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Öztürk Ö, Bagis H, Bolu S. Osteogenesis Imperfecta and Split Foot Malformation due to 7q21.2q21.3 Deletion Including COL1A2, DLX5/6 Genes: Review of the Literature. J Pediatr Genet 2024; 13:69-79. [PMID: 38567169 PMCID: PMC10984717 DOI: 10.1055/s-0041-1736613] [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: 04/11/2021] [Accepted: 09/22/2021] [Indexed: 10/19/2022]
Abstract
Copy number variation in loss of 7q21 is a genetic disorder characterized by split hand/foot malformation, hearing loss, developmental delay, myoclonus, dystonia, joint laxity, and psychiatric disorders. Osteogenesis imperfecta caused by whole gene deletions of COL1A2 is a very rare condition. We report a Turkish girl with ectrodactyly, joint laxity, multiple bone fractures, blue sclera, early teeth decay, mild learning disability, and depression. A copy number variant in loss of 4.8 Mb at chromosome 7 (q21.2q21.3) included the 58 genes including DLX5, DLX6, DYNC1I1, SLC25A13, SGCE, and COL1A2 . They were identified by chromosomal microarray analysis. We compared the findings in our patients with those previously reported. This case report highlights the importance of using microarray to identify the genetic etiology in patients with ectrodactyly and osteogenesis imperfecta.
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Affiliation(s)
- Özden Öztürk
- Department of Medical Genetics, Medical School of Adiyaman University, Adiyaman, Türkiye
| | - Haydar Bagis
- Department of Medical Genetics, Medical School of Adiyaman University, Adiyaman, Türkiye
| | - Semih Bolu
- Department of Pediatrics, Division of Pediatric Endocrinology, Medical School of Adiyaman University, Adiyaman, Türkiye
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2
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Truong BT, Shull LC, Lencer E, Bend EG, Field M, Blue EE, Bamshad MJ, Skinner C, Everman D, Schwartz CE, Flanagan-Steet H, Artinger KB. PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in split hand/foot malformation. Dis Model Mech 2023; 16:dmm049977. [PMID: 37083955 PMCID: PMC10151829 DOI: 10.1242/dmm.049977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/09/2023] [Indexed: 04/22/2023] Open
Abstract
Split hand/foot malformation (SHFM) is a rare limb abnormality with clefting of the fingers and/or toes. For many individuals, the genetic etiology is unknown. Through whole-exome and targeted sequencing, we detected three novel variants in a gene encoding a transcription factor, PRDM1, that arose de novo in families with SHFM or segregated with the phenotype. PRDM1 is required for limb development; however, its role is not well understood and it is unclear how the PRDM1 variants affect protein function. Using transient and stable overexpression rescue experiments in zebrafish, we show that the variants disrupt the proline/serine-rich and DNA-binding zinc finger domains, resulting in a dominant-negative effect. Through gene expression assays, RNA sequencing, and CUT&RUN in isolated pectoral fin cells, we demonstrate that Prdm1a directly binds to and regulates genes required for fin induction, outgrowth and anterior/posterior patterning, such as fgfr1a, dlx5a, dlx6a and smo. Taken together, these results improve our understanding of the role of PRDM1 in the limb gene regulatory network and identified novel PRDM1 variants that link to SHFM in humans.
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Affiliation(s)
- Brittany T. Truong
- Human Medical Genetics & Genomics Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lomeli C. Shull
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ezra Lencer
- Biology Department, Lafayette College, Easton, PA 18042, USA
| | - Eric G. Bend
- Greenwood Genetics Center, Greenwood, SC 29646, USA
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, AUS
| | - Elizabeth E. Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | - Kristin B. Artinger
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
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3
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Gudkov M, Thibaut L, Khushi M, Blue GM, Winlaw DS, Dunwoodie SL, Giannoulatou E. ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data. BMC Bioinformatics 2023; 24:49. [PMID: 36792982 PMCID: PMC9930243 DOI: 10.1186/s12859-023-05154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/19/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND A wide range of tools are available for the detection of copy number variants (CNVs) from whole-genome sequencing (WGS) data. However, none of them focus on clinically-relevant CNVs, such as those that are associated with known genetic syndromes. Such variants are often large in size, typically 1-5 Mb, but currently available CNV callers have been developed and benchmarked for the discovery of smaller variants. Thus, the ability of these programs to detect tens of real syndromic CNVs remains largely unknown. RESULTS Here we present ConanVarvar, a tool which implements a complete workflow for the targeted analysis of large germline CNVs from WGS data. ConanVarvar comes with an intuitive R Shiny graphical user interface and annotates identified variants with information about 56 associated syndromic conditions. We benchmarked ConanVarvar and four other programs on a dataset containing real and simulated syndromic CNVs larger than 1 Mb. In comparison to other tools, ConanVarvar reports 10-30 times less false-positive variants without compromising sensitivity and is quicker to run, especially on large batches of samples. CONCLUSIONS ConanVarvar is a useful instrument for primary analysis in disease sequencing studies, where large CNVs could be the cause of disease.
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Affiliation(s)
- Mikhail Gudkov
- grid.1057.30000 0000 9472 3971Victor Chang Cardiac Research Institute, Sydney, NSW 2010 Australia ,grid.1013.30000 0004 1936 834XSchool of Biomedical Engineering, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1005.40000 0004 4902 0432St Vincent’s Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2010 Australia
| | - Loïc Thibaut
- grid.1057.30000 0000 9472 3971Victor Chang Cardiac Research Institute, Sydney, NSW 2010 Australia ,grid.1005.40000 0004 4902 0432School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052 Australia
| | - Matloob Khushi
- grid.1013.30000 0004 1936 834XSchool of Computer Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Gillian M. Blue
- grid.1013.30000 0004 1936 834XSydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia ,grid.413973.b0000 0000 9690 854XHeart Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145 Australia
| | - David S. Winlaw
- grid.1013.30000 0004 1936 834XSydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia ,grid.413973.b0000 0000 9690 854XHeart Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145 Australia
| | - Sally L. Dunwoodie
- grid.1057.30000 0000 9472 3971Victor Chang Cardiac Research Institute, Sydney, NSW 2010 Australia ,grid.1005.40000 0004 4902 0432St Vincent’s Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2010 Australia ,grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052 Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia. .,St Vincent's Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, 2010, Australia.
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4
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Nikolić I, Samardžić J, Stevanović S, Miljuš-Đukić J, Milisavljević M, Timotijević G. CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response. Int J Mol Sci 2023; 24:ijms24032442. [PMID: 36768765 PMCID: PMC9916663 DOI: 10.3390/ijms24032442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 01/28/2023] Open
Abstract
Global climate change has a detrimental effect on plant growth and health, causing serious losses in agriculture. Investigation of the molecular mechanisms of plant responses to various environmental pressures and the generation of plants tolerant to abiotic stress are imperative to modern plant science. In this paper, we focus on the application of the well-established technology CRISPR/Cas9 genome editing to better understand the functioning of the intrinsically disordered protein DSS1 in plant response to oxidative stress. The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were phenotypically characterized during plant development and their sensitivity to oxidative stress was analyzed. The characterization of mutant lines revealed differences in root and stem lengths, and rosette area size. Plants with a disrupted AtDSS1(V) gene exhibited lower survival rates and increased levels of oxidized proteins in comparison to WT plants exposed to oxidative stress induced by hydrogen peroxide. In this work, the dss1 double mutant was not obtained due to embryonic lethality. These results suggest that the DSS1(V) protein could be an important molecular component in plant abiotic stress response.
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Pesce F, Newcombe EA, Seiffert P, Tranchant EE, Olsen JG, Grace CR, Kragelund BB, Lindorff-Larsen K. Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins. Biophys J 2023; 122:310-321. [PMID: 36518077 PMCID: PMC9892621 DOI: 10.1016/j.bpj.2022.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Diffusion measurements by pulsed-field gradient NMR and fluorescence correlation spectroscopy can be used to probe the hydrodynamic radius of proteins, which contains information about the overall dimension of a protein in solution. The comparison of this value with structural models of intrinsically disordered proteins is nonetheless impaired by the uncertainty of the accuracy of the methods for computing the hydrodynamic radius from atomic coordinates. To tackle this issue, we here build conformational ensembles of 11 intrinsically disordered proteins that we ensure are in agreement with measurements of compaction by small-angle x-ray scattering. We then use these ensembles to identify the forward model that more closely fits the radii derived from pulsed-field gradient NMR diffusion experiments. Of the models we examined, we find that the Kirkwood-Riseman equation provides the best description of the hydrodynamic radius probed by pulsed-field gradient NMR experiments. While some minor discrepancies remain, our results enable better use of measurements of the hydrodynamic radius in integrative modeling and for force field benchmarking and parameterization.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Estella A Newcombe
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Pernille Seiffert
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Emil E Tranchant
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christy R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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6
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The molecular genetics of human appendicular skeleton. Mol Genet Genomics 2022; 297:1195-1214. [PMID: 35907958 DOI: 10.1007/s00438-022-01930-1] [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: 07/07/2021] [Accepted: 07/09/2022] [Indexed: 10/16/2022]
Abstract
Disorders that result from de-arrangement of growth, development and/or differentiation of the appendages (limbs and digit) are collectively called as inherited abnormalities of human appendicular skeleton. The bones of appendicular skeleton have central role in locomotion and movement. The different types of appendicular skeletal abnormalities are well described in the report of "Nosology and Classification of Genetic skeletal disorders: 2019 Revision". In the current article, we intend to present the embryology, developmental pathways, disorders and the molecular genetics of the appendicular skeletal malformations. We mainly focused on the polydactyly, syndactyly, brachydactyly, split-hand-foot malformation and clubfoot disorders. To our knowledge, only nine genes of polydactyly, five genes of split-hand-foot malformation, nine genes for syndactyly, eight genes for brachydactyly and only single gene for clubfoot have been identified to be involved in disease pathophysiology. The current molecular genetic data will help life sciences researchers working on the rare skeletal disorders. Moreover, the aim of present systematic review is to gather the published knowledge on molecular genetics of appendicular skeleton, which would help in genetic counseling and molecular diagnosis.
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7
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Levi G, de Lombares C, Giuliani C, Iannuzzi V, Aouci R, Garagnani P, Franceschi C, Grimaud-Hervé D, Narboux-Nême N. DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution. Mol Biol Evol 2021; 38:4748-4764. [PMID: 34132815 PMCID: PMC8557472 DOI: 10.1093/molbev/msab181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech.
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Affiliation(s)
- Giovanni Levi
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Camille de Lombares
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - Vincenzo Iannuzzi
- Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Italy
| | - Rym Aouci
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Dominique Grimaud-Hervé
- Histoire Naturelle de l’Homme Préhistorique, CNRS UMR 7194, Département H&E, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Narboux-Nême
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
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8
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Ruidiaz SF, Dreier JE, Hartmann-Petersen R, Kragelund BB. The disordered PCI-binding human proteins CSNAP and DSS1 have diverged in structure and function. Protein Sci 2021; 30:2069-2082. [PMID: 34272906 PMCID: PMC8442969 DOI: 10.1002/pro.4159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) regularly constitute components of larger protein assemblies contributing to architectural stability. Two small, highly acidic IDPs have been linked to the so-called PCI complexes carrying PCI-domain subunits, including the proteasome lid and the COP9 signalosome. These two IDPs, DSS1 and CSNAP, have been proposed to have similar structural propensities and functions, but they display differences in their interactions and interactome sizes. Here we characterized the structural properties of human DSS1 and CSNAP at the residue level using NMR spectroscopy and probed their propensities to bind ubiquitin. We find that distinct structural features present in DSS1 are completely absent in CSNAP, and vice versa, with lack of relevant ubiquitin binding to CSNAP, suggesting the two proteins to have diverged in both structure and function. Our work additionally highlights that different local features of seemingly similar IDPs, even subtle sequence variance, may endow them with different functional traits. Such traits may underlie their potential to engage in multiple interactions thereby impacting their interactome sizes.
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Affiliation(s)
- Sarah F Ruidiaz
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Jesper E Dreier
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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9
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Nikolić IP, Nešić SB, Samardžić JT, Timotijević GS. Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress. PROTOPLASMA 2021; 258:779-792. [PMID: 33404921 DOI: 10.1007/s00709-020-01598-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
DSS1 is a small protein, highly conserved across different species. As a member of the intrinsically disordered protein family, DSS1 interacts with different protein partners, thus forming complexes involved in diverse biological mechanisms: DNA repair, regulation of protein homeostasis, mRNA export, etc. Additionally, DSS1 has a novel intriguing role in the post-translational protein modification named DSSylation. Oxidatively damaged proteins are targeted for removal with DSS1 and then degraded by proteasome. Yet, DSS1 involvement in the maintenance of genome integrity through homologous recombination is the only function well studied in Arabidopsis research. The fact that animal DSS1 shows wide multifunctionality imposes a need to investigate the additional roles of two Arabidopsis thaliana DSS1 homologs. Having in mind the universality of various biological processes, we considered the possibility of plant DSS1 involvement in cellular homeostasis maintenance during stress exposure. Using real-time PCR and immunoblot analysis, we investigated the profiles of DSS1 gene and protein expression under oxidative stress. We grew and selected the homozygous Arabidopsis mutant line, carrying the T-DNA intron insertion in the DSS1(V) gene. The mutant line was phenotypically described during plant development, and its sensitivity to oxidative stress was characterized. This is the first report which indicates that plant DSS1 gene expression has an altered profile under the influence of oxidative stress. dss1(V)-/- plants showed an increased sensitivity to oxidative stress, germinated faster than WT, but generally showed developmental delay in further stages. Our results indicate that the DSS1 protein could be a crucial player in the molecular mechanisms underlying plant abiotic stress responses.
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Affiliation(s)
- Ivana P Nikolić
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia
| | - Sofija B Nešić
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia
| | - Jelena T Samardžić
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia
| | - Gordana S Timotijević
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia.
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Lai S, Zhang X, Feng L, He M, Wang S. The prenatal diagnosis and genetic counseling of chromosomal micro-duplication on 10q24.3 in a fetus: A case report and a brief review of the literature. Medicine (Baltimore) 2020; 99:e22533. [PMID: 33080687 PMCID: PMC7571886 DOI: 10.1097/md.0000000000022533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Split-hand/split-foot malformation (SHFM), also known as ectrodactyly, is a congenital limb malformation affecting the central rays of the autopod extending to syndactyly, median clefts of the hands and feet, aplasia/hypoplasia of phalanges, metacarpals and metatarsals. Duplication of this 10q24 region is associated with SHFM3. While the clinical and genetic heterogeneity of SHFM makes the prenatal diagnosis and genetic counseling more challenging and difficult. PATIENT CONCERNS A physically normal pregnant woman had a systemic ultrasound at the second trimester, only identified the deformity of both hands and feet on the fetus. DIAGNOSES The fetus was diagnosed as sporadic SHFM3. INTERVENTIONS After seeking advice from genetic counseling, she decided to terminate the pregnancy. The induction of infant was done after appearance of bipedal clefts, lobster-claw appearance and partial loss of phalanges and metacarpals, leaving behind 2nd finger in the left hand and the 5th in the right hand. Furthermore, collection of umbilical cord is recommended to this fetus for genome-wide detection. OUTCOMES An outcome of the gene detection from abortion shows that there is variation in copy number in genome of chromosome 1 and chromosome 10. LESSONS This case study confirms an association between SHFM3 and chromosomal micro-duplication on 10q24.3, and the extension of clinical spectrum of SHFM3. It also proposes some prenatal diagnosis and genetic counseling to help in planning and management in affected pregnancy. This will reduce the congenital and development abnormalities in birth rate, as well as relive the economic, psychological, and physical burden to the affected families.
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Affiliation(s)
- Shaoyang Lai
- Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen
| | - Xueqin Zhang
- Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen
| | - Ling Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengzhou He
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaoshuai Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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11
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Integrative genomic analysis predicts novel functional enhancer-SNPs for bone mineral density. Hum Genet 2019; 138:167-185. [PMID: 30656451 DOI: 10.1007/s00439-019-01971-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/03/2019] [Indexed: 01/20/2023]
Abstract
Osteoporosis is a skeletal disorder characterized by low bone mineral density (BMD) and deterioration of bone microarchitecture. To identify novel genetic loci underlying osteoporosis, an effective strategy is to focus on scanning of variants with high potential functional impacts. Enhancers play a crucial role in regulating cell-type-specific transcription. Therefore, single-nucleotide polymorphisms (SNPs) located in enhancers (enhancer-SNPs) may represent strong candidate functional variants. Here, we performed a targeted analysis for potential functional enhancer-SNPs that may affect gene expression and biological processes in bone-related cells, specifically, osteoblasts, and peripheral blood monocytes (PBMs), using five independent cohorts (n = 5905) and the genetics factors for osteoporosis summary statistics, followed by comprehensive integrative genomic analyses of chromatin states, transcription, and metabolites. We identified 15 novel enhancer-SNPs associated with femoral neck and lumbar spine BMD, including 5 SNPs mapped to novel genes (e.g., rs10840343 and rs10770081 in IGF2 gene) and 10 novel SNPs mapped to known BMD-associated genes (e.g., rs2941742 in ESR1 gene, and rs10249092 and rs4342522 in SHFM1 gene). Interestingly, enhancer-SNPs rs10249092 and rs4342522 in SHFM1 were tightly linked, but annotated to different enhancers in PBMs and osteoblasts, respectively, suggesting that even tightly linked SNPs may regulate the same target gene and contribute to the phenotype variation in cell-type-specific manners. Importantly, ten enhancer-SNPs may also regulate BMD variation by affecting the serum metabolite levels. Our findings revealed novel susceptibility loci that may regulate BMD variation and provided intriguing insights into the genetic mechanisms of osteoporosis.
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12
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Mazumdar J, Chowdhury P, Bhattacharya T, Mondal BC, Ghosh U. Patients with Congenital Limb Anomaly Show Short Telomere, Shutdown of Telomerase and Deregulated Expression of Various Telomere-Associated Proteins in Peripheral Blood Mononuclear Cells-A Case Series. J Clin Diagn Res 2017; 11:GR01-GR06. [PMID: 28969156 DOI: 10.7860/jcdr/2017/26960.10516] [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: 02/28/2017] [Accepted: 05/24/2017] [Indexed: 11/24/2022]
Abstract
Congenital limb anomalies are outcome of improper bone formation during embryonic development when cells divide, differentiate with high rate. So, telomerase activity is essential to maintain telomere length for such highly dividing cells. Here, we report four cases of congenital limb anomalies with detailed structures of limbs along with other clinical manifestations of age less than two years. We compared telomere length, expression of telomerase and telomere-associated genes of Peripheral Blood Mononuclear Cells (PBMC) in patient and four age-matched normal individual. Patient-1 was diagnosed with congenital limb hypogenesis ectrodactyly sequence, an autosomal dominant disorder, showing absence of digits and fibula in upper and lower limb respectively. Both mother and grandmother of Patient-1 showed similar hypogenesis of limbs. Patient-2 showed bilateral clenched hand with arthrogryposis, microcephaly and holoprosencephaly. Both Patient-3 and Patient-4 has no radius in upper limb. Additionally, Paient-3 showed right sided orbital Space Occupying Lesion (SOL) and Paranasal Sinuses (PNS) whereas Patient-4 showed fused kidney with fanconi anaemia. Furthermore, all the patients showed shorter telomere length, inactive telomerase and de-regulated expression of telomere-associated proteins in PBMC compared with age-matched control group. So, we can conclude that congenital limb anomalies may be linked with telomeropathy and a study with large number of samples is required to firmly establish such association.
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Affiliation(s)
- Jayitri Mazumdar
- Senior Resident, Department of Paediatrics, Calcutta National Medical College and Hospital, Kolkata, West Bengal, India
| | - Priyanka Chowdhury
- Resaerch Scholar, Department of Biochemistry and Biophysics, University of Kalyani, West Bengal, India
| | - Tunisha Bhattacharya
- RMO Cum Clinical Tutor, Department of Paediatrics, Calcutta National Medical College and Hospital, Kolkata, West Bengal, India
| | - Badal Chandra Mondal
- Professor, Department of Paediatrics, Murshidabad Medical College, Berhampore, West Bengal, India
| | - Utpal Ghosh
- Assistant Professor, Department of Biochemistry and Biophysics, University of Kalyani, West Bengal, India
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13
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Cao L, Yang W, Wang S, Chen C, Zhang X, Luo Y. Molecular Genetic Characterization of a Chinese Family with Severe Split Hand/Foot Malformation. Genet Test Mol Biomarkers 2017; 21:357-362. [PMID: 28422522 DOI: 10.1089/gtmb.2016.0415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Split hand/foot malformation (SHFM) is a congenital limb malformation characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM is a genetically heterogeneous disease; the aim of this study was to identify pathogenic variations in a Chinese family with SHFM. MATERIALS AND METHODS Haplotype analyses with microsatellite markers covering the five SHFM loci were performed to localize the causative locus. Real-time quantitative polymerase chain reaction (qPCR) assays and inverse PCR were performed to determine the copy number variations and to amplify junction breakpoints in affected individuals. Candidate genes were further screened for mutations through Sanger sequencing. RESULTS A potential haplotype in the SHFM3 locus was shared by all affected individuals. qPCR and inverse PCR showed a microduplication at chromosome 10q24 spanning 488,859 bp and encompassing five entire genes, LBX1, BTRC, POLL, DPCD, and FBXW4, that co-segregated with the SHFM phenotype. No coding or splice-site mutations of these genes were found. CONCLUSION We determined the molecular basis of SHFM in a Chinese family by haplotype analysis, qPCR, inverse PCR, and Sanger sequencing. Our work extends the clinical spectrum of SHFM3; provides a fine-scale delineation of the chromosomal breakpoints helping to narrow the critical region of SHFM3; and facilitates an understanding of the mechanisms underlying abnormal limb development and extraskeletal anomalies.
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Affiliation(s)
- Lihua Cao
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
| | - Wei Yang
- 2 McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, China
| | - Shusen Wang
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
| | - Chen Chen
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
| | - Xue Zhang
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China .,2 McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, China
| | - Yang Luo
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
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14
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Abstract
Ankyloblepharon-ectodermal defects-cleft lip/palate (AEC) syndrome, also known as Hay-Wells syndrome, is an autosomal genetic disease with the main features of ankyloblepharon filiforme adnatum, ectodermal defects, and cleft lip/palate. The authors report a patient with 17 months old girl with AEC syndrome having ankyloblepharon, cleft and palate, and ectrodactyly with some associated features. Etiology, clinical features, differential diagnosis, and treatment have been elaborated in this clinical report.
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15
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Klar AJS. Split hand/foot malformation genetics supports the chromosome 7 copy segregation mechanism for human limb development. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150415. [PMID: 27821526 PMCID: PMC5104513 DOI: 10.1098/rstb.2015.0415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/17/2022] Open
Abstract
Genetic aberrations of several unlinked loci cause human congenital split hand/foot malformation (SHFM) development. Mutations of the DLX5 (distal-less) transcription factor-encoding gene in chromosome 7 cause SHFM through haploinsufficiency, but the vast majority of cases result from heterozygous chromosomal aberrations of the region without mutating the DLX5 gene. To resolve this paradox, we invoke a chromosomal epigenetic mechanism for limb development. It is composed of a monochromatid gene expression phenomenon that we discovered in two fission yeasts with the selective chromosome copy segregation phenomenon that we discovered in mouse cells. Accordingly, one daughter cell inherits both expressed DLX5 copies while the other daughter inherits both epigenetically silenced ones from a single deterministic cell of the developing limb. Thus, differentiated daughter cells after further proliferation will correspondingly produce proximal/distal-limb tissues. Published results of a Chr. 7 translocation with a centromere-proximal breakpoint situated over 41 million bases away from the DLX locus, centromeric and DLX5-region inversions have satisfied key genetic and developmental biology predictions of the mechanism. Further genetic tests of the mechanism are proposed. We propose that the DNA double helical structure itself causes the development of sister cells' gene regulation asymmetry. We also argue against the conventionally invoked morphogen model of development.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.
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Affiliation(s)
- Amar J S Klar
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Building 539, Room 154, Frederick, MD 21702-1201, USA
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16
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Kelso AA, Goodson SD, Watts LE, Ledford LL, Waldvogel SM, Diehl JN, Shah SB, Say AF, White JD, Sehorn MG. The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing. Nucleic Acids Res 2016; 45:711-725. [PMID: 27694622 PMCID: PMC5314795 DOI: 10.1093/nar/gkw877] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/08/2016] [Accepted: 09/21/2016] [Indexed: 12/17/2022] Open
Abstract
Homologous recombination (HR) is a template-driven repair pathway that mends DNA double-stranded breaks (DSBs), and thus helps to maintain genome stability. The RAD51 recombinase facilitates DNA joint formation during HR, but to accomplish this task, RAD51 must be loaded onto the single-stranded DNA. DSS1, a candidate gene for split hand/split foot syndrome, provides the ability to recognize RPA-coated ssDNA to the tumor suppressor BRCA2, which is complexed with RAD51. Together BRCA2-DSS1 displace RPA and load RAD51 onto the ssDNA. In addition, the BRCA2 interacting protein BCCIP normally colocalizes with chromatin bound BRCA2, and upon DSB induction, RAD51 colocalizes with BRCA2-BCCIP foci. Down-regulation of BCCIP reduces DSB repair and disrupts BRCA2 and RAD51 foci formation. While BCCIP is known to interact with BRCA2, the relationship between BCCIP and RAD51 is not known. In this study, we investigated the biochemical role of the β-isoform of BCCIP in relation to the RAD51 recombinase. We demonstrate that BCCIPβ binds DNA and physically and functionally interacts with RAD51 to stimulate its homologous DNA pairing activity. Notably, this stimulatory effect is not the result of RAD51 nucleoprotein filament stabilization; rather, we demonstrate that BCCIPβ induces a conformational change within the RAD51 filament that promotes release of ADP to help maintain an active presynaptic filament. Our findings reveal a functional role for BCCIPβ as a RAD51 accessory factor in HR.
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Affiliation(s)
- Andrew A Kelso
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Steven D Goodson
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Leah E Watts
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - LeAnna L Ledford
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Sarah M Waldvogel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - J Nathaniel Diehl
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Shivani B Shah
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Amanda F Say
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Julie D White
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Michael G Sehorn
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, SC 29634, USA
- Clemson University School of Health Research, Clemson, SC 29634, USA
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17
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Aspen Cancer Conference Fellows. Toxicol Pathol 2016. [DOI: 10.1080/01926230490882358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Rivadeneira F, Mäkitie O. Osteoporosis and Bone Mass Disorders: From Gene Pathways to Treatments. Trends Endocrinol Metab 2016; 27:262-281. [PMID: 27079517 DOI: 10.1016/j.tem.2016.03.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 12/28/2022]
Abstract
Genomic technologies have evolved rapidly contributing to the understanding of diseases. Genome-wide association studies (GWAS) and whole-exome sequencing have aided the identification of the genetic determinants of monogenic and complex conditions including osteoporosis and bone mass disorders. Overlap exists between the genes implicated in monogenic and complex forms of bone mass disorders, largely explained by the clustering of genes encoding factors in signaling pathways crucial for mesenchymal cell differentiation, skeletal development, and bone remodeling and metabolism. Numerous of the remaining discovered genes merit functional follow-up studies to elucidate their role in bone biology. The insight provided by genetic studies is serving the identification of biomarkers predictive of disease, redefining disease, response to treatment, and discovery of novel drug targets for skeletal disorders.
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Affiliation(s)
- Fernando Rivadeneira
- Musculoskeletal Genomics, Health and Metabolism, Departments of Internal Medicine and Epidemiology, Erasmus University Medical Center, 3000CA Rotterdam, The Netherlands.
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Molecular Medicine and Surgery, Karolinska Institutet, and Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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19
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Kragelund BB, Schenstrøm SM, Rebula CA, Panse VG, Hartmann-Petersen R. DSS1/Sem1, a Multifunctional and Intrinsically Disordered Protein. Trends Biochem Sci 2016; 41:446-459. [PMID: 26944332 DOI: 10.1016/j.tibs.2016.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 01/24/2023]
Abstract
DSS1/Sem1 is a versatile intrinsically disordered protein. Besides being a bona fide subunit of the 26S proteasome, DSS1 associates with other protein complexes, including BRCA2-RPA, involved in homologous recombination; the Csn12-Thp3 complex, involved in RNA splicing; the integrator, involved in transcription; and the TREX-2 complex, involved in nuclear export of mRNA and transcription elongation. As a subunit of the proteasome, DSS1 functions both in complex assembly and possibly as a ubiquitin receptor. Here, we summarise structural and functional aspects of DSS1/Sem1 with particular emphasis on its multifunctional and disordered properties. We suggest that DSS1/Sem1 can act as a polyanionic adhesive to prevent nonproductive interactions during construction of protein assemblies, uniquely employing different structures when associating with the diverse multisubunit complexes.
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Affiliation(s)
- Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Signe M Schenstrøm
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Caio A Rebula
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Vikram Govind Panse
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Rasmus Hartmann-Petersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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20
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Sivasankaran A, Srikanth A, Kulshreshtha PS, Anuradha D, Kadandale JS, Samuel CR. Split Hand/Foot Malformation Associated with 7q21.3 Microdeletion: A Case Report. Mol Syndromol 2016; 6:287-96. [PMID: 27022330 DOI: 10.1159/000443708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2015] [Indexed: 11/19/2022] Open
Abstract
Split hand/foot malformation (SHFM) or ectrodactyly is a rare genetic condition affecting limb development. SHFM shows clinical and genetic heterogeneity. It can present as an isolated form or in combination with additional anomalies affecting the long bones (nonsyndromic form) or other organ systems including the craniofacial, genitourinary and ectodermal structures (syndromic ectrodactyly). This study reports a girl with SHFM who also exhibited developmental delay, mild dysmorphic facial features and sensorineural hearing loss. High-resolution banding analysis indicated an interstitial deletion within the 7q21 band. FISH using locus-specific BAC probes confirmed the microdeletion of 7q21.3. Chromosomal microarray analysis also revealed a microdeletion of 1.856 Mb in 7q21.3. However, a larger 8.44-Mb deletion involving bands 7q21.11q21.2 was observed, and the breakpoints were refined. The phenotype and the candidate genes underlying the pathogenesis of this disorder are discussed.
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Affiliation(s)
- Aswini Sivasankaran
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, India
| | - Ambika Srikanth
- Center for Human Genetics, Biotech Park, Electronic City Phase I, Bangalore, India
| | - Pooja S Kulshreshtha
- Center for Human Genetics, Biotech Park, Electronic City Phase I, Bangalore, India
| | - Deenadayalu Anuradha
- Department of Medical Genetics, Institute of Obstetrics and Gynecology, Government Hospital for Women and Children, Madras Medical College, Chennai, India
| | - Jayarama S Kadandale
- Center for Human Genetics, Biotech Park, Electronic City Phase I, Bangalore, India
| | - Chandra R Samuel
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, India
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21
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Rasmussen MB, Kreiborg S, Jensen P, Bak M, Mang Y, Lodahl M, Budtz-Jørgensen E, Tommerup N, Tranebjærg L, Rendtorff ND. Phenotypic subregions within the split-hand/foot malformation 1 locus. Hum Genet 2016; 135:345-57. [DOI: 10.1007/s00439-016-1635-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/13/2016] [Indexed: 11/29/2022]
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22
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Proudfoot A, Axelrod HL, Geralt M, Fletterick RJ, Yumoto F, Deacon AM, Elsliger MA, Wilson IA, Wüthrich K, Serrano P. Dlx5 Homeodomain:DNA Complex: Structure, Binding and Effect of Mutations Related to Split Hand and Foot Malformation Syndrome. J Mol Biol 2016; 428:1130-1141. [PMID: 26829219 DOI: 10.1016/j.jmb.2016.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/20/2016] [Accepted: 01/24/2016] [Indexed: 12/18/2022]
Abstract
The Dlx5 homeodomain is a transcription factor related to the Drosophila distal-less gene that is associated with breast and lung cancer, lymphoma, Rett syndrome and osteoporosis in humans. Mutations in the DLX5 gene have been linked to deficiencies in craniofacial and limb development in higher eukaryotes, including split hand and foot malformation 1 in humans. Our characterization of a Dlx5 homeodomain:(CGACTAATTAGTCG)2 complex by NMR spectroscopy paved the way for determination of its crystal structure at 1.85Å resolution that enabled rationalization of the effects of disease-related mutations on the protein function. A Q186H mutation linked to split hand and foot malformation 1 likely affects affinity of DNA binding by disrupting water-mediated interactions with the DNA major groove. A more subtle effect is implicated for the Q178P mutation, which is not in direct contact with the DNA. Our data indicate that these mutations diminish the ability of the Dlx5 homeodomain to recognize and bind target DNAs, and they likely destabilize the formation of functional complexes.
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Affiliation(s)
- Andrew Proudfoot
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Herbert L Axelrod
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robert J Fletterick
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Fumiaki Yumoto
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Ashley M Deacon
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute of Molecular Biology and Biophysics, ETH Zürich, CH 8093, Zürich, Switzerland
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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23
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Hsueh YL, Su YN, Lin HY, Lee CN, Shih JC. Array comparative genomic hybridization characterization of multiple interstitial deletions involving 7p22.1, 7q11.23, 7q21.3-q22.1, 19p13.3-p12, and 19q13.11-q13.43 in a fetus associated with split hand-foot malformation. Role of EPS15L1 in pathogenesis. Taiwan J Obstet Gynecol 2015; 54:455-8. [PMID: 26384072 DOI: 10.1016/j.tjog.2014.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2014] [Indexed: 11/26/2022] Open
Affiliation(s)
- Ya-Lien Hsueh
- Department of Obstetrics and Gynecology, Cardinal Tien Hospital Yunghe Branch, New Taipei City, Taiwan
| | - Yi-Ning Su
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsin-Yu Lin
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Nan Lee
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jin-Chung Shih
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
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24
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Zhao W, Vaithiyalingam S, San Filippo J, Maranon DG, Jimenez-Sainz J, Fontenay GV, Kwon Y, Leung SG, Lu L, Jensen RB, Chazin WJ, Wiese C, Sung P. Promotion of BRCA2-Dependent Homologous Recombination by DSS1 via RPA Targeting and DNA Mimicry. Mol Cell 2015; 59:176-87. [PMID: 26145171 PMCID: PMC4506714 DOI: 10.1016/j.molcel.2015.05.032] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/21/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
The tumor suppressor BRCA2 is thought to facilitate the handoff of ssDNA from replication protein A (RPA) to the RAD51 recombinase during DNA break and replication fork repair by homologous recombination. However, we find that RPA-RAD51 exchange requires the BRCA2 partner DSS1. Biochemical, structural, and in vivo analyses reveal that DSS1 allows the BRCA2-DSS1 complex to physically and functionally interact with RPA. Mechanistically, DSS1 acts as a DNA mimic to attenuate the affinity of RPA for ssDNA. A mutation in the solvent-exposed acidic domain of DSS1 compromises the efficacy of RPA-RAD51 exchange. Thus, by targeting RPA and mimicking DNA, DSS1 functions with BRCA2 in a two-component homologous recombination mediator complex in genome maintenance and tumor suppression. Our findings may provide a paradigm for understanding the roles of DSS1 in other biological processes.
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Affiliation(s)
- Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sivaraja Vaithiyalingam
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Joseph San Filippo
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - David G Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Judit Jimenez-Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gerald V Fontenay
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Stanley G Leung
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lucy Lu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
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25
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Rattanasopha S, Tongkobpetch S, Srichomthong C, Kitidumrongsook P, Suphapeetiporn K, Shotelersuk V. Absent expression of the osteoblast-specific maternally imprinted genes,DLX5andDLX6,causes split hand/split foot malformation type I. J Med Genet 2014; 51:817-23. [DOI: 10.1136/jmedgenet-2014-102576] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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26
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Restelli M, Lopardo T, Lo Iacono N, Garaffo G, Conte D, Rustighi A, Napoli M, Del Sal G, Perez-Morga D, Costanzo A, Merlo GR, Guerrini L. DLX5, FGF8 and the Pin1 isomerase control ΔNp63α protein stability during limb development: a regulatory loop at the basis of the SHFM and EEC congenital malformations. Hum Mol Genet 2014; 23:3830-42. [PMID: 24569166 PMCID: PMC4065156 DOI: 10.1093/hmg/ddu096] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ectrodactyly, or Split-Hand/Foot Malformation (SHFM), is a congenital condition characterized by the loss of central rays of hands and feet. The p63 and the DLX5;DLX6 transcription factors, expressed in the embryonic limb buds and ectoderm, are disease genes for these conditions. Mutations of p63 also cause the ectodermal dysplasia–ectrodactyly–cleft lip/palate (EEC) syndrome, comprising SHFM. Ectrodactyly is linked to defects of the apical ectodermal ridge (AER) of the developing limb buds. FGF8 is the key signaling molecule in this process, able to direct proximo-distal growth and patterning of the skeletal primordial of the limbs. In the limb buds of both p63 and Dlx5;Dlx6 murine models of SHFM, the AER is poorly stratified and FGF8 expression is severely reduced. We show here that the FGF8 locus is a downstream target of DLX5 and that FGF8 counteracts Pin1–ΔNp63α interaction. In vivo, lack of Pin1 leads to accumulation of the p63 protein in the embryonic limbs and ectoderm. We show also that ΔNp63α protein stability is negatively regulated by the interaction with the prolyl-isomerase Pin1, via proteasome-mediated degradation; p63 mutant proteins associated with SHFM or EEC syndromes are resistant to Pin1 action. Thus, DLX5, p63, Pin1 and FGF8 participate to the same time- and location-restricted regulatory loop essential for AER stratification, hence for normal patterning and skeletal morphogenesis of the limb buds. These results shed new light on the molecular mechanisms at the basis of the SHFM and EEC limb malformations.
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Affiliation(s)
- Michela Restelli
- Department of Biosciences, University of Milano, Milano I-20133, Italy
| | - Teresa Lopardo
- Department of Biosciences, University of Milano, Milano I-20133, Italy
| | - Nadia Lo Iacono
- Department of Biosciences, University of Milano, Milano I-20133, Italy
| | - Giulia Garaffo
- Telethon Laboratory, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino I-10126, Italy
| | - Daniele Conte
- Telethon Laboratory, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino I-10126, Italy
| | | | - Marco Napoli
- Department of Biochemistry and Molecular Biology, Center for Genetics & Genomics, and Center for Stem Cell & Developmental Biology, MD Anderson, Houston, TX, USA
| | - Giannino Del Sal
- Molecular Oncology Unit, LNCIB Area Science Park, Trieste I-34149, Italy
| | - David Perez-Morga
- Laboratoire de Parasitologie Moléculaire, IBMM-DBM, Université Libre de Bruxelles, Gosselies B-6041, Belgium and
| | - Antonio Costanzo
- Department of Dermatology, University of Rome 'Tor Vergata', Rome I-00133, Italy
| | - Giorgio Roberto Merlo
- Telethon Laboratory, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino I-10126, Italy
| | - Luisa Guerrini
- Department of Biosciences, University of Milano, Milano I-20133, Italy
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Zhang Y, Chang FM, Huang J, Junco JJ, Maffi SK, Pridgen HI, Catano G, Dang H, Ding X, Yang F, Kim DJ, Slaga TJ, He R, Wei SJ. DSSylation, a novel protein modification targets proteins induced by oxidative stress, and facilitates their degradation in cells. Protein Cell 2014; 5:124-40. [PMID: 24515614 PMCID: PMC3956975 DOI: 10.1007/s13238-013-0018-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 12/19/2013] [Indexed: 02/02/2023] Open
Abstract
Timely removal of oxidatively damaged proteins is critical for cells exposed to oxidative stresses; however, cellular mechanism for clearing oxidized proteins is not clear. Our study reveals a novel type of protein modification that may play a role in targeting oxidized proteins and remove them. In this process, DSS1 (deleted in split hand/split foot 1), an evolutionally conserved small protein, is conjugated to proteins induced by oxidative stresses in vitro and in vivo, implying oxidized proteins are DSS1 clients. A subsequent ubiquitination targeting DSS1-protein adducts has been observed, suggesting the client proteins are degraded through the ubiquitin-proteasome pathway. The DSS1 attachment to its clients is evidenced to be an enzymatic process modulated by an unidentified ATPase. We name this novel protein modification as DSSylation, in which DSS1 plays as a modifier, whose attachment may render target proteins a signature leading to their subsequent ubiquitination, thereby recruits proteasome to degrade them.
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Affiliation(s)
- Yinghao Zhang
- Medical Research Division, Regional Academic Health Center, Edinburg, TX 78541 USA
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fang-Mei Chang
- Medical Research Division, Regional Academic Health Center, Edinburg, TX 78541 USA
| | - Jianjun Huang
- Medical Research Division, Regional Academic Health Center, Edinburg, TX 78541 USA
- Department of Clinical Biochemistry, Xiangya Medical College, Central South University, Changsha, 410013 China
| | - Jacob J. Junco
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Shivani K. Maffi
- Medical Research Division, Regional Academic Health Center, Edinburg, TX 78541 USA
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Hannah I. Pridgen
- Medical Research Division, Regional Academic Health Center, Edinburg, TX 78541 USA
| | - Gabriel Catano
- Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Hong Dang
- Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Xiang Ding
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Dae Joon Kim
- Medical Research Division, Regional Academic Health Center, Edinburg, TX 78541 USA
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
- The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Thomas J. Slaga
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
- The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Rongqiao He
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Sung-Jen Wei
- Medical Research Division, Regional Academic Health Center, Edinburg, TX 78541 USA
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
- The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
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28
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Wang X, Xin Q, Li L, Li J, Zhang C, Qiu R, Qian C, Zhao H, Liu Y, Shan S, Dang J, Bian X, Shao C, Gong Y, Liu Q. Exome sequencing reveals a heterozygous DLX5 mutation in a Chinese family with autosomal-dominant split-hand/foot malformation. Eur J Hum Genet 2014; 22:1105-10. [PMID: 24496061 DOI: 10.1038/ejhg.2014.7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 12/17/2022] Open
Abstract
Split-hand/foot malformation (SHFM) is a congenital limb deformity due to the absence or dysplasia of central rays of the autopod. Six SHFM loci have already been identified. Here we describe a Chinese family with autosomal-dominant SHFM1 that has previously been mapped to 7q21.2-21.3. The two affected family members, mother and son, showed deep median clefts between toes, ectrodactyly and syndactyly; the mother also showed triphalangeal thumbs. Exome sequencing and variant screening of candidate genes in the six loci known to be responsible for SHFM revealed a novel heterozygous mutation, c.558G>T (p.(Gln186His)), in distal-less homeobox 5 (DLX5). As DLX5 encodes a transcription factor capable of transactivating MYC, we also tested whether the mutation could affect DLX5 transcription acitivity. Results from luciferase reporter assay revealed that a mutation in DLX5 compromised its transcriptional activity. This is the first report of a mutation in DLX5 leading to autosomal-dominant SHFM1.
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Affiliation(s)
- Xue Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Qian Xin
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Lin Li
- Department of Medical Genetics, Linyi People's Hospital, Linyi, China
| | - Jiangxia Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Changwu Zhang
- Department of Orthopedics, Cangshan People's Hospital, Cangshan, China
| | - Rongfang Qiu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Chenmin Qian
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hailing Zhao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Yongchao Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Shan Shan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Jie Dang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Xianli Bian
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Changshun Shao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Yaoqin Gong
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
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29
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Affiliation(s)
- Cheng-Xin Gong
- Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, 10314, USA,
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30
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Lu J, Vaidya N, Meng H, Dai Q, Romine LE, Jones MC, Pretorius DH. Prenatally diagnosed fetal split-hand/foot malformations often accompany a spectrum of anomalies. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2014; 33:167-176. [PMID: 24371113 DOI: 10.7863/ultra.33.1.167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The purpose of this series was to identify cases that appeared on sonography to be split-hand/foot malformations (SHFMs) in fetuses and correlate the sonographic findings, including 2-dimensional (2D) and 3-dimensional (3D) sonography, to outcomes. A retrospective review was conducted of sonographic studies from 2002 to 2012 at 2 fetal care centers. Data were collected with respect to the morphologic characteristics of split-hand/foot abnormalities, the utility of 3D sonography, associated anatomic abnormalities, family histories, gestational ages at diagnosis, fetal outcomes, karyotype, and autopsy results. Ten cases were identified with gestational ages ranging from 15 to 29 weeks. Three-dimensional sonography was helpful in defining anatomy in 7 of 9 cases in which it was performed. Bilateral SHFMs were found in 7 cases (3 cases involving both hands and feet, 2 cases isolated to hands, and 2 cases isolated to feet), whereas 3 cases showed unilateral split-hand malformations. Associated anatomic anomalies were present in 6 cases, and 4 of these had recognized syndromes, including 2 with abnormal karyotypes, specifically, del(22q11) and del(7q31). Two cases occurred in the context of a positive family history of SHFM. Three cases were delivered at term, and 7 cases were electively terminated. In conclusion, SHFMs often occur with a broad range of chromosomal abnormalities, single-gene disorders, and other congenital anomalies. Some apparent SHFMs turn out to be other limb anomalies, such as complex syndactyly. Prenatal screening using 2D sonography can identify SHFMs, and 3D sonography often further clarifies them.
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Affiliation(s)
- Jia Lu
- Thornton Hospital, 9300 Campus Point Dr, 7756, La Jolla, CA 92037 USA.
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31
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Emmett SD, West KP. Gestational vitamin A deficiency: a novel cause of sensorineural hearing loss in the developing world? Med Hypotheses 2014; 82:6-10. [PMID: 24120698 PMCID: PMC4391953 DOI: 10.1016/j.mehy.2013.09.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
Abstract
Hearing loss is a substantial public health problem with profound social and economic consequences in the developing world. The World Health Organization (WHO) estimates that there are 360 million people living with disabling hearing loss globally, and 80% of these individuals are from low- and middle-income countries. The epidemiology of hearing impairment remains poorly defined in most impoverished societies. Middle ear infections in childhood are a key determinant; however, congenital anomalies may also comprise an important etiology and may arise from gestational malnutrition. While evidence exists that preventable vitamin A deficiency exacerbates the severity of ear infections and, consequently, hearing loss, antenatal vitamin A deficiency during sensitive periods of fetal development may represent an etiologically distinct and virtually unexplored causal pathway. Evidence from multiple animal systems clearly shows that fetal inner ear development requires adequate vitamin A nutriture to proceed normally. Inner ear malformations occur in experimentally imposed maternal vitamin A deficiency in multiple species in a dose-response manner. These anomalies are likely due to the loss of retinoic acid-dependent regulation of both hindbrain development and otic morphogenic processes. Based on in vivo evidence in experimental animals, we hypothesize that preventable gestational vitamin A deficiency, especially during early stages of fetal development, may predispose offspring to inner ear malformations and sensorineural hearing loss. As vitamin A deficiency affects an estimated 20 million pregnant women globally, we hypothesize that, in undernourished settings, routine provision of supplemental vitamin A at the recommended allowance throughout pregnancy may promote normal inner ear development and reduce risk of an as yet unknown fraction of sensorineural hearing loss. If our hypothesis proves correct, gestational vitamin A deficiency would represent a potentially preventable etiology of sensorineural hearing loss of substantial public health significance.
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Affiliation(s)
- Susan D Emmett
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline Street, Baltimore, MD 21287, USA; Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street, W2041, Baltimore, MD 21205, USA.
| | - Keith P West
- Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street, W2041, Baltimore, MD 21205, USA
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32
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Split-hand/foot malformation - molecular cause and implications in genetic counseling. J Appl Genet 2013; 55:105-15. [PMID: 24163146 PMCID: PMC3909621 DOI: 10.1007/s13353-013-0178-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 09/21/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022]
Abstract
Split-hand/foot malformation (SHFM) is a congenital limb defect affecting predominantly the central rays of the autopod and occurs either as an isolated trait or part of a multiple congenital anomaly syndrome. SHFM is usually sporadic, familial forms are uncommon. The condition is clinically and genetically heterogeneous and shows mostly autosomal dominant inheritance with variable expressivity and reduced penetrance. To date, seven chromosomal loci associated with isolated SHFM have been described, i.e., SHFM1 to 6 and SHFM/SHFLD. The autosomal dominant mode of inheritance is typical for SHFM1, SHFM3, SHFM4, SHFM5. Autosomal recessive and X-linked inheritance is very uncommon and have been noted only in a few families. Most of the known SHFM loci are associated with chromosomal rearrangements that involve small deletions or duplications of the human genome. In addition, three genes, i.e., TP63, WNT10B, and DLX5 are known to carry point mutations in patients affected by SHFM. In this review, we focus on the known molecular basis of isolated SHFM. We provide clinical and molecular information about each type of abnormality as well as discuss the underlying pathways and mechanism that contribute to their development. Recent progress in the understanding of SHFM pathogenesis currently allows for the identification of causative genetic changes in about 50 % of the patients affected by this condition. Therefore, we propose a diagnostic flow-chart helpful in the planning of molecular genetic tests aimed at identifying disease causing mutation. Finally, we address the issue of genetic counseling, which can be extremely difficult and challenging especially in sporadic SHFM cases.
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33
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Gurrieri F, Everman DB. Clinical, genetic, and molecular aspects of split-hand/foot malformation: an update. Am J Med Genet A 2013; 161A:2860-72. [PMID: 24115638 DOI: 10.1002/ajmg.a.36239] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 08/26/2013] [Indexed: 12/26/2022]
Abstract
We here provide an update on the clinical, genetic, and molecular aspects of split-hand/foot malformation (SHFM). This rare condition, affecting 1 in 8,500-25,000 newborns, is extremely complex because of its variability in clinical presentation, irregularities in its inheritance pattern, and the heterogeneity of molecular genetic alterations that can be found in affected individuals. Both syndromal and nonsyndromal forms are reviewed and the major molecular genetic alterations thus far reported in association with SHFM are discussed. This updated overview should be helpful for clinicians in their efforts to make an appropriate clinical and genetic diagnosis, provide an accurate recurrence risk assessment, and formulate a management plan.
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Affiliation(s)
- Fiorella Gurrieri
- Istituto di Genetica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
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34
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Bohn S, Sakata E, Beck F, Pathare GR, Schnitger J, Nágy I, Baumeister W, Förster F. Localization of the regulatory particle subunit Sem1 in the 26S proteasome. Biochem Biophys Res Commun 2013; 435:250-4. [PMID: 23643786 DOI: 10.1016/j.bbrc.2013.04.069] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
Abstract
The ubiquitin-proteasome system is responsible for regulated protein degradation in the cell with the 26S proteasome acting as its executive arm. The molecular architecture of this 2.5 MDa complex has been established recently, with the notable exception of the small acidic subunit Sem1. Here, we localize the C-terminal helix of Sem1 binding to the PCI domain of the subunit Rpn7 using cryo-electron microscopy single particle reconstruction of proteasomes purified from yeast cells with sem1 deletion. The approximate position of the N-terminal region of Sem1 bridging the cleft between Rpn7 and Rpn3 was inferred based on site-specific cross-linking data of the 26S proteasome. Our structural studies indicate that Sem1 can assume different conformations in different contexts, which supports the idea that Sem1 functions as a molecular glue stabilizing the Rpn3/Rpn7 heterodimer.
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Affiliation(s)
- Stefan Bohn
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany
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35
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Williams RW, Xue B, Uversky VN, Dunker AK. Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25724. [PMID: 28516017 PMCID: PMC5424788 DOI: 10.4161/idp.25724] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/02/2013] [Accepted: 07/11/2013] [Indexed: 11/19/2022]
Abstract
The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1–3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information.
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Affiliation(s)
- Robert W Williams
- Department of Biomedical Informatics; Uniformed Services University; Bethesda, MD USA
| | - Bin Xue
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA
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36
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Bonache S, de la Hoya M, Gutierrez-Enriquez S, Tenés A, Masas M, Balmaña J, Diez O. Mutation analysis of the SHFM1 gene in breast/ovarian cancer families. J Cancer Res Clin Oncol 2013; 139:529-32. [DOI: 10.1007/s00432-013-1385-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/21/2013] [Indexed: 11/25/2022]
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37
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Velinov M, Ahmad A, Brown-Kipphut B, Shafiq M, Blau J, Cooma R, Roth P, Iqbal MA. A 0.7 Mb de novo duplication at 7q21.3 including the genes DLX5 and DLX6 in a patient with split-hand/split-foot malformation. Am J Med Genet A 2012; 158A:3201-6. [PMID: 23169702 DOI: 10.1002/ajmg.a.35644] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 08/08/2012] [Indexed: 12/13/2022]
Abstract
Split-hand/split-foot malformation (SHFM1) has been reported to be caused by deletions, duplications or rearrangements involving the 7q21.3 region harboring DSS1, DLX5, and DLX6. We report on a female patient with unilateral syndactyly of the third and fourth fingers of the right hand and overgrowth and lateral deviation of the right great toe. There was a split foot malformation on the right, with absent fifth toe. The left hand was apparently normal and left foot was intact. The patient has no hearing loss. We performed conventional G-banding karyotype analysis, array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). G-banding karyotype result was normal 46,XX. However, a duplication of 719 kb (96,303,736-97,022,335; NCBI build36/hg18, March 2006) was identified at the 7q21.3 region by aCGH. The array result was also confirmed by FISH analysis. The duplicated region harbors only DLX5 and DLX6, which are known for their role in SHFM1. Additionally, FISH analysis of parental samples showed de novo origin of this abnormality in the patient. This is the first report that highlights the duplication of 719 kb at 7q21.3, harboring only DLX5 and DLX6 associated with the SHFM1 phenotype.
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Affiliation(s)
- Milen Velinov
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
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38
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Ma YY, Lin H, Chang FM, Chang TC, Trieu T, Pridgen HI, Zhang Y, Huang J, Patiño-Guzman K, Diab N, Cantu A, Slaga TJ, Wei SJ. Identification of the deleted in split hand/split foot 1 protein as a novel biomarker for human cervical cancer. Carcinogenesis 2012; 34:68-78. [PMID: 23024267 DOI: 10.1093/carcin/bgs279] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The morphological detection of early neoplastic transformation leading to cervical cancer remains problematic. In this work, we have identified deleted in split hand/split foot 1 protein (DSS1) as an early biomarker that is specifically upregulated in premalignant and malignant cervical epithelial cells, but is low or undetectable in non-malignant cells. DSS1 mRNA and protein levels are significantly increased in cultured human cervical carcinoma cell lines originating from primary and metastatic tumors. In fact, > 96% of patient tumor tissues were found to have cells with elevated DSS1 when compared with tumor-adjacent normal cells. In histological sections of cervical tissue containing either invasive cervical carcinoma or its precursor lesions, DSS1 was readily detected in the tumor cells. Steady-state DSS1 expression by immortalized cervical cancer cell lines was found to be necessary for maintenance of their transformed phenotype, since stable shRNA-mediated depletion of DSS1 in HeLa cells inhibited their proliferation and colony-forming activity in monolayer cultures and prevented division of these cells in soft agar. When DSS1 levels are reduced using shRNA, the cells ultimately undergo apoptosis via activation of p53 and the p53 downstream targets, and cleavage of apoptosis-associated proteins including CPP32/caspase-3, poly(ADP-ribose)polymerase and DNA-PKcs. In addition, silencing of DSS1 makes cervical cancer cells sensitive to cell death after treatment with cisplatin. We conclude that the DSS1 protein is critically involved in the maintenance of the transformed phenotype in cervical cancer cells, and that it might be a specific, robust and reliable marker for early detection, diagnosis and treatment.
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Affiliation(s)
- Yen-Ying Ma
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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39
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Zarnegar BJ, Webster DE, Lopez-Pajares V, Vander Stoep Hunt B, Qu K, Yan KJ, Berk DR, Sen GL, Khavari PA. Genomic profiling of a human organotypic model of AEC syndrome reveals ZNF750 as an essential downstream target of mutant TP63. Am J Hum Genet 2012; 91:435-43. [PMID: 22922031 DOI: 10.1016/j.ajhg.2012.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/06/2012] [Accepted: 07/09/2012] [Indexed: 11/16/2022] Open
Abstract
The basis for impaired differentiation in TP63 mutant ankyloblepharon-ectodermal dysplasia-clefting (AEC) syndrome is unknown. Human epidermis harboring AEC TP63 mutants recapitulated this impairment, along with downregulation of differentiation activators, including HOPX, GRHL3, KLF4, PRDM1, and ZNF750. Gene-set enrichment analysis indicated that disrupted expression of epidermal differentiation programs under the control of ZNF750 and KLF4 accounted for the majority of disrupted epidermal differentiation resulting from AEC mutant TP63. Chromatin immunoprecipitation (ChIP) analysis and ChIP-sequencing of TP63 binding in differentiated keratinocytes revealed ZNF750 as a direct target of wild-type and AEC mutant TP63. Restoring ZNF750 to AEC model tissue rescued activator expression and differentiation, indicating that AEC TP63-mediated ZNF750 inhibition contributes to differentiation defects in AEC. Incorporating disease-causing mutants into regenerated human tissue can thus dissect pathomechanisms and identify targets that reverse disease features.
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Affiliation(s)
- Brian J Zarnegar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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40
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Birnbaum RY, Everman DB, Murphy KK, Gurrieri F, Schwartz CE, Ahituv N. Functional characterization of tissue-specific enhancers in the DLX5/6 locus. Hum Mol Genet 2012; 21:4930-8. [PMID: 22914741 DOI: 10.1093/hmg/dds336] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Disruption of distaless homeobox 5 and 6 (Dlx5/6) in mice results in brain, craniofacial, genital, ear and limb defects. In humans, chromosomal aberrations in the DLX5/6 region, some of which do not encompass DLX5/6, are associated with split hand/foot malformation 1 (SHFM1) as well as intellectual disability, craniofacial anomalies and hearing loss, suggesting that the disruption of DLX5/6 regulatory elements could lead to these abnormalities. Here, we characterized enhancers in the DLX5/6 locus whose tissue-specific expression and genomic location along with previously characterized enhancers correlate with phenotypes observed in individuals with chromosomal abnormalities. By analyzing chromosomal aberrations at 7q21, we refined the minimal SHFM1 critical region and used comparative genomics to select 26 evolutionary conserved non-coding sequences in this critical region for zebrafish enhancer assays. Eight of these sequences were shown to function as brain, olfactory bulb, branchial arch, otic vesicle and fin enhancers, recapitulating dlx5a/6a expression. Using a mouse enhancer assay, several of these zebrafish enhancers showed comparable expression patterns in the branchial arch, otic vesicle, forebrain and/or limb at embryonic day 11.5. Examination of the coordinates of various chromosomal rearrangements in conjunction with the genomic location of these tissue-specific enhancers showed a correlation with the observed clinical abnormalities. Our findings suggest that chromosomal abnormalities that disrupt the function of these tissue-specific enhancers could be the cause of SHFM1 and its associated phenotypes. In addition, they highlight specific enhancers in which mutations could lead to non-syndromic hearing loss, craniofacial defects or limb malformations.
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Affiliation(s)
- Ramon Y Birnbaum
- Department of Bioengineering and Therapeutic Sciences and 2Institute for Human Genetics, University of California-San Francisco, CA, USA
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41
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Vera-Carbonell A, Moya-Quiles MR, Ballesta-Martínez M, López-González V, Bafallíu JA, Guillén-Navarro E, López-Expósito I. Rapp–Hodgkin syndrome and SHFM1 patients: Delineating the p63–Dlx5/Dlx6 pathway. Gene 2012; 497:292-7. [DOI: 10.1016/j.gene.2012.01.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 01/27/2012] [Accepted: 01/29/2012] [Indexed: 11/29/2022]
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Caburet S, Zavadakova P, Ben-Neriah Z, Bouhali K, Dipietromaria A, Charon C, Besse C, Laissue P, Chalifa-Caspi V, Christin-Maitre S, Vaiman D, Levi G, Veitia RA, Fellous M. Genome-wide linkage in a highly consanguineous pedigree reveals two novel loci on chromosome 7 for non-syndromic familial Premature Ovarian Failure. PLoS One 2012; 7:e33412. [PMID: 22428046 PMCID: PMC3302824 DOI: 10.1371/journal.pone.0033412] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 02/08/2012] [Indexed: 01/08/2023] Open
Abstract
Background The human condition known as Premature Ovarian Failure (POF) is characterized by loss of ovarian function before the age of 40. A majority of POF cases are sporadic, but 10–15% are familial, suggesting a genetic origin of the disease. Although several causal mutations have been identified, the etiology of POF is still unknown for about 90% of the patients. Methodology/Principal Findings We report a genome-wide linkage and homozygosity analysis in one large consanguineous Middle-Eastern POF-affected family presenting an autosomal recessive pattern of inheritance. We identified two regions with a LODmax of 3.26 on chromosome 7p21.1-15.3 and 7q21.3-22.2, which are supported as candidate regions by homozygosity mapping. Sequencing of the coding exons and known regulatory sequences of three candidate genes (DLX5, DLX6 and DSS1) included within the largest region did not reveal any causal mutations. Conclusions/Significance We detect two novel POF-associated loci on human chromosome 7, opening the way to the identification of new genes involved in the control of ovarian development and function.
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Affiliation(s)
- Sandrine Caburet
- Institut Jacques Monod, Université Denis Diderot, CNRS UMR7592, Paris, France
- Université Paris Diderot-Paris VII, Paris, France
- * E-mail: (SC); (MF)
| | - Petra Zavadakova
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Ziva Ben-Neriah
- Department of Genetics, Hadassah University Hospital, Jerusalem, Israel
| | - Kamal Bouhali
- Évolution des Régulations Endocriniennes, CNRS UMR7221, Muséum National d'Histoire Naturelle, Paris, France
| | - Aurélie Dipietromaria
- Évolution des Régulations Endocriniennes, CNRS UMR7221, Muséum National d'Histoire Naturelle, Paris, France
| | | | | | - Paul Laissue
- Institut Cochin, Université Paris Descartes, CNRS UMR 8104, Paris, France
- Inserm, U1016, Paris, France
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sophie Christin-Maitre
- Inserm U933 Génétique de la Reproduction, Service d'Endocrinologie de la Reproduction, Hôpital Saint-Antoine, Université Pierre-et-Marie-Curie, Paris, France
| | - Daniel Vaiman
- Institut Cochin, Université Paris Descartes, CNRS UMR 8104, Paris, France
- Inserm, U1016, Paris, France
| | - Giovanni Levi
- Évolution des Régulations Endocriniennes, CNRS UMR7221, Muséum National d'Histoire Naturelle, Paris, France
| | - Reiner A. Veitia
- Institut Jacques Monod, Université Denis Diderot, CNRS UMR7592, Paris, France
- Université Paris Diderot-Paris VII, Paris, France
| | - Marc Fellous
- Institut Cochin, Université Paris Descartes, CNRS UMR 8104, Paris, France
- Inserm, U1016, Paris, France
- * E-mail: (SC); (MF)
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Trapp O, Seeliger K, Puchta H. Homologs of breast cancer genes in plants. FRONTIERS IN PLANT SCIENCE 2011; 2:19. [PMID: 22629260 PMCID: PMC3355568 DOI: 10.3389/fpls.2011.00019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/02/2011] [Indexed: 05/22/2023]
Abstract
Since the initial discovery of genes involved in hereditary breast cancer in humans, a vast wealth of information has been published. Breast cancer proteins were shown to work as tumor suppressors primarily through their involvement in DNA-damage repair. Surprisingly, homologs of these genes can be found in plant genomes, as well. Here, we want to give an overview of the identification and characterization of the biological roles of these proteins, in plants. In addition to the conservation of their function in DNA repair, new plant-specific characteristics have been revealed. BRCA1 is required for the efficient repair of double strand breaks (DSB) by homologous recombination in somatic cells of the model plant Arabidopsis thaliana. Bioinformatic analysis indicates that, whereas most homologs of key components of the different mammalian BRCA1 complexes are present in plant genomes, homologs of most factors involved in the recruitment of BRCA1 to the DSB cannot be identified. Thus, it is not clear at the moment whether differences exist between plants and animals at this important step. The most conserved region of BRCA1 and BARD1 homologs in plants is a PHD domain which is absent in mammals and which, in AtBARD1, might be involved in the transcriptional regulation of plant development. The presence of a plant-specific domain prompted us to reevaluate the current model for the evolution of BRCA1 homologs and to suggest a new hypothesis, in which we postulate that plant BRCA1 and BARD1 have one common predecessor that gained a PHD domain before duplication. Furthermore, work in Arabidopsis demonstrates that - as in animals - BRCA2 homologs are important for meiotic DNA recombination. Surprisingly, recent research has revealed that AtBRCA2 also has an important role in systemic acquired resistance. In Arabidopsis, BRCA2 is involved in the transcriptional regulation of pathogenesis-related (PR) genes via its interaction with the strand exchange protein RAD51.
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Affiliation(s)
- Oliver Trapp
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
| | - Katharina Seeliger
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
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Obenauf AC, Schwarzbraun T, Auer M, Hoffmann EM, Waldispuehl-Geigl J, Ulz P, Günther B, Duba HC, Speicher MR, Geigl JB. Mapping of balanced chromosome translocation breakpoints to the basepair level from microdissected chromosomes. J Cell Mol Med 2011; 14:2078-84. [PMID: 20597996 PMCID: PMC3822999 DOI: 10.1111/j.1582-4934.2010.01116.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes. There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome. Here we demonstrate that we have advanced both the microdissection and the subsequent unbiased amplification to an extent that breakpoint mapping to the basepair level has become possible. As a case in point we analysed the two breakpoints of a t(7;13) translocation observed in a patient with split hand/foot malformation (SHFM1). The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level. Consequently, our results will also contribute to a further delineation of causative mechanisms underlying SHFM1 which are currently unknown.
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Affiliation(s)
- Anna C Obenauf
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
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45
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Hall M, Misra S, Chaudhuri M, Chaudhuri G. Peptide aptamer mimicking RAD51-binding domain of BRCA2 inhibits DNA damage repair and survival in Trypanosoma brucei. Microb Pathog 2011; 50:252-62. [PMID: 21296653 DOI: 10.1016/j.micpath.2010.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Revised: 11/26/2010] [Accepted: 11/30/2010] [Indexed: 10/18/2022]
Abstract
The eukaryotic DNA recombination repair protein BRCA2 is functional in the parasitic protozoan Trypanosoma brucei. The mechanism of the involvement of BRCA2 in homologous recombination includes its interaction with the DNA recombinase proteins of the RAD51 family. BRCA2 is known to interact with RAD51 through its unique and essential BRC sequence motifs. T. brucei BRCA2 homolog (TbBRCA2) has fifteen repeating BRC motifs as compared to mammalian BRCA2 that has only eight. We report here our yeast 2-hybrid analysis studies on the interactions of TbBRCA2 BRC motifs with five different RAD51 paralogues of T. brucei. Our study revealed that a single BRC motif is sufficient to bind to these RAD51 paralogues. To test the possibility whether a single 44 amino acid long repeating unit of the TbBRCA2 BRC motif may be exploited as an inhibitor of T. brucei growth, we ectopically expressed this peptide segment in the procyclic form of the parasite and evaluated its effects on cell survival as well as the sensitivity of these cells to the DNA damaging agent methyl methane sulfonate (MMS). Expression of a single BRC motif led to MMS sensitivity and inhibited cellular proliferation in T. brucei.
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Affiliation(s)
- Mack Hall
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN 37208, USA
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46
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Drozdov I, Tsoka S, Ouzounis CA, Shah AM. Genome-wide expression patterns in physiological cardiac hypertrophy. BMC Genomics 2010; 11:557. [PMID: 20937113 PMCID: PMC3091706 DOI: 10.1186/1471-2164-11-557] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Accepted: 10/11/2010] [Indexed: 01/28/2023] Open
Abstract
Background Genome-wide expression patterns in physiological cardiac hypertrophy. Co-expression patterns in physiological cardiac hypertrophy Results In this study, the first large-scale analysis of publicly available genome-wide expression data of several in vivo murine models of physiological LVH was carried out using network analysis. On evaluating 3 million gene co-expression patterns across 141 relevant microarray experiments, it was found that physiological adaptation is an evolutionarily conserved processes involving preservation of the function of cytochrome c oxidase, induction of autophagy compatible with cell survival, and coordinated regulation of angiogenesis. Conclusion This analysis not only identifies known biological pathways involved in physiological LVH, but also offers novel insights into the molecular basis of this phenotype by identifying key networks of co-expressed genes, as well as their topological and functional properties, using relevant high-quality microarray experiments and network inference.
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Affiliation(s)
- Ignat Drozdov
- King's College London (KCL) BHF Centre of Research Excellence - Cardiovascular Division - School of Medicine - James Black Centre - 125 Coldharbour Lane, London, UK
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47
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Hung T, Chang HY. Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol 2010; 7:582-5. [PMID: 20930520 DOI: 10.4161/rna.7.5.13216] [Citation(s) in RCA: 444] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are pervasively transcribed and critical regulators of the epigenome[1, 2]. These long, polyadenylated RNAs do not code for proteins, but function directly as RNAs, recruiting chromatin modifiers to mediate transcriptional changes in processes ranging from X-inactivation (XIST) to imprinting (H19)[3]. The recent discovery that lncRNA HOTAIR can link chromatin changes to cancer metastasis[4] furthers the relevance of lncRNAs to human disease. Here, we discuss lncRNAs as regulatory modules and explore the implications for disease pathogenesis. Although large-scale analyses of mammalian transcriptomes have revealed that more than 50% of transcripts have no protein coding potential[2, 5, 6], the functions of these putative transcripts are largely unknown. A subset of these noncoding transcripts are termed long noncoding RNAs (lncRNAs), based on an arbitrary minimum length of 200 nucleotides. LncRNAs are roughly classified based on their position relative to protein-coding genes: intergenic (between genes), intragenic/intronic (within genes), and antisense[2]. Initial efforts to characterize these molecules demonstrated that they function in cis, regulating their immediate genomic neighbors. Examples include AIR, XIST, and Kcnq1ot (reviewed in [1, 7, 8]), which recruit chromatin modifying complexes to silence adjacent sites. The scope of lncRNAs in gene regulation was advanced with the finding that lncRNA HOTAIR exhibited trans regulatory capacities. HOTAIR is transcribed at the intersection of opposing chromatin domains in the HOXC locus, but targets Polycomb Repressive Complex 2 (PRC2) to silence 40 kilobases of HOXD[9], a locus involved in developmental patterning. A subsequent study revealed that HOTAIR is overexpressed in approximately one quarter of human breast cancers, directing PRC2 to approximately 800 ectopic sites in the genome, which leads to histone H3 lysine 27 trimethylation and changes in gene expression[4]. The impacts of lncRNA-mediated chromatin changes are noteworthy: not only did HOTAIR drive metastasis in a mouse model, but HOTAIR expression in human breast cancer was found to be an independent prognostic marker for death and metastasis[4]. The fact that HOTAIR drives chromatin reprogramming genome-wide suggests that long-range regulation by lncRNAs may be a widespread mechanism. This is supported by a study showing that > 20% of tested lncRNAs are bound by PRC2 and other chromatin modifiers[10]. Furthermore, this is an underestimate of the total RNAs involved in chromatin modification, as PRC2 target genes also transcribe smaller 50-200 nt RNAs that interact with SUZ12 to mediate gene repression[11]. These findings provoke questions regarding the initial triggers for HOTAIR overexpression and whether understanding of lncRNA mechanics may have clinical relevance.
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Affiliation(s)
- Tiffany Hung
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
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48
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Kouwenhoven EN, van Heeringen SJ, Tena JJ, Oti M, Dutilh BE, Alonso ME, de la Calle-Mustienes E, Smeenk L, Rinne T, Parsaulian L, Bolat E, Jurgelenaite R, Huynen MA, Hoischen A, Veltman JA, Brunner HG, Roscioli T, Oates E, Wilson M, Manzanares M, Gómez-Skarmeta JL, Stunnenberg HG, Lohrum M, van Bokhoven H, Zhou H. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. PLoS Genet 2010; 6:e1001065. [PMID: 20808887 PMCID: PMC2924305 DOI: 10.1371/journal.pgen.1001065] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 07/12/2010] [Indexed: 12/04/2022] Open
Abstract
Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM), orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders. We performed genome-wide DNA–binding profiling by chromatin immunoprecipitation (ChIP), followed by deep sequencing (ChIP–seq) in primary human keratinocytes, and identified potential target genes and regulatory elements controlled by p63. We show that p63 binds to an enhancer element in the SHFM1 locus on chromosome 7q and that this element controls expression of DLX6 and possibly DLX5, both of which are important for limb development. A unique micro-deletion including this enhancer element, but not the DLX5/DLX6 genes, was identified in a patient with SHFM. Our study strongly indicates disruption of a non-coding cis-regulatory element located more than 250 kb from the DLX5/DLX6 genes as a novel disease mechanism in SHFM1. These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes. Mammalian embryonic development requires precise control of gene expression in the right place at the right time. One level of control of gene expression is through cis-regulatory elements controlled by transcription factors. Deregulation of gene expression by mutations in such cis-regulatory elements has been described in developmental disorders. Heterozygous mutations in the transcription factor p63 are found in patients with limb malformations, cleft lip/palate, and defects in skin and other epidermal appendages, through disruption of normal ectodermal development during embryogenesis. We reasoned that the identification of target genes and cis-regulatory elements controlled by p63 would provide candidate genes for defects arising from abnormally regulated ectodermal development. To test our hypothesis, we carried out a genome-wide binding site analysis and identified a large number of target genes and regulatory elements regulated by p63. We further showed that one of these regulatory elements controls expression of DLX6 and possibly DLX5 in the apical ectodermal ridge in the developing limbs. Loss of this element through a micro-deletion was associated with split hand foot malformation (SHFM1). The list of p63 binding sites provides a resource for the identification of mutations that cause ectodermal dysplasias and malformations in humans.
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MESH Headings
- Animals
- Base Sequence
- Binding Sites
- Cells, Cultured
- Child, Preschool
- Chromatin Immunoprecipitation
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Enhancer Elements, Genetic
- Female
- Gene Expression Regulation, Developmental
- Genome-Wide Association Study
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Keratinocytes/metabolism
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/metabolism
- Male
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Molecular Sequence Data
- Proteasome Endopeptidase Complex/genetics
- Proteasome Endopeptidase Complex/metabolism
- Protein Binding
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Zebrafish
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Affiliation(s)
- Evelyn N. Kouwenhoven
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Simon J. van Heeringen
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Martin Oti
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bas E. Dutilh
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - M. Eva Alonso
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Leonie Smeenk
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Lilian Parsaulian
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Emine Bolat
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Rasa Jurgelenaite
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Tony Roscioli
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Emily Oates
- Department of Clinical Genetics, Children's Hospital at Westmead, Westmead, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Westmead, Australia
| | - Miguel Manzanares
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marion Lohrum
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail: (HZ); (HvB)
| | - Huiqing Zhou
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail: (HZ); (HvB)
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Chatterjee S, Kraus P, Lufkin T. A symphony of inner ear developmental control genes. BMC Genet 2010; 11:68. [PMID: 20637105 PMCID: PMC2915946 DOI: 10.1186/1471-2156-11-68] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 07/16/2010] [Indexed: 01/21/2023] Open
Abstract
The inner ear is one of the most complex and detailed organs in the vertebrate body and provides us with the priceless ability to hear and perceive linear and angular acceleration (hence maintain balance). The development and morphogenesis of the inner ear from an ectodermal thickening into distinct auditory and vestibular components depends upon precise temporally and spatially coordinated gene expression patterns and well orchestrated signaling cascades within the otic vesicle and upon cellular movements and interactions with surrounding tissues. Gene loss of function analysis in mice has identified homeobox genes along with other transcription and secreted factors as crucial regulators of inner ear morphogenesis and development. While otic induction seems dependent upon fibroblast growth factors, morphogenesis of the otic vesicle into the distinct vestibular and auditory components appears to be clearly dependent upon the activities of a number of homeobox transcription factors. The Pax2 paired-homeobox gene is crucial for the specification of the ventral otic vesicle derived auditory structures and the Dlx5 and Dlx6 homeobox genes play a major role in specification of the dorsally derived vestibular structures. Some Micro RNAs have also been recently identified which play a crucial role in the inner ear formation.
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Affiliation(s)
- Sumantra Chatterjee
- Stem Cell and Developmental Biology, Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore
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50
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Cortajarena AL, Liu TY, Hochstrasser M, Regan L. Designed proteins to modulate cellular networks. ACS Chem Biol 2010; 5:545-52. [PMID: 20020775 DOI: 10.1021/cb9002464] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major challenge of protein design is to create useful new proteins that interact specifically with biological targets in living cells. Such binding modules have many potential applications, including the targeted perturbation of protein networks. As a general approach to create such modules, we designed a library with approximately 10(9) different binding specificities based on a small 3-tetratricopeptide repeat (TPR) motif framework. We employed a novel strategy, based on split GFP reassembly, to screen the library for modules with the desired binding specificity. Using this approach, we identified modules that bind tightly and specifically to Dss1, a small human protein that interacts with the tumor suppressor protein BRCA2. We showed that these modules also bind the yeast homologue of Dss1, Sem1. Furthermore, we demonstrated that these modules inhibit Sem1 activity in yeast. This strategy will be generally applicable to make novel genetically encoded tools for systems/synthetic biology applications.
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Affiliation(s)
| | - Tina Y. Liu
- Department of Molecular Biophysics & Biochemistry
| | | | - Lynne Regan
- Department of Molecular Biophysics & Biochemistry
- Department of Chemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520
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