAX6 genomic interactions. METHODS We screened PAX6 in 372 individuals with bilateral microphthalmia, anophthalmia, or coloboma (MAC) from the Medical Research Council Human Genetics Unit eye malformation cohort (HGUeye) and reviewed data from the Deciphering Developmental Disorders study. We performed cluster analysis on PAX6-associated ocular phenotypes by variant type and molecular modeling of the structural impact of 86 different PAX6 causative missense variants. RESULTS Eight different PAX6 missense variants were identified in 17 individuals (15 families) with MAC, accounting for 4% (15/372) of our cohort. Seven altered the paired domain (p.[Arg26Gln]x1, p.[Gly36Val]x1, p.[Arg38Trp]x2, p.[Arg38Gln]x1, p.[Gly51Arg]x2, p.[Ser54Arg]x2, p.[Asn124Lys]x5) and one the homeodomain (p.[Asn260Tyr]x1). p.Ser54Arg and p.Asn124Lys were exclusively associated with severe bilateral microphthalmia. MAC-associated variants were predicted to alter but not ablate DNA interaction, consistent with the electrophoretic mobility shifts observed using mutant paired domains with well-characterized PAX6-binding sites. We found no strong evidence for novel PAX6-associated extraocular disease. CONCLUSION Altering the affinity and specificity of PAX6-binding genome-wide provides a plausible mechanism for the worse-than-null effects of MAC-associated missense variants.
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Affiliation(s)
- Kathleen A Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - H Nikki Hall
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Liusaidh J Owen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Benjamin J Livesey
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Isabel M Hanson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Simon Bodek
- Department of Clinical Genetics, St Michael's Hospital, Southwell Street, Bristol, UK
| | - Patrick Calvas
- CHU Toulouse, Service de Génétique Médicale, Hôpital Purpan, Toulouse, France
| | - Bruce Castle
- Peninsula Clinical Genetics, Royal Devon and Exeter Hospitals (Heavitree), Exeter, UK
| | - Michael Clarke
- Newcastle Eye Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Royal Victoria Infirmary, Newcastle Upon Tyne, UK
| | - Alexander T Deng
- Clinical Genetics, Guys and St Thomas NHS Trust, Great Maze Pond, London, UK
| | - Patrick Edery
- Hospices Civils de Lyon, Genetic Department and National HHT Reference Center, Femme-Mère-Enfants Hospital, Bron, France
| | - Richard Fisher
- Teeside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | | | - Elise Heon
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, ON, Canada
| | - Jane Hurst
- Department of Clinical Genetics, Great Ormond Street Hospital for Children, London, UK
| | - Dragana Josifova
- Clinical Genetics, Guys and St Thomas NHS Trust, Great Maze Pond, London, UK
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Shane McKee
- Northern Ireland Regional Genetics Service (NIRGS), Belfast City Hospital, Belfast, UK
| | - Francoise Meire
- Department of Ophthalmology, Hôpital Universitaire des Enfants Reine Fabiola, Brussels, Belgium
| | | | - Michael Parker
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Charlotte M Reiff
- Department of Ophthalmology, University of Freiburg, Freiburg, Germany
| | - Jay Self
- University Hospital Southampton, Southampton, UK
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Edward S Tobias
- Academic Medical Genetics and Pathology, University of Glasgow, Queen Elizabeth University Hospital, Glasgow, UK
| | - Joke B G M Verheij
- Department of Genetics, University of Groningen, University Medical Center, Groningen, The Netherlands
| | | | - Denise Williams
- Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham, UK
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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Lima Cunha D, Arno G, Corton M, Moosajee M. The Spectrum of PAX6 Mutations and Genotype-Phenotype Correlations in the Eye. Genes (Basel) 2019; 10:genes10121050. [PMID: 31861090 PMCID: PMC6947179 DOI: 10.3390/genes10121050] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022] Open
Abstract
The transcription factor PAX6 is essential in ocular development in vertebrates, being considered the master regulator of the eye. During eye development, it is essential for the correct patterning and formation of the multi-layered optic cup and it is involved in the developing lens and corneal epithelium. In adulthood, it is mostly expressed in cornea, iris, and lens. PAX6 is a dosage-sensitive gene and it is highly regulated by several elements located upstream, downstream, and within the gene. There are more than 500 different mutations described to affect PAX6 and its regulatory regions, the majority of which lead to PAX6 haploinsufficiency, causing several ocular and systemic abnormalities. Aniridia is an autosomal dominant disorder that is marked by the complete or partial absence of the iris, foveal hypoplasia, and nystagmus, and is caused by heterozygous PAX6 mutations. Other ocular abnormalities have also been associated with PAX6 changes, and genotype-phenotype correlations are emerging. This review will cover recent advancements in PAX6 regulation, particularly the role of several enhancers that are known to regulate PAX6 during eye development and disease. We will also present an updated overview of the mutation spectrum, where an increasing number of mutations in the non-coding regions have been reported. Novel genotype-phenotype correlations will also be discussed.
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Affiliation(s)
| | - Gavin Arno
- Institute of Ophthalmology, UCL, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital—Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Mariya Moosajee
- Institute of Ophthalmology, UCL, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- Correspondence:
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6
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Vasilyeva TA, Voskresenskaya AA, Pozdeyeva NA, Marakhonov AV, Zinchenko RA. PAX6 Gene Characteristic and Causative Role of PAX6 Mutations in Inherited Eye Pathologies. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Steinmetz EL, Dewald DN, Walldorf U. Homeodomain-interacting protein kinase phosphorylates the Drosophila Paired box protein 6 (Pax6) homologues Twin of eyeless and Eyeless. INSECT MOLECULAR BIOLOGY 2018; 27:198-211. [PMID: 29205612 DOI: 10.1111/imb.12363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Homeodomain-interacting protein kinase (Hipk), the Drosophila homologue of mammalian HIPK2, plays several important roles in regulating differentiation, proliferation, apoptosis, and stress responses and acts as a mediator for signals of diverse pathways, such as Notch or Wingless signalling. The Paired box protein 6 (Pax6) has two Drosophila homologues, Twin of eyeless (Toy) and Eyeless (Ey). Both stand atop the retinal determination gene network (RDGN), which is essential for proper eye development in Drosophila. Here, we set Hipk and the master regulators Toy and Ey in an enzyme-substrate relationship. Furthermore, we prove a physical interaction between Toy and Hipk in vivo using bimolecular fluorescence complementation. Using in vitro kinase assays with different truncated Toy constructs and mutational analyses, we mapped four Hipk phosphorylation sites of Toy, one in the paired domain (Ser121 ) and three in the C-terminal transactivation domain of Toy (Thr395 , Ser410 and Thr452 ). The interaction and phosphorylation of the master regulator Toy by Hipk may be important for precise tuning of signalling within the RDGN and therefore for Drosophila eye development.
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Affiliation(s)
- E L Steinmetz
- Developmental Biology, Saarland University, Homburg, Germany
| | - D N Dewald
- Developmental Biology, Saarland University, Homburg, Germany
| | - U Walldorf
- Developmental Biology, Saarland University, Homburg, Germany
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8
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Kim CH, An MJ, Kim DH, Kim JW. Histone deacetylase 1 (HDAC1) regulates retinal development through a PAX6-dependent pathway. Biochem Biophys Res Commun 2016; 482:735-741. [PMID: 27871855 DOI: 10.1016/j.bbrc.2016.11.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022]
Abstract
Cell fate determination is tightly controlled by the expression of transcription factors and gene regulatory networks. PAX6 is a transcription factor containing a DNA-binding paired-box domain and homeobox domain that plays a key role in the development of the eye, brain, and pancreas. Here, we showed that histone deacetyltransferase 1 (HDAC1) is a novel binding partner of PAX6 in newborn mouse retinas. We also showed that HDAC1 specifically binds to the paired and transactivation domains of PAX6, and these physical interactions were required for effective repression of PAX6 transcriptional activity during retinal development. Furthermore, HDAC1 preferentially regulates the transcriptional activity of PAX6 when it binds to paired-domain (P6CON and chimeric pCON/P3) PAX6 responsive elements compared to homeodomain (pP3) PAX6 responsive elements. The repressive effect of HDAC1 on the transcriptional activity of PAX6 was reversed by knockdown of HDAC1 or treatment with an HDAC inhibitor, TSA. Taken together, these results show that HDAC1 binds PAX6 and that protein-protein interaction leads to transcriptional repression of PAX6 target genes during mouse retinal development.
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Affiliation(s)
- Chul-Hong Kim
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Mi-Jin An
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae-Hyun Kim
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jung-Woong Kim
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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Di Lascio S, Belperio D, Benfante R, Fornasari D. Alanine Expansions Associated with Congenital Central Hypoventilation Syndrome Impair PHOX2B Homeodomain-mediated Dimerization and Nuclear Import. J Biol Chem 2016; 291:13375-93. [PMID: 27129232 PMCID: PMC4933246 DOI: 10.1074/jbc.m115.679027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 11/30/2022] Open
Abstract
Heterozygous mutations of the human PHOX2B gene, a key regulator of autonomic nervous system development, lead to congenital central hypoventilation syndrome (CCHS), a neurodevelopmental disorder characterized by a failure in the autonomic control of breathing. Polyalanine expansions in the 20-residues region of the C terminus of PHOX2B are the major mutations responsible for CCHS. Elongation of the alanine stretch in PHOX2B leads to a protein with altered DNA binding, transcriptional activity, and nuclear localization and the possible formation of cytoplasmic aggregates; furthermore, the findings of various studies support the idea that CCHS is not due to a pure loss of function mechanism but also involves a dominant negative effect and/or toxic gain of function for PHOX2B mutations. Because PHOX2B forms homodimers and heterodimers with its paralogue PHOX2A in vitro, we tested the hypothesis that the dominant negative effects of the mutated proteins are due to non-functional interactions with the wild-type protein or PHOX2A using a co-immunoprecipitation assay and the mammalian two-hybrid system. Our findings show that PHOX2B forms homodimers and heterodimerizes weakly with mutated proteins, exclude the direct involvement of the polyalanine tract in dimer formation, and indicate that mutated proteins retain partial ability to form heterodimers with PHOX2A. Moreover, in this study, we investigated the effects of the longest polyalanine expansions on the homeodomain-mediated nuclear import, and our data clearly show that the expanded C terminus interferes with this process. These results provide novel insights into the effects of the alanine tract expansion on PHOX2B folding and activity.
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Affiliation(s)
- Simona Di Lascio
- From the Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129 Milan, Italy and
| | - Debora Belperio
- From the Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129 Milan, Italy and
| | - Roberta Benfante
- From the Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129 Milan, Italy and the National Research Council (CNR) Neuroscience Institute, 20129 Milan, Italy
| | - Diego Fornasari
- From the Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129 Milan, Italy and the National Research Council (CNR) Neuroscience Institute, 20129 Milan, Italy
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10
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Forsdahl S, Kiselev Y, Hogseth R, Mjelle JE, Mikkola I. Pax6 regulates the expression of Dkk3 in murine and human cell lines, and altered responses to Wnt signaling are shown in FlpIn-3T3 cells stably expressing either the Pax6 or the Pax6(5a) isoform. PLoS One 2014; 9:e102559. [PMID: 25029272 PMCID: PMC4100929 DOI: 10.1371/journal.pone.0102559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/19/2014] [Indexed: 02/07/2023] Open
Abstract
Pax6 is a transcription factor important for early embryo development. It is expressed in several cancer cell lines and tumors. In glioblastoma, PAX6 has been shown to function as a tumor suppressor. Dickkopf 3 (Dkk3) is well established as a tumor suppressor in several tumor types, but not much is known about the regulation of its expression. We have previously found that Pax6 and Pax6(5a) increase the expression of the Dkk3 gene in two stably transfected mouse fibroblast cell lines. In this study the molecular mechanism behind this regulation is looked at. Western blot and reverse transcriptase quantitative PCR (RT-qPCR) confirmed higher level of Dkk3 expression in both Pax6 and Pax6(5a) expressing cell lines compared to the control cell line. By the use of bioinformatics and electrophoretic mobility shift assay (EMSA) we have mapped a functional Pax6 binding site in the mouse Dkk3 promoter. The minimal Dkk3 promoter fragment required for transcriptional activation by Pax6 and Pax6(5a) was a 200 bp region just upstream of the transcriptional start site. Mutation of the evolutionary conserved binding site in this region abrogated transcriptional activation and binding of Pax6/Pax6(5a) to the mouse Dkk3 promoter. Since the identified Pax6 binding site in this promoter is conserved, RT-qPCR and Western blot were used to look for regulation of Dkk3/REIC expression in human cell lines. Six of eight cell lines tested showed changes in Dkk3/REIC expression after PAX6 siRNA knockdown. Interestingly, we observed that the Pax6/Pax6(5a) expressing mouse fibroblast cell lines were less responsive to canonical Wnt pathway stimulation than the control cell line when TOP/FOP activity and the levels of active β-catenin and GSK3-β Ser9 phosphorylation were measured after LiCl stimulation.
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Affiliation(s)
- Siri Forsdahl
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
| | - Yury Kiselev
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
- Norwegian Translational Cancer Research Center, Department of Medical Biology, UiT – The Arctic University of Norway, Tromsoe, Norway
| | - Rune Hogseth
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
| | - Janne E. Mjelle
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
| | - Ingvild Mikkola
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
- * E-mail:
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11
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Mussar K, Tucker A, McLennan L, Gearhart A, Jimenez-Caliani AJ, Cirulli V, Crisa L. Macrophage/epithelium cross-talk regulates cell cycle progression and migration in pancreatic progenitors. PLoS One 2014; 9:e89492. [PMID: 24586821 PMCID: PMC3929706 DOI: 10.1371/journal.pone.0089492] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 01/21/2014] [Indexed: 01/06/2023] Open
Abstract
Macrophages populate the mesenchymal compartment of all organs during embryogenesis and have been shown to support tissue organogenesis and regeneration by regulating remodeling of the extracellular microenvironment. Whether this mesenchymal component can also dictate select developmental decisions in epithelia is unknown. Here, using the embryonic pancreatic epithelium as model system, we show that macrophages drive the epithelium to execute two developmentally important choices, i.e. the exit from cell cycle and the acquisition of a migratory phenotype. We demonstrate that these developmental decisions are effectively imparted by macrophages activated toward an M2 fetal-like functional state, and involve modulation of the adhesion receptor NCAM and an uncommon "paired-less" isoform of the transcription factor PAX6 in the epithelium. Over-expression of this PAX6 variant in pancreatic epithelia controls both cell motility and cell cycle progression in a gene-dosage dependent fashion. Importantly, induction of these phenotypes in embryonic pancreatic transplants by M2 macrophages in vivo is associated with an increased frequency of endocrine-committed cells emerging from ductal progenitor pools. These results identify M2 macrophages as key effectors capable of coordinating epithelial cell cycle withdrawal and cell migration, two events critical to pancreatic progenitors' delamination and progression toward their differentiated fates.
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Affiliation(s)
- Kristin Mussar
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Andrew Tucker
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Linsey McLennan
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Addie Gearhart
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Antonio J. Jimenez-Caliani
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Vincenzo Cirulli
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Laura Crisa
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
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12
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Kim CH, Kim JW, Jang SM, An JH, Song KH, Choi KH. Transcriptional activity of paired homeobox Pax6 is enhanced by histone acetyltransferase Tip60 during mouse retina development. Biochem Biophys Res Commun 2012; 424:427-32. [PMID: 22766506 DOI: 10.1016/j.bbrc.2012.06.126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 06/25/2012] [Indexed: 10/28/2022]
Abstract
Pax6 is a member of the Pax family of transcription factors that contains a DNA binding paired-box and homeobox domain. In animals, including humans, Pax6 plays a key role in development, regulating organogenesis of the eye and brain. The current data show that histone acetyltransferase Tip60 physically interacts with Pax6 in developing post-natal day 4 (P4) mouse retinas. We also found that Tip60 binds with paired-domain of Pax6 using its chromo- and zinc-finger-containing regions, and that these protein interactions were needed for the effective full-transcriptional activation of Pax6. Furthermore, among the combinations of Pax6-target gene interactions using its two DNA binding domain, paired- and homeobox domain, Tip60 significantly enhanced the transcriptional activity of Pax6 on the paired-domain binding sequence (P6CON) containing reporter construct (pCON) than other homeo domain and chimera binding containing pP3 and pCON/P3 constructs. Taken together, these results suggest that Tip60 binds with Pax6 and that this physical interaction leads to the full-transcriptional activation of Pax6 during retina development.
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Affiliation(s)
- Chul-Hong Kim
- Department of Life Science (BK21 Program), College of Natural Sciences, Chung-Ang University, Seoul 156-756, South Korea
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13
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Shukla S, Mishra R. Predictions on impact of missense mutations on structure function relationship of PAX6 and its alternatively spliced isoform PAX6(5a). Interdiscip Sci 2012; 4:54-73. [PMID: 22392277 DOI: 10.1007/s12539-012-0114-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 04/11/2011] [Accepted: 05/17/2011] [Indexed: 05/31/2023]
Abstract
The PAX6 contains two DNA-binding domains, paired domain (PD), homeodomain (HD), and a transactivation domain (TD). Only the crystal structure of PD and the solution structure of HD of PAX6 are known. Mutations in PAX6 show variable penetrance, and expressivity of ocular and neural diseases, but the mechanism is poorly understood. Its alternatively spliced isoform PAX6(5a), is also required in a specific ratio for optimal functions. To understand impact of missense mutations on stability, and conformation of PAX6, whose functional analyses are described in PAX6 allelic variant database, were considered. Representative mutations like PAX6-L46R, -C52R, -V126D, -R128C, -R242T, -P375Q, -Q422R, -V256E, and -S259P from PD, HD, and TD of PAX6 were explored. The secondary structures were analyzed through PSIPRED, and relative solvent accessibilities (RSA) of the mutant and the wild type amino acid residues were compared through SABLE. The change in the contact residues and calculations of energy level were studied through SVMcon, MUpro, and FoldX, respectively. The 3D modeling was performed with the help of MODELLER and models were visualized in Chimera. Predictions suggest mutation induced alterations in local conformation or misfolding in DNA-binding domains of PAX6 and PAX6(5a). The predicted impact of mutations via secondary structure, changes in free energy, stability, conformation, and experimental reports on DNA-binding and transactivation, necessarily provides a strong background to explain structure-function relationship of PAX6 and PAX6(5a). However, because of their predictive nature, these findings need to be validated with other experimental evidences when structure of full length PAX6 is available.
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Affiliation(s)
- Sachin Shukla
- Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
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14
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Elvenes J, Thomassen EIS, Johnsen SS, Kaino K, Sjøttem E, Johansen T. Pax6 represses androgen receptor-mediated transactivation by inhibiting recruitment of the coactivator SPBP. PLoS One 2011; 6:e24659. [PMID: 21935435 PMCID: PMC3174178 DOI: 10.1371/journal.pone.0024659] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 08/16/2011] [Indexed: 11/29/2022] Open
Abstract
The androgen receptor (AR) has a central role in development and maintenance of the male reproductive system and in the etiology of prostate cancer. The transcription factor Pax6 has recently been reported to act as a repressor of AR and to be hypermethylated in prostate cancer cells. SPBP is a transcriptional regulator that previously has been shown to enhance the activity of Pax6. In this study we have identified SPBP to act as a transcriptional coactivator of AR. We also show that Pax6 inhibits SPBP-mediated enhancement of AR activity on the AR target gene probasin promoter, a repression that was partly reversed by increased expression of SPBP. Enhanced expression of Pax6 reduced the amount of SPBP associated with the probasin promoter when assayed by ChIP in HeLa cells. We mapped the interaction between both AR and SPBP, and AR and Pax6 to the DNA-binding domains of the involved proteins. Further binding studies revealed that Pax6 and SPBP compete for binding to AR. These results suggest that Pax6 represses AR activity by displacing and/or inhibiting recruitment of coactivators to AR target promoters. Understanding the mechanism for inhibition of AR coactivators can give rise to molecular targeted drugs for treatment of prostate cancer.
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Affiliation(s)
- Julianne Elvenes
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
| | | | - Sylvia Sagen Johnsen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
| | - Katrine Kaino
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
| | - Eva Sjøttem
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
- * E-mail:
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, Tromsø, Norway
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Kozmikova I, Smolikova J, Vlcek C, Kozmik Z. Conservation and diversification of an ancestral chordate gene regulatory network for dorsoventral patterning. PLoS One 2011; 6:e14650. [PMID: 21304903 PMCID: PMC3033397 DOI: 10.1371/journal.pone.0014650] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 01/04/2011] [Indexed: 12/24/2022] Open
Abstract
Formation of a dorsoventral axis is a key event in the early development of most animal embryos. It is well established that bone morphogenetic proteins (Bmps) and Wnts are key mediators of dorsoventral patterning in vertebrates. In the cephalochordate amphioxus, genes encoding Bmps and transcription factors downstream of Bmp signaling such as Vent are expressed in patterns reminiscent of those of their vertebrate orthologues. However, the key question is whether the conservation of expression patterns of network constituents implies conservation of functional network interactions, and if so, how an increased functional complexity can evolve. Using heterologous systems, namely by reporter gene assays in mammalian cell lines and by transgenesis in medaka fish, we have compared the gene regulatory network implicated in dorsoventral patterning of the basal chordate amphioxus and vertebrates. We found that Bmp but not canonical Wnt signaling regulates promoters of genes encoding homeodomain proteins AmphiVent1 and AmphiVent2. Furthermore, AmphiVent1 and AmphiVent2 promoters appear to be correctly regulated in the context of a vertebrate embryo. Finally, we show that AmphiVent1 is able to directly repress promoters of AmphiGoosecoid and AmphiChordin genes. Repression of genes encoding dorsal-specific signaling molecule Chordin and transcription factor Goosecoid by Xenopus and zebrafish Vent genes represents a key regulatory interaction during vertebrate axis formation. Our data indicate high evolutionary conservation of a core Bmp-triggered gene regulatory network for dorsoventral patterning in chordates and suggest that co-option of the canonical Wnt signaling pathway for dorsoventral patterning in vertebrates represents one of the innovations through which an increased morphological complexity of vertebrate embryo is achieved.
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Elvenes J, Sjøttem E, Holm T, Bjørkøy G, Johansen T. Pax6 localizes to chromatin-rich territories and displays a slow nuclear mobility altered by disease mutations. Cell Mol Life Sci 2010; 67:4079-94. [PMID: 20577777 PMCID: PMC11115490 DOI: 10.1007/s00018-010-0429-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 01/02/2023]
Abstract
The transcription factor Pax6 is crucial for the embryogenesis of multiple organs, including the eyes, parts of the brain and the pancreas. Mutations in one allele of PAX6 lead to eye diseases including Peter's anomaly and aniridia. Here, we use fluorescence recovery after photobleaching to show that Pax6 and also other Pax family proteins display a strikingly low nuclear mobility compared to other transcriptional regulators. For Pax6, the slow mobility is largely due to the presence of two DNA-binding domains, but protein-protein interactions also contribute. Consistently, the subnuclear localization of Pax6 suggests that it interacts preferentially with chromatin-rich territories. Some aniridia-causing missense mutations in Pax6 have impaired DNA-binding affinity. Interestingly, when these mutants were analyzed by FRAP, they displayed a pronounced increased mobility compared to wild-type Pax6. Hence, our results support the conclusion that disease mutations result in proteins with impaired function because of altered DNA- and protein-interaction capabilities.
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Affiliation(s)
- Julianne Elvenes
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, 9037 Tromso, Norway
| | - Eva Sjøttem
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, 9037 Tromso, Norway
| | - Turid Holm
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, 9037 Tromso, Norway
| | - Geir Bjørkøy
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, 9037 Tromso, Norway
- University College of Sør-Trøndelag, 7006 Trondheim, Norway
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, 9037 Tromso, Norway
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Alibés A, Nadra AD, De Masi F, Bulyk ML, Serrano L, Stricher F. Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res 2010; 38:7422-31. [PMID: 20685816 PMCID: PMC2995082 DOI: 10.1093/nar/gkq683] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Quite often a single or a combination of protein mutations is linked to specific diseases. However, distinguishing from sequence information which mutations have real effects in the protein’s function is not trivial. Protein design tools are commonly used to explain mutations that affect protein stability, or protein–protein interaction, but not for mutations that could affect protein–DNA binding. Here, we used the protein design algorithm FoldX to model all known missense mutations in the paired box domain of Pax6, a highly conserved transcription factor involved in eye development and in several diseases such as aniridia. The validity of FoldX to deal with protein–DNA interactions was demonstrated by showing that high levels of accuracy can be achieved for mutations affecting these interactions. Also we showed that protein-design algorithms can accurately reproduce experimental DNA-binding logos. We conclude that 88% of the Pax6 mutations can be linked to changes in intrinsic stability (77%) and/or to its capabilities to bind DNA (30%). Our study emphasizes the importance of structure-based analysis to understand the molecular basis of diseases and shows that protein–DNA interactions can be analyzed to the same level of accuracy as protein stability, or protein–protein interactions.
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Affiliation(s)
- Andreu Alibés
- EMBL/CRG Systems Biology Research Unit, Center for Genomic Regulation, UPF, Barcelona, Spain.
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18
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Hill A, Boll W, Ries C, Warner L, Osswalt M, Hill M, Noll M. Origin of Pax and Six gene families in sponges: Single PaxB and Six1/2 orthologs in Chalinula loosanoffi. Dev Biol 2010; 343:106-23. [DOI: 10.1016/j.ydbio.2010.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 02/11/2010] [Accepted: 03/16/2010] [Indexed: 11/25/2022]
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19
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Wang Y, Groppe JC, Wu J, Ogawa T, Mues G, D'Souza RN, Kapadia H. Pathogenic mechanisms of tooth agenesis linked to paired domain mutations in human PAX9. Hum Mol Genet 2009; 18:2863-74. [PMID: 19429910 DOI: 10.1093/hmg/ddp221] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mutations in the paired-domain transcription factor PAX9 are associated with non-syndromic tooth agenesis that preferentially affects posterior dentition. Of the 18 mutations identified to date, eight are phenotypically well-characterized missense mutations within the DNA-binding paired domain. We determined the structural and functional consequences of these paired domain missense mutations and correlated our findings with the associated dental phenotype variations. In vitro testing included subcellular localization, protein-protein interactions between MSX1 and mutant PAX9 proteins, binding of PAX9 mutants to a DNA consensus site and transcriptional activation from the Pax9 effector promoters Bmp4 and Msx1 with and without MSX1 as co-activator. All mutant PAX9 proteins were localized in the nucleus of transfected cells and physically interacted with MSX1 protein. Three of the mutants retained the ability to bind the consensus paired domain recognition sequence; the others were unable or only partly able to interact with this DNA fragment and also showed a similarly impaired capability for activation of transcription from the Msx1 and Bmp4 promoters. For seven of the eight mutants, the degree of loss of DNA-binding and promoter activation correlated quite well with the severity of the tooth agenesis pattern seen in vivo. One of the mutants however showed neither reduction in DNA-binding nor decrease in transactivation; instead, a loss of responsiveness to synergism with MSX1 in target promoter activation and a dominant negative effect when expressed together with wild-type PAX9 could be observed. Our structure-based studies, which modeled DNA binding and subdomain stability, were able to predict functional consequences quite reliably.
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Affiliation(s)
- Ying Wang
- Department of Biomedical Sciences, Texas A&M University Health Science Center, Baylor College of Dentistry, Dallas, TX 75246, USA
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20
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Twigg SR, Versnel SL, Nürnberg G, Lees MM, Bhat M, Hammond P, Hennekam RC, Hoogeboom AJM, Hurst JA, Johnson D, Robinson AA, Scambler PJ, Gerrelli D, Nürnberg P, Mathijssen IM, Wilkie AO. Frontorhiny, a distinctive presentation of frontonasal dysplasia caused by recessive mutations in the ALX3 homeobox gene. Am J Hum Genet 2009; 84:698-705. [PMID: 19409524 PMCID: PMC2681074 DOI: 10.1016/j.ajhg.2009.04.009] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 04/03/2009] [Accepted: 04/14/2009] [Indexed: 01/06/2023] Open
Abstract
We describe a recessively inherited frontonasal malformation characterized by a distinctive facial appearance, with hypertelorism, wide nasal bridge, short nasal ridge, bifid nasal tip, broad columella, widely separated slit-like nares, long philtrum with prominent bilateral swellings, and midline notch in the upper lip and alveolus. Additional recurrent features present in a minority of individuals have been upper eyelid ptosis and midline dermoid cysts of craniofacial structures. Assuming recessive inheritance, we mapped the locus in three families to chromosome 1 and identified mutations in ALX3, which is located at band 1p13.3 and encodes the aristaless-related ALX homeobox 3 transcription factor. In total, we identified seven different homozygous pathogenic mutations in seven families. These mutations comprise missense substitutions at critical positions within the conserved homeodomain as well as nonsense, frameshift, and splice-site mutations, all predicting severe or complete loss of function. Our findings contrast with previous studies of the orthologous murine gene, which showed no phenotype in Alx3(-/-) homozygotes, apparently as a result of functional redundancy with the paralogous Alx4 gene. We conclude that ALX3 is essential for normal facial development in humans and that deficiency causes a clinically recognizable phenotype, which we term frontorhiny.
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Affiliation(s)
- Stephen R.F. Twigg
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah L. Versnel
- Department of Plastic and Reconstructive Surgery, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands
| | - Gudrun Nürnberg
- Cologne Center for Genomics and Institute for Genetics, University of Cologne, D-50674 Cologne, Germany
| | - Melissa M. Lees
- Department of Clinical Genetics, Great Ormond Street Hospital for Children, London WC1N 3JH, UK
- North Thames Cleft Centre, Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | | | - Peter Hammond
- Molecular Medicine Unit, Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Raoul C.M. Hennekam
- Department of Clinical Genetics, Great Ormond Street Hospital for Children, London WC1N 3JH, UK
- Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London WC1N 1EH, UK
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | | | - Jane A. Hurst
- Department of Clinical Genetics, Oxford Radcliffe Hospitals NHS Trust, Oxford OX3 9DU, UK
- Department of Plastic and Reconstructive Surgery, Oxford Radcliffe Hospitals NHS Trust, Oxford OX3 9DU, UK
| | - David Johnson
- Department of Plastic and Reconstructive Surgery, Oxford Radcliffe Hospitals NHS Trust, Oxford OX3 9DU, UK
| | - Alexis A. Robinson
- Neural Development Unit, Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Peter J. Scambler
- Molecular Medicine Unit, Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Dianne Gerrelli
- Human Developmental Biology Resource, Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Peter Nürnberg
- Cologne Center for Genomics and Institute for Genetics, University of Cologne, D-50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, D-50674 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, D-50931 Cologne, Germany
| | - Irene M.J. Mathijssen
- Department of Plastic and Reconstructive Surgery, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands
| | - Andrew O.M. Wilkie
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Clinical Genetics, Oxford Radcliffe Hospitals NHS Trust, Oxford OX3 9DU, UK
- Department of Plastic and Reconstructive Surgery, Oxford Radcliffe Hospitals NHS Trust, Oxford OX3 9DU, UK
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21
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Nardmann J, Reisewitz P, Werr W. Discrete shoot and root stem cell-promoting WUS/WOX5 functions are an evolutionary innovation of angiosperms. Mol Biol Evol 2009; 26:1745-55. [PMID: 19387013 DOI: 10.1093/molbev/msp084] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The morphologically diverse bodies of seed plants comprising gymnosperms and angiosperms, which separated some 350 Ma, grow by the activity of meristems containing stem cell niches. In the dicot model Arabidopsis thaliana, these are maintained by the stem cell-promoting functions of WUS and WUSCHEL-related homeobox 5 (WOX5) in the shoot and the root, respectively. Both genes are members of the WOX gene family, which has a monophyletic origin in green algae. The establishment of the WOX gene phylogeny from basal land plants through gymnosperms to basal and higher angiosperms reveals three major branches: a basal clade consisting of WOX13-related genes present in some green algae and throughout all land plant genomes, a second clade containing WOX8/9/11/12 homologues, and a modern clade restricted to seed plants. The analysis of the origin of the modern branch in two basal angiosperms (Amborella trichopoda and Nymphaea jamesoniana) and three gymnosperms (Pinus sylvestris, Ginkgo biloba, and Gnetum gnemon) shows that all members of the modern clade consistently found in monocots and dicots exist at the base of the angiosperm lineage, including WUS and WOX5 orthologues. In contrast, our analyses identify a single WUS/WOX5 homologue in all three gymnosperm genomes, consistent with a monophyletic origin in the last common ancestor of gymnosperms and angiosperms. Phylogenetic data, WUS- and WOX5-specific evolutionary signatures, as well as the expression pattern and stem cell-promoting function of the single gymnosperm WUS/WOX5 pro-orthologue in Arabidopsis indicate a gene duplication event followed by subfunctionalization at the base of angiosperms.
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Affiliation(s)
- Judith Nardmann
- Institut für Entwicklungsbiologie, Universität zu Köln, Köln, Germany
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22
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Relationship of Pax6 activity levels to the extent of eye development in the mouse, Mus musculus. Genetics 2008; 179:1345-55. [PMID: 18562673 DOI: 10.1534/genetics.108.088591] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In this study we extend the mouse Pax6 mutant allelic series to include a homozygous and hemizygous viable hypomorph allele. The Pax6(132-14Neu) allele is a Phe272Ile missense mutation within the third helix of the homeodomain. The mutant Pax6 homeodomain shows greatly reduced binding activity to the P3 DNA binding target. Glucagon-promoter activation by the entire mutant Pax6 product of a reporter gene driven by the G1 paired and homeodomain DNA binding target was slightly increased. We constructed mutant Pax6 genotypes such that Pax6 activity ranged between 100 and 0% and show that the extent of eye development is progressively reduced as Pax6 activity decreased. Two apparent thresholds identify three groups in which the extent of eye development abruptly shifted from complete eye at the highest levels of Pax6 to a rudimentary eye at intermediate levels of Pax6 to very early termination of eye development at the lowest levels of Pax6. Of the two Pax6-positive regions that participate in eye development, the surface ectoderm, which develops into the lens vesicle and the cornea, is more sensitive to reduced levels of Pax6 activity than the optic vesicle, which develops into the inner and outer retinal layers.
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The Evolution of Alternative Splicing in the Pax Family: The View from the Basal Chordate Amphioxus. J Mol Evol 2008; 66:605-20. [DOI: 10.1007/s00239-008-9113-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 04/16/2008] [Accepted: 04/22/2008] [Indexed: 10/22/2022]
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24
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Qin Y, Choi Y, Zhao H, Simpson JL, Chen ZJ, Rajkovic A. NOBOX homeobox mutation causes premature ovarian failure. Am J Hum Genet 2007; 81:576-81. [PMID: 17701902 PMCID: PMC1950834 DOI: 10.1086/519496] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Accepted: 05/07/2007] [Indexed: 12/14/2022] Open
Abstract
NOBOX (newborn ovary homeobox gene) is an oocyte-specific homeobox gene that plays a critical role in early folliculogenesis and represents a candidate gene for nonsyndromic ovarian failure. We investigated whether mutations in the NOBOX gene cause premature ovarian failure (POF). We sequenced the NOBOX gene in 96 white women with POF and discovered seven known single-nucleotide polymorphisms and four novel variations, two of which, p.Arg355His and p.Arg360Gln, cause missense mutations in the homeobox domain. Electrophoretic mobility shift assay (EMSA) confirmed that the missense mutation, p.Arg355His, disrupted NOBOX homeodomain binding to NOBOX DNA-binding element (NBE) and had a dominant negative effect on the binding of wild-type NOBOX to DNA. Our findings demonstrate that NOBOX mutations can cause POF.
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Affiliation(s)
- Yingying Qin
- Center for Reproductive Medicine, Shandong Provincial Hospital of Shandong University, Jinan, China
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25
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Grocott T, Frost V, Maillard M, Johansen T, Wheeler GN, Dawes LJ, Wormstone IM, Chantry A. The MH1 domain of Smad3 interacts with Pax6 and represses autoregulation of the Pax6 P1 promoter. Nucleic Acids Res 2007; 35:890-901. [PMID: 17251190 PMCID: PMC1807973 DOI: 10.1093/nar/gkl1105] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Pax6 transcription is under the control of two main promoters (P0 and P1), and these are autoregulated by Pax6. Additionally, Pax6 expression is under the control of the TGFβ superfamily, although the precise mechanisms of such regulation are not understood. The effect of TGFβ on Pax6 expression was studied in the FHL124 lens epithelial cell line and was found to cause up to a 50% reduction in Pax6 mRNA levels within 24 h. Analysis of luciferase reporters showed that Pax6 autoregulation of the P1 promoter, and its induction of a synthetic promoter encoding six paired domain-binding sites, were significantly repressed by both an activated TGFβ receptor and TGFβ ligand stimulation. Subsequently, a novel Pax6 binding site in P1 was shown to be necessary for autoregulation, indicating a direct influence of Pax6 protein on P1. In transfected cells, and endogenously in FHL124 cells, Pax6 co-immunoprecipitated with Smad3 following TGFβ receptor activation, while in GST pull-down experiments, the MH1 domain of Smad3 was observed binding the RED sub-domain of the Pax6 paired domain. Finally, in DNA adsorption assays, activated Smad3 inhibited Pax6 from binding the consensus paired domain recognition sequence. We hypothesize that the Pax6 autoregulatory loop is targeted for repression by the TGFβ/Smad pathway, and conclude that this involves diminished paired domain DNA-binding function resulting from a ligand-dependant interaction between Pax6 and Smad3.
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Affiliation(s)
- Timothy Grocott
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
| | - Victoria Frost
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
| | - Marjorie Maillard
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
| | - Terje Johansen
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
| | - Grant N. Wheeler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
| | - Lucy J. Dawes
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
| | - I. Michael Wormstone
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
| | - Andrew Chantry
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK and Department of Biochemistry, Institute of Medical Biology, University of Tromso, 9037 Tromso, Norway
- *To whom correspondence should be addressed. Tel: 44 1603 593551; Fax: 44 1603 592250;
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Calon A, Gross I, Davidson I, Kedinger M, Duluc I, Domon-Dell C, Freund JN. Functional interaction between the homeoprotein CDX1 and the transcriptional machinery containing the TATA-binding protein. Nucleic Acids Res 2006; 35:175-85. [PMID: 17158164 PMCID: PMC1802564 DOI: 10.1093/nar/gkl1034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have previously reported that the CDX1 homeoprotein interacts with the TATA-box binding protein (TBP) on the promoter of the glucose-6-phosphatase (G6Pase) gene. We show here that CDX1 interacts with TBP via the homeodomain and that the transcriptional activity additionally requires the N-terminal domain upstream of the homeodomain. CDX1 interacting with TBP is connected to members of the TFIID and Mediator complexes, two major elements of the general transcriptional machinery. Transcription luciferase assays performed using an altered-specificity mutant of TBP provide evidence for the functionality of the interaction between CDX1 and TBP. Unlike CDX1, CDX2 does not interact with TBP nor does it transactivate the G6Pase promoter. Swapping experiments between the domains of CDX1 and CDX2 indicate that, despite opposite functional effects of the homeoproteins on the G6Pase promoter, the N-terminal domains and homeodomains of both CDX1 and CDX2 have the intrinsic ability to activate transcription and to interact with TBP. However, the carboxy domains define the specificity of CDX1 and CDX2. Thus, intra-molecular interactions control the activity and partner recruitment of CDX1 and CDX2, leading to different molecular functions.
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Affiliation(s)
| | | | - Irwin Davidson
- CNRS UMR7104, IGBMC and University Louis PasteurIllkirch, France
| | | | | | | | - Jean-Noël Freund
- To whom correspondence should be addressed at INSERM U682, 3 Avenue Molière, 67200 Strasbourg, France. Tel: +33 388 27 77 27; Fax: +33 388 26 35 38;
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Livne-bar I, Pacal M, Cheung MC, Hankin M, Trogadis J, Chen D, Dorval KM, Bremner R. Chx10 is required to block photoreceptor differentiation but is dispensable for progenitor proliferation in the postnatal retina. Proc Natl Acad Sci U S A 2006; 103:4988-93. [PMID: 16547132 PMCID: PMC1458782 DOI: 10.1073/pnas.0600083103] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Indexed: 11/18/2022] Open
Abstract
In the Chx10-null ocular retardation (or(J)) mouse, retinal progenitor cell (RPC) proliferation is impaired, and bipolar neurons, a late born cell type, fail to differentiate. It is unclear whether Chx10 is required to maintain proliferation throughout retinogenesis or whether the bipolar cell defect is an indirect effect of growth arrest. We show that Chx10 is dispensable for late-stage RPC proliferation but is essential to promote bipolar cell genesis in place of rods. Ectopic Chx10 expression drove bipolar instead of rod cell differentiation without affecting division. Converting Chx10 to an activator impaired bipolar cell differentiation, implying that repression is important for Chx10 activity. In the Chx10 null or(J) retina, only a small fraction of cells expressing mutated Chx10 mRNA were rods, but this fraction increased after p27(Kip1) inactivation, which partially rescues proliferation. Most significantly, acute Chx10 knockdown in the postnatal retina promoted rods in place of bipolar neurons without affecting division. Thus, Chx10 directly controls bipolar cell genesis by inhibiting rod differentiation independent of its temporally limited early effect on RPC proliferation.
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Affiliation(s)
- Izzy Livne-bar
- *Toronto Western Research Institute, University Health Network
- Vision Science Research Program
| | - Marek Pacal
- *Toronto Western Research Institute, University Health Network
- Vision Science Research Program
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5T 2S8; and
| | - Melissa C. Cheung
- *Toronto Western Research Institute, University Health Network
- Vision Science Research Program
| | - Mark Hankin
- Department of Anatomy and Neurobiology, Medical College of Ohio, Toledo, OH 43614
| | - Judy Trogadis
- *Toronto Western Research Institute, University Health Network
- Vision Science Research Program
| | - Danian Chen
- *Toronto Western Research Institute, University Health Network
- Vision Science Research Program
| | - Kimberley M. Dorval
- *Toronto Western Research Institute, University Health Network
- Vision Science Research Program
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5T 2S8; and
| | - Rod Bremner
- *Toronto Western Research Institute, University Health Network
- Vision Science Research Program
- Departments of Ophthalmology and Vision Science, and
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5T 2S8; and
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Corry GN, Underhill DA. Pax3 target gene recognition occurs through distinct modes that are differentially affected by disease-associated mutations. ACTA ACUST UNITED AC 2006; 18:427-38. [PMID: 16280008 DOI: 10.1111/j.1600-0749.2005.00275.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paired box protein Pax3 is an essential regulator of muscle and neural crest-derived cell types, including melanocytes. Within this lineage, Pax3 has been shown to regulate the genes encoding microphthalmia-associated transcription factor (Mitf) and tyrosinase-related protein-1 (Trp-1), despite each having dissimilar Pax3 recognition sequences. We have, therefore, examined the structural requirements for Pax3 binding to the MITF and TRP-1 promoter elements, focusing on the contribution of the paired domain and homeodomain to Pax3 target site recognition. Unexpectedly, although the MITF element is characterized by suboptimal recognition motifs for the paired domain and homeodomain, it sustains a higher level of Pax3 binding than TRP-1, which contains a canonical paired domain site. The basis for this difference involves a context-dependent cooperative binding event requiring both the paired domain and homeodomain, while the paired domain alone is sufficient for TRP-1 recognition. Significantly, the analysis of Waardenburg syndrome mutations reveals marked disparity in their effects on MITF and TRP-1 binding that further underscores mechanistic differences in their interaction with Pax3. Importantly, these mutations also exert distinct effects on the ability of Pax3 to regulate reporter genes fused to either the MITF or TRP-1 promoters. Our results, therefore, establish that Pax3 can regulate target genes through alternate modes of DNA recognition that are differentially impacted by disease-causing mutations, which together have important implications for understanding Pax3-regulated gene networks.
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Affiliation(s)
- Gareth N Corry
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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