1
|
Cova G, Glaser J, Schöpflin R, Prada-Medina CA, Ali S, Franke M, Falcone R, Federer M, Ponzi E, Ficarella R, Novara F, Wittler L, Timmermann B, Gentile M, Zuffardi O, Spielmann M, Mundlos S. Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3. Nat Commun 2023; 14:1475. [PMID: 36928426 PMCID: PMC10020157 DOI: 10.1038/s41467-023-37057-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Split-Hand/Foot Malformation type 3 (SHFM3) is a congenital limb malformation associated with tandem duplications at the LBX1/FGF8 locus. Yet, the disease patho-mechanism remains unsolved. Here we investigate the functional consequences of SHFM3-associated rearrangements on chromatin conformation and gene expression in vivo in transgenic mice. We show that the Lbx1/Fgf8 locus consists of two separate, but interacting, regulatory domains. Re-engineering of a SHFM3-associated duplication and a newly reported inversion in mice results in restructuring of the chromatin architecture. This leads to ectopic activation of the Lbx1 and Btrc genes in the apical ectodermal ridge (AER) in an Fgf8-like pattern induced by AER-specific enhancers of Fgf8. We provide evidence that the SHFM3 phenotype is the result of a combinatorial effect on gene misexpression in the developing limb. Our results reveal insights into the molecular mechanism underlying SHFM3 and provide conceptual framework for how genomic rearrangements can cause gene misexpression and disease.
Collapse
Affiliation(s)
- Giulia Cova
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Department of Pathology, New York University School of Medicine, Langone Health Medical Center, New York, NY, 10016, USA.
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Cesar Augusto Prada-Medina
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Salaheddine Ali
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Rita Falcone
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Miriam Federer
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Universität Innsbruck, Innsbruck, 6020, Austria
| | - Emanuela Ponzi
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Romina Ficarella
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | | | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Mattia Gentile
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, 27100, Italy
| | - Malte Spielmann
- Institute of Human Genetics, Universitätsklinikum Schleswig Holstein Campus Kiel and Christian-Albrechts-Universität, Kiel, 24118, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, 13353, Germany.
| |
Collapse
|
2
|
Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:v12080810. [PMID: 32727076 PMCID: PMC7472028 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
Collapse
|
3
|
Han Q, Zhang Q, Song H, Bamme Y, Song C, Ge Z. FBXW4 Is Highly Expressed and Associated With Poor Survival in Acute Myeloid Leukemia. Front Oncol 2020; 10:149. [PMID: 32175272 PMCID: PMC7056870 DOI: 10.3389/fonc.2020.00149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/28/2020] [Indexed: 12/12/2022] Open
Abstract
The F-box and WD repeat domain-containing (FBXW) proteins play an important role in ubiquitin proteasome by inducing protein degradation. Ten FBXW proteins have been identified in humans. The functions of FBXW proteins, like FBXW7, have been well-established in many human cancers. However, little is known about their transcriptional expression profiles and relationship with prognosis in acute myeloid leukemia (AML). Here we investigated the roles of FBXW proteins in AML by analyzing their mRNA expression profiles and association with clinical features using data from EMBL-EBI, the Cancer Cell Line Encyclopedia, Gene Expression Profiling Interactive Analysis, and cBioPortal databases. Our results showed that the mRNA level of FBXW proteins were highly detected by microarray in 14 AML cell lines, although there were no obvious differences. The expression of FBXW4 was significantly higher in AML patients compared with that in normal controls (P < 0.01). Patients whose age was ≥60 years old had a higher FBXW4 expression when compared with those who were <60 years old (P < 0.05). Cytogenetic favorable-risk group patients had a much lower FBXW4 expression than the intermediate- and poor-risk group patients (P < 0.0001). Moreover, patients with high FBXW4 expression exhibited significantly shorter event-free survival (EFS) and overall survival (OS) than those with low FBXW4 expression (median EFS: 5.3 vs. 10.0 months, P = 0.025; median OS: 8.1 vs. 19.0 months, P= 0.015). A multivariate analysis indicated that high FBXW4 expression was an independent risk factor for poor EFS in AML patients who received intensive chemotherapy followed by allo-SCT. In summary, our data suggested that FBXW4 is aberrantly expressed in AML and high FBXW4 expression might be a poor prognostic biomarker; future functional and mechanistic studies will further illuminate the roles of FBXW4 in AML.
Collapse
Affiliation(s)
- Qi Han
- Department of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Institute of Hematology Southeast University, Nanjing, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Qi Zhang
- Department of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Institute of Hematology Southeast University, Nanjing, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Huihui Song
- Department of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Institute of Hematology Southeast University, Nanjing, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Yevgeniya Bamme
- Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA, United States
| | - Chunhua Song
- International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China.,Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA, United States
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Institute of Hematology Southeast University, Nanjing, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| |
Collapse
|
4
|
Gagnier L, Belancio VP, Mager DL. Mouse germ line mutations due to retrotransposon insertions. Mob DNA 2019; 10:15. [PMID: 31011371 PMCID: PMC6466679 DOI: 10.1186/s13100-019-0157-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
Collapse
Affiliation(s)
- Liane Gagnier
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L. Mager
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| |
Collapse
|
5
|
Holder-Espinasse M, Jamsheer A, Escande F, Andrieux J, Petit F, Sowinska-Seidler A, Socha M, Jakubiuk-Tomaszuk A, Gerard M, Mathieu-Dramard M, Cormier-Daire V, Verloes A, Toutain A, Plessis G, Jonveaux P, Baumann C, David A, Farra C, Colin E, Jacquemont S, Rossi A, Mansour S, Ghali N, Moncla A, Lahiri N, Hurst J, Pollina E, Patch C, Ahn JW, Valat AS, Mezel A, Bourgeot P, Zhang D, Manouvrier-Hanu S. Duplication of 10q24 locus: broadening the clinical and radiological spectrum. Eur J Hum Genet 2019; 27:525-534. [PMID: 30622331 PMCID: PMC6460637 DOI: 10.1038/s41431-018-0326-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/25/2017] [Accepted: 12/04/2018] [Indexed: 01/21/2023] Open
Abstract
Split-hand-split-foot malformation (SHFM) is a rare condition that occurs in 1 in 8500-25,000 newborns and accounts for 15% of all limb reduction defects. SHFM is heterogeneous and can be isolated, associated with other malformations, or syndromic. The mode of inheritance is mostly autosomal dominant with incomplete penetrance, but can be X-linked or autosomal recessive. Seven loci are currently known: SHFM1 at 7q21.2q22.1 (DLX5 gene), SHFM2 at Xq26, SHFM3 at 10q24q25, SHFM4 at 3q27 (TP63 gene), SHFM5 at 2q31 and SHFM6 as a result of variants in WNT10B (chromosome 12q13). Duplications at 17p13.3 are seen in SHFM when isolated or associated with long bone deficiency. Tandem genomic duplications at chromosome 10q24 involving at least the DACTYLIN gene are associated with SHFM3. No point variant in any of the genes residing within the region has been identified so far, but duplication of exon 1 of the BTRC gene may explain the phenotype, with likely complex alterations of gene regulation mechanisms that would impair limb morphogenesis. We report on 32 new index cases identified by array-CGH and/or by qPCR, including some prenatal ones, leading to termination for the most severe. Twenty-two cases were presenting with SHFM and 7 with monodactyly only. Three had an overlapping phenotype. Additional findings were identified in 5 (renal dysplasia, cutis aplasia, hypogonadism and agenesis of corpus callosum with hydrocephalus). We present their clinical and radiological findings and review the literature on this rearrangement that seems to be one of the most frequent cause of SHFM.
Collapse
MESH Headings
- Adult
- Child, Preschool
- Chromosomes, Human, Pair 10/genetics
- Comparative Genomic Hybridization/methods
- F-Box Proteins/genetics
- Female
- Gene Rearrangement/genetics
- Genetic Predisposition to Disease
- Hand Deformities, Congenital/diagnostic imaging
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/physiopathology
- Humans
- Infant
- Limb Deformities, Congenital/diagnostic imaging
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/physiopathology
- Male
- Pedigree
- Phenotype
- Proteasome Endopeptidase Complex/genetics
- Proto-Oncogene Proteins/genetics
- Radiography
- Segmental Duplications, Genomic/genetics
- Wnt Proteins/genetics
- Young Adult
Collapse
Affiliation(s)
| | - Aleksander Jamsheer
- Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Fabienne Escande
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille, France
- RADEME, EA 7364, Lille University, Lille, France
| | - Joris Andrieux
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille, France
| | - Florence Petit
- RADEME, EA 7364, Lille University, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| | | | - Magdalena Socha
- Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Anna Jakubiuk-Tomaszuk
- Department of Pediatric Neurology and Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | | | | | | | - Alain Verloes
- Service de Génétique, Hôpital Robert Debré, Paris, France
| | | | | | | | | | - Albert David
- Service de Génétique, CHU Nantes, Nantes, France
| | - Chantal Farra
- American University of Beirut Medical Centre, Beirut, Lebanon
| | | | - Sébastien Jacquemont
- Department of Paediatrics, Faculty of Medicine, University of Montréal, Montreal, Canada
| | - Annick Rossi
- Laboratoire de Cytogénétique, EFS Normandie, Bois Guillaume, France
| | | | - Neeti Ghali
- North West Thames Regional Genetics Service, Harrow, UK
| | - Anne Moncla
- Laboratoire de Génétique Chromosomique, CHU Marseille, Marseille, France
| | | | - Jane Hurst
- Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Elena Pollina
- Pathology Department, Queen Elizabeth Hospital, Woolwich, UK
| | | | - Joo Wook Ahn
- Genetics Laboratories, Guy's Hospital, London, UK
| | - Anne-Sylvie Valat
- Centre Pluridisciplinaire de Diagnostic Prénatal, CHRU Lille, Lille, France
| | - Aurélie Mezel
- Service de Chirurgie Orthopédique, CHRU Lille, Lille, France
| | - Philippe Bourgeot
- Centre Pluridisciplinaire de Diagnostic Prénatal, CHRU Lille, Lille, France
| | - David Zhang
- Institute of Neurology, University College London, London, UK
| | - Sylvie Manouvrier-Hanu
- RADEME, EA 7364, Lille University, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Friedli M, Trono D. The developmental control of transposable elements and the evolution of higher species. Annu Rev Cell Dev Biol 2015; 31:429-51. [PMID: 26393776 DOI: 10.1146/annurev-cellbio-100814-125514] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transposable elements (TEs) account for at least 50% of the human genome. They constitute essential motors of evolution through their ability to modify genomic architecture, mutate genes and regulate gene expression. Accordingly, TEs are subject to tight epigenetic control during the earliest phases of embryonic development via histone and DNA methylation. Key to this process is recognition by sequence-specific RNA- and protein-based repressors. Collectively, these mediators are responsible for silencing a very broad range of TEs in an evolutionarily dynamic fashion. As a consequence, mobile elements and their controllers exert a marked influence on transcriptional networks in embryonic stem cells and a variety of adult tissues. The emerging picture is not that of a simple arms race but rather of a massive and sophisticated enterprise of TE domestication for the evolutionary benefit of the host.
Collapse
Affiliation(s)
- Marc Friedli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; ,
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; ,
| |
Collapse
|
8
|
Sp6 and Sp8 transcription factors control AER formation and dorsal-ventral patterning in limb development. PLoS Genet 2014; 10:e1004468. [PMID: 25166858 PMCID: PMC4148220 DOI: 10.1371/journal.pgen.1004468] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 05/14/2014] [Indexed: 12/27/2022] Open
Abstract
The formation and maintenance of the apical ectodermal ridge (AER) is critical for the outgrowth and patterning of the vertebrate limb. The induction of the AER is a complex process that relies on integrated interactions among the Fgf, Wnt, and Bmp signaling pathways that operate within the ectoderm and between the ectoderm and the mesoderm of the early limb bud. The transcription factors Sp6 and Sp8 are expressed in the limb ectoderm and AER during limb development. Sp6 mutant mice display a mild syndactyly phenotype while Sp8 mutants exhibit severe limb truncations. Both mutants show defects in AER maturation and in dorsal-ventral patterning. To gain further insights into the role Sp6 and Sp8 play in limb development, we have produced mice lacking both Sp6 and Sp8 activity in the limb ectoderm. Remarkably, the elimination or significant reduction in Sp6;Sp8 gene dosage leads to tetra-amelia; initial budding occurs, but neither Fgf8 nor En1 are activated. Mutants bearing a single functional allele of Sp8 (Sp6−/−;Sp8+/−) exhibit a split-hand/foot malformation phenotype with double dorsal digit tips probably due to an irregular and immature AER that is not maintained in the center of the bud and on the abnormal expansion of Wnt7a expression to the ventral ectoderm. Our data are compatible with Sp6 and Sp8 working together and in a dose-dependent manner as indispensable mediators of Wnt/βcatenin and Bmp signaling in the limb ectoderm. We suggest that the function of these factors links proximal-distal and dorsal-ventral patterning. In this report we examined the functional roles of Sp6 and Sp8 during limb development using compound loss-of-function mutants. Sp6 and Sp8, two members of the Sp gene family, are expressed in the limb bud ectoderm and function downstream of WNT/βcatenin signaling for Fgf8 induction. The analysis of the allelic series shows that the progressive reduction in the dose of Sp6 and Sp8 gene products leads to predictable morphology, from syndactyly, to split hand/foot malformation, oligodactyly, truncation and finally amelia, indicating that these two factors act in a complementary manner. The molecular characterization of the mutant limbs reveal that Sp6/Sp8 are required in a dose-dependent manner for Fgf8 and En1 induction, thereby placing them as an important link between the induction of the AER and the establishment of dorsal-ventral patterning during limb development.
Collapse
|
9
|
Schwarzer W, Spitz F. The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains. Curr Opin Genet Dev 2014; 27:74-82. [PMID: 24907448 DOI: 10.1016/j.gde.2014.03.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 02/06/2023]
Abstract
Specificity and precision of expression are essential for the genes that regulate developmental processes. The specialized cis-acting modules, such as enhancers, that define gene expression patterns can be distributed across large regions, raising questions about the nature of the mechanisms that underline their action. Recent data has exposed the structural 3D context in which these long-range enhancers are operating. Here, we present how these studies shed new light on principles driving long-distance regulatory relationships. We discuss the molecular mechanisms that enable and accompany the action of long-range acting elements and the integration of multiple distributed regulatory inputs into the coherent and specific regulatory programs that are key to embryonic development.
Collapse
Affiliation(s)
- Wibke Schwarzer
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Fiorella Gurrieri
- Istituto di Genetica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | |
Collapse
|
12
|
Weischenfeldt J, Symmons O, Spitz F, Korbel JO. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet 2013; 14:125-38. [PMID: 23329113 DOI: 10.1038/nrg3373] [Citation(s) in RCA: 376] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genomic structural variants have long been implicated in phenotypic diversity and human disease, but dissecting the mechanisms by which they exert their functional impact has proven elusive. Recently however, developments in high-throughput DNA sequencing and chromosomal engineering technology have facilitated the analysis of structural variants in human populations and model systems in unprecedented detail. In this Review, we describe how structural variants can affect molecular and cellular processes, leading to complex organismal phenotypes, including human disease. We further present advances in delineating disease-causing elements that are affected by structural variants, and we discuss future directions for research on the functional consequences of structural variants.
Collapse
Affiliation(s)
- Joachim Weischenfeldt
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | | | | | | |
Collapse
|
13
|
Rowe HM, Friedli M, Offner S, Verp S, Mesnard D, Marquis J, Aktas T, Trono D. De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development 2013; 140:519-29. [PMID: 23293284 DOI: 10.1242/dev.087585] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Endogenous retroviruses (ERVs) undergo de novo DNA methylation during the first few days of mammalian embryogenesis, although the factors that control the targeting of this process are largely unknown. We asked whether KAP1 (KRAB-associated protein 1) is involved in this mechanism because of its previously defined role in maintaining the silencing of ERVs through the histone methyltransferase ESET and histone H3 lysine 9 trimethylation. Here, we demonstrate that introduced ERV sequences are sufficient to direct rapid de novo methylation of a flanked promoter in embryonic stem (ES) cells. This mechanism requires the presence of an ERV sequence-recognizing KRAB zinc-finger protein (ZFP) and both KAP1 and ESET. Furthermore, this process can also take place on a strong cellular promoter and leads to methylation signatures that are subsequently maintained in vivo throughout embryogenesis. Finally, we show that methylation of ERVs residing in the genome is affected by knockout of KAP1 in early embryos. KRAB-ZFPs, KAP1 and ESET are thus likely to be responsible for the early embryonic instatement of stable epigenetic marks at ERV-containing loci.
Collapse
Affiliation(s)
- Helen M Rowe
- School of Life Sciences and Frontiers in Genetics Program, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Marinić M, Aktas T, Ruf S, Spitz F. An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev Cell 2013; 24:530-42. [PMID: 23453598 DOI: 10.1016/j.devcel.2013.01.025] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 11/26/2012] [Accepted: 01/31/2013] [Indexed: 12/26/2022]
Abstract
Fgf8 encodes a key signaling factor, and its precise regulation is essential for embryo patterning. Here, we identified the regulatory modules that control Fgf8 expression during mammalian embryogenesis. These enhancers are interspersed with unrelated genes along a large region of 220 kb; yet they act on Fgf8 only. Intriguingly, this region also contains additional genuine enhancer activities that are not transformed into gene expression. Using genomic engineering strategies, we showed that these multiple and distinct regulatory modules act as a coherent unit and influence genes depending on their position rather than on their promoter sequence. These findings highlight how the structure of a locus regulates the autonomous intrinsic activities of the regulatory elements it contains and contributes to their tissue and target specificities. We discuss the implications of such regulatory systems regarding the evolution of gene expression and the impact of human genomic structural variations.
Collapse
Affiliation(s)
- Mirna Marinić
- Developmental Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | | | | | | |
Collapse
|
15
|
Vergult S, Hoogeboom AJM, Bijlsma EK, Sante T, Klopocki E, De Wilde B, Jongmans M, Thiel C, Verheij JBGM, Perez-Aytes A, Van Esch H, Kuechler A, Barge-Schaapveld DQCM, Sznajer Y, Mortier G, Menten B. Complex genetics of radial ray deficiencies: screening of a cohort of 54 patients. Genet Med 2012; 15:195-202. [DOI: 10.1038/gim.2012.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
|
16
|
Park JS, Ma W, O'Brien LL, Chung E, Guo JJ, Cheng JG, Valerius MT, McMahon JA, Wong WH, McMahon AP. Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks. Dev Cell 2012; 23:637-51. [PMID: 22902740 DOI: 10.1016/j.devcel.2012.07.008] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 05/24/2012] [Accepted: 07/15/2012] [Indexed: 01/09/2023]
Abstract
A balance between Six2-dependent self-renewal and canonical Wnt signaling-directed commitment regulates mammalian nephrogenesis. Intersectional studies using chromatin immunoprecipitation and transcriptional profiling identified direct target genes shared by each pathway within nephron progenitors. Wnt4 and Fgf8 are essential for progenitor commitment; cis-regulatory modules flanking each gene are cobound by Six2 and β-catenin and are dependent on conserved Lef/Tcf binding sites for activity. In vitro and in vivo analyses suggest that Six2 and Lef/Tcf factors form a regulatory complex that promotes progenitor maintenance while entry of β-catenin into this complex promotes nephrogenesis. Alternative transcriptional responses associated with Six2 and β-catenin cobinding events occur through non-Lef/Tcf DNA binding mechanisms, highlighting the regulatory complexity downstream of Wnt signaling in the developing mammalian kidney.
Collapse
Affiliation(s)
- Joo-Seop Park
- Division of Pediatric Urology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Rowe HM, Trono D. Dynamic control of endogenous retroviruses during development. Virology 2011; 411:273-87. [PMID: 21251689 DOI: 10.1016/j.virol.2010.12.007] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 12/06/2010] [Indexed: 02/07/2023]
Abstract
Close to half of the human genome encompasses mobile genetic elements, most of which are retrotransposons. These genetic invaders are formidable evolutionary forces that have shaped the architecture of the genomes of higher organisms, with some conserving the ability to induce new integrants within their hosts' genome. Expectedly, the control of endogenous retroviruses is tight and multi-pronged. It is most crucially established in the germ line and during the first steps of embryogenesis, primarily through transcriptional mechanisms that have likely evolved under their very pressure, but are now engaged in controlling gene expression at large, notably during early development.
Collapse
Affiliation(s)
- Helen M Rowe
- National Program, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | |
Collapse
|