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Tiukacheva EA, Ulianov SV, Karpukhina A, Razin SV, Vassetzky Y. 3D genome alterations and editing in pathology. Mol Ther 2023; 31:924-933. [PMID: 36755493 PMCID: PMC10124079 DOI: 10.1016/j.ymthe.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The human genome is folded into a multi-level 3D structure that controls many nuclear functions including gene expression. Recently, alterations in 3D genome organization were associated with several genetic diseases and cancer. As a consequence, experimental approaches are now being developed to modify the global 3D genome organization and that of specific loci. Here, we discuss emerging experimental approaches of 3D genome editing that may prove useful in biomedicine.
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Affiliation(s)
- Eugenia A Tiukacheva
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Institute of Gene Biology, Moscow 119334, Russia; Moscow Institute of Physics and Technology, Moscow 141700, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; Koltzov Institute of Developmental Biology, Moscow 119334, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Moscow 119334, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anna Karpukhina
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Koltzov Institute of Developmental Biology, Moscow 119334, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Moscow 119334, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yegor Vassetzky
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Koltzov Institute of Developmental Biology, Moscow 119334, Russia.
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2
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ANT1 overexpression models: Some similarities with facioscapulohumeral muscular dystrophy. Redox Biol 2022; 56:102450. [PMID: 36030628 PMCID: PMC9434167 DOI: 10.1016/j.redox.2022.102450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 11/20/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant disorder characterized by progressive muscle weakness. Adenine nucleotide translocator 1 (ANT1), the only 4q35 gene involved in mitochondrial function, is strongly expressed in FSHD skeletal muscle biopsies. However, its role in FSHD is unclear. In this study, we evaluated ANT1 overexpression effects in primary myoblasts from healthy controls and during Xenopus laevis organogenesis. We also compared ANT1 overexpression effects with the phenotype of FSHD muscle cells and biopsies. Here, we report that the ANT1 overexpression-induced phenotype presents some similarities with FSHD muscle cells and biopsies. ANT1-overexpressing muscle cells showed disorganized morphology, altered cytoskeletal arrangement, enhanced mitochondrial respiration/glycolysis, ROS production, oxidative stress, mitochondrial fragmentation and ultrastructure alteration, as observed in FSHD muscle cells. ANT1 overexpression in Xenopus laevis embryos affected skeletal muscle development, impaired skeletal muscle, altered mitochondrial ultrastructure and led to oxidative stress as observed in FSHD muscle biopsies. Moreover, ANT1 overexpression in X. laevis embryos affected heart structure and mitochondrial ultrastructure leading to cardiac arrhythmia, as described in some patients with FSHD. Overall our data suggest that ANT1 could contribute to mitochondria dysfunction and oxidative stress in FSHD muscle cells by modifying their bioenergetic profile associated with ROS production. Such interplay between energy metabolism and ROS production in FSHD will be of significant interest for future prospects.
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3
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Karpukhina A, Tiukacheva E, Dib C, Vassetzky YS. Control of DUX4 Expression in Facioscapulohumeral Muscular Dystrophy and Cancer. Trends Mol Med 2021; 27:588-601. [PMID: 33863674 DOI: 10.1016/j.molmed.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
DUX4, a gene encoding a transcription factor involved in early embryogenesis, is located within the D4Z4 subtelomeric repeat on chromosome 4q35. In most healthy somatic tissues, DUX4 is heavily repressed by multiple genetic and epigenetic mechanisms, and its aberrant expression is linked to facioscapulohumeral muscular dystrophy (FSHD) where it has been extensively studied. Recently, DUX4 expression has been implicated in oncogenesis, although this is much less explored. In this review, we discuss multiple levels of control of DUX4 expression, including enhancer-promoter interactions, DNA methylation, histone modifications, noncoding RNAs, and telomere positioning effect. We also connect disparate data on intrachromosomal contacts involving DUX4 and emphasize the feedback loops in DUX4 regulation. Finally, we bridge data on DUX4 in FSHD and cancer and discuss prospective approaches for future FSHD therapies and the potential outcomes of DUX4 inhibition in cancer.
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Affiliation(s)
- Anna Karpukhina
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France; Koltzov Institute of Developmental Biology, Moscow 117334, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Eugenia Tiukacheva
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France
| | - Carla Dib
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France; Stanford University School of Medicine, Stanford, CA 94305-510, USA
| | - Yegor S Vassetzky
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France; Koltzov Institute of Developmental Biology, Moscow 117334, Russia.
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4
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Abstract
Neuromuscular disorders are a heterogeneous group of conditions affecting the neuromuscular system. The aim of this article is to review the major epigenetic findings in motor neuron diseases and major hereditary muscular dystrophies. DNA methylation changes are observed in both hereditary and sporadic forms, and combining DNA methylation analysis with mutational screening holds the potential for better diagnostic and prognostic accuracy. Novel, less toxic and more selective epigenetic drugs are designed and tested in animal and cell culture models of neuromuscular disorders, and non-coding RNAs are being investigated as either disease biomarkers or targets of therapeutic approaches to restore gene expression levels. Overall, neuromuscular disorder epigenetic biomarkers have a strong potential for clinical applications in the near future.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
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5
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Salsi V, Magdinier F, Tupler R. Does DNA Methylation Matter in FSHD? Genes (Basel) 2020; 11:E258. [PMID: 32121044 PMCID: PMC7140823 DOI: 10.3390/genes11030258] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) has been associated with the genetic and epigenetic molecular features of the CpG-rich D4Z4 repeat tandem array at 4q35. Reduced DNA methylation of D4Z4 repeats is considered part of the FSHD mechanism and has been proposed as a reliable marker in the FSHD diagnostic procedure. We considered the assessment of D4Z4 DNA methylation status conducted on distinct cohorts using different methodologies. On the basis of the reported results we conclude that the percentage of DNA methylation detected at D4Z4 does not correlate with the disease status. Overall, data suggest that in the case of FSHD1, D4Z4 hypomethylation is a consequence of the chromatin structure present in the contracted allele, rather than a proxy of its function. Besides, CpG methylation at D4Z4 DNA is reduced in patients presenting diseases unrelated to muscle progressive wasting, like Bosma Arhinia and Microphthalmia syndrome, a developmental disorder, as well as ICF syndrome. Consistent with these observations, the analysis of epigenetic reprogramming at the D4Z4 locus in human embryonic and induced pluripotent stem cells indicate that other mechanisms, independent from the repeat number, are involved in the control of the epigenetic structure at D4Z4.
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Affiliation(s)
- Valentina Salsi
- Department of Life Sciences, University of Modena and Reggio Emilia, 4, 41121 Modena, Italy;
| | | | - Rossella Tupler
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 4, 41121 Modena, Italy
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, 4, 41121 Modena, Italy
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01003, USA
- Li Weibo Institute for Rare Diseases Research at the University of Massachusetts Medical School, Worcester, MA 01003, USA
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6
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Narwade N, Patel S, Alam A, Chattopadhyay S, Mittal S, Kulkarni A. Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise. Nucleic Acids Res 2019; 47:7247-7261. [PMID: 31265077 PMCID: PMC6698742 DOI: 10.1093/nar/gkz562] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/08/2019] [Accepted: 06/27/2019] [Indexed: 11/14/2022] Open
Abstract
Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. Therefore, genome-wide understanding of these elements holds great therapeutic promise. Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. However, a comprehensive genome-wide map of human S/MARs is yet not available. Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. Along with co-ordinate (location) details of S/MARs, the dataset also revealed details of S/MAR features, namely, length, inter-SMAR length (the chromatin loop size), nucleotide repeats, motif abundance, chromosomal distribution and genomic context. S/MARs identified in present study and their subsequent analysis also suggests that these elements act as hotspots for integration of retroviruses. Therefore, these data will help toward better understanding of genome functioning and designing effective anti-viral therapeutics. In order to facilitate user friendly browsing and retrieval of the data obtained in present study, a web interface, MARome (http://bioinfo.net.in/MARome), has been developed.
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Affiliation(s)
- Nitin Narwade
- Bioinformatics Centre, Savitribai Phule Pune University, Pune - 411 007, Maharashtra, India
| | - Sonal Patel
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Pune - 411 007, Maharashtra, India
| | - Aftab Alam
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Pune - 411 007, Maharashtra, India
| | - Samit Chattopadhyay
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Pune - 411 007, Maharashtra, India.,Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata - 700 032, West Bengal, India
| | - Smriti Mittal
- Department of Biotechnology, Savitribai Phule Pune University, Pune - 411 007, Maharashtra, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune - 411 007, Maharashtra, India
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7
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Gaillard MC, Broucqsault N, Morere J, Laberthonnière C, Dion C, Badja C, Roche S, Nguyen K, Magdinier F, Robin JD. Analysis of the 4q35 chromatin organization reveals distinct long-range interactions in patients affected with Facio-Scapulo-Humeral Dystrophy. Sci Rep 2019; 9:10327. [PMID: 31316120 PMCID: PMC6637155 DOI: 10.1038/s41598-019-46861-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
Facio-Scapulo Humeral dystrophy (FSHD) is the third most common myopathy, affecting 1 amongst 10,000 individuals (FSHD1, OMIM #158900). This autosomal dominant pathology is associated in 95% of cases with genetic and epigenetic alterations in the subtelomeric region at the extremity of the long arm of chromosome 4 (q arm). A large proportion of the remaining 5% of cases carry a mutation in the SMCHD1 gene (FSHD2, OMIM #158901). Here, we explored the 3D organization of the 4q35 locus by three-dimensions DNA in situ fluorescent hybridization (3D-FISH) in primary fibroblasts isolated from patients and healthy donors. We found that D4Z4 contractions and/or SMCHD1 mutations impact the spatial organization of the 4q35 region and trigger changes in the expression of different genes. Changes in gene expression were corroborated in muscle biopsies suggesting that the modified chromatin landscape impelled a modulation in the level of expression of a number of genes across the 4q35 locus in FSHD. Using induced pluripotent stem cells (hIPSC), we further examined whether chromatin organization is inherited after reprogramming or acquired during differentiation and showed that folding of the 4q35 region is modified upon differentiation. These results together with previous findings highlight the role of the D4Z4 macrosatellite repeat in the topological organization of chromatin and further indicate that the D4Z4-dependent 3D structure induces transcriptional changes of 4q35 genes expression.
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Affiliation(s)
| | | | - Julia Morere
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | | | - Camille Dion
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Cherif Badja
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Stéphane Roche
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France.,APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, France
| | | | - Jérôme D Robin
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France.
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8
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Cortesi A, Pesant M, Sinha S, Marasca F, Sala E, Gregoretti F, Antonelli L, Oliva G, Chiereghin C, Soldà G, Bodega B. 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy. Genome Res 2019; 29:883-895. [PMID: 31097473 PMCID: PMC6581056 DOI: 10.1101/gr.233288.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
Despite increasing insights in genome structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human genome, remains elusive. Facioscapulohumeral muscular dystrophy (FSHD) is associated with deletion of D4Z4 repeat array below 11 units at 4q35.2. It is known that the deletion alters chromatin structure in cis, leading to gene up-regulation. Here we show a genome-wide role of 4q-D4Z4 array in modulating gene expression via 3D nuclear contacts. We have developed an integrated strategy of 4q-D4Z4–specific 4C-seq and chromatin segmentation analyses, showing that 4q-D4Z4 3D interactome and chromatin states of interacting genes are impaired in FSHD1 condition; in particular, genes that have lost the 4q-D4Z4 interaction and with a more active chromatin state are enriched for muscle atrophy transcriptional signature. Expression level of these genes is restored by the interaction with an ectopic 4q-D4Z4 array, suggesting that the repeat directly modulates the transcription of contacted targets. Of note, the up-regulation of atrophic genes is a common feature of several FSHD1 and FSHD2 patients, indicating that we have identified a core set of deregulated genes involved in FSHD pathophysiology.
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Affiliation(s)
- Alice Cortesi
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Matthieu Pesant
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Shruti Sinha
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Federica Marasca
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Eleonora Sala
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Francesco Gregoretti
- CNR Institute for High Performance Computing and Networking (ICAR), 8013, Naples, Italy
| | - Laura Antonelli
- CNR Institute for High Performance Computing and Networking (ICAR), 8013, Naples, Italy
| | - Gennaro Oliva
- CNR Institute for High Performance Computing and Networking (ICAR), 8013, Naples, Italy
| | - Chiara Chiereghin
- Department of Biomedical Sciences, Humanitas University, 20090, Pieve Emanuele, Milan, Italy.,Humanitas Clinical and Research Center, 20089, Rozzano, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, 20090, Pieve Emanuele, Milan, Italy.,Humanitas Clinical and Research Center, 20089, Rozzano, Milan, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
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9
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Diament A, Tuller T. Modeling three-dimensional genomic organization in evolution and pathogenesis. Semin Cell Dev Biol 2018; 90:78-93. [PMID: 30030143 DOI: 10.1016/j.semcdb.2018.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 12/17/2022]
Abstract
The regulation of gene expression is mediated via the complex three-dimensional (3D) conformation of the genetic material and its interactions with various intracellular factors. Various experimental and computational approaches have been developed in recent years for understating the relation between the 3D conformation of the genome and the phenotypes of cells in normal condition and diseases. In this review, we will discuss novel approaches for analyzing and modeling the 3D genomic conformation, focusing on deciphering disease-causing mutations that affect gene expression. We conclude that as this is a very challenging mission, an important direction should involve the comparative analysis of various 3D models from various organisms or cells.
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Affiliation(s)
- Alon Diament
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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10
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DeSimone AM, Pakula A, Lek A, Emerson CP. Facioscapulohumeral Muscular Dystrophy. Compr Physiol 2017; 7:1229-1279. [PMID: 28915324 DOI: 10.1002/cphy.c160039] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Facioscapulohumeral Muscular Dystrophy is a common form of muscular dystrophy that presents clinically with progressive weakness of the facial, scapular, and humeral muscles, with later involvement of the trunk and lower extremities. While typically inherited as autosomal dominant, facioscapulohumeral muscular dystrophy (FSHD) has a complex genetic and epigenetic etiology that has only recently been well described. The most prevalent form of the disease, FSHD1, is associated with the contraction of the D4Z4 microsatellite repeat array located on a permissive 4qA chromosome. D4Z4 contraction allows epigenetic derepression of the array, and possibly the surrounding 4q35 region, allowing misexpression of the toxic DUX4 transcription factor encoded within the terminal D4Z4 repeat in skeletal muscles. The less common form of the disease, FSHD2, results from haploinsufficiency of the SMCHD1 gene in individuals carrying a permissive 4qA allele, also leading to the derepression of DUX4, further supporting a central role for DUX4. How DUX4 misexpression contributes to FSHD muscle pathology is a major focus of current investigation. Misexpression of other genes at the 4q35 locus, including FRG1 and FAT1, and unlinked genes, such as SMCHD1, has also been implicated as disease modifiers, leading to several competing disease models. In this review, we describe recent advances in understanding the pathophysiology of FSHD, including the application of MRI as a research and diagnostic tool, the genetic and epigenetic disruptions associated with the disease, and the molecular basis of FSHD. We discuss how these advances are leading to the emergence of new approaches to enable development of FSHD therapeutics. © 2017 American Physiological Society. Compr Physiol 7:1229-1279, 2017.
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Affiliation(s)
- Alec M DeSimone
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Anna Pakula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA
| | - Angela Lek
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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11
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Razin SV, Gavrilov AA, Kos P, Ulianov SV. Self-organization of a chromatin fibril into topologically-associated domains. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Sharma V, Pandey SN, Khawaja H, Brown KJ, Hathout Y, Chen YW. PARP1 Differentially Interacts with Promoter region of DUX4 Gene in FSHD Myoblasts. JOURNAL OF GENETIC SYNDROMES & GENE THERAPY 2016; 7:303. [PMID: 27722032 PMCID: PMC5051271 DOI: 10.4172/2157-7412.1000303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE The goal of the study is to identity proteins, which interact with the promoter region of double homeobox protein 4 (DUX4) gene known to be causative for the autosomal dominant disorder Facioscapulohumeral Muscular Dystrophy (FSHD). METHODS We performed a DNA pull down assay coupled with mass spectrometry analysis to identify proteins that interact with a DUX4 promoter probe in Rhabdomyosarcomca (RD) cells. We selected the top ranked protein poly (ADP-ribose) polymerase 1 (PARP1) from our mass spectrometry data for further ChIP-qPCR validation using patients' myoblasts. We then treated FSHD myoblasts with PARP1 inhibitors to investigate the role of PARP1 in the FSHD myoblasts. RESULTS In our mass spectrometry analysis, PARP1 was found to be the top ranked protein interacting preferentially with the DUX4 promoter probe in RD cells. We further validated this interaction by immunoblotting in RD cells (2-fold enrichment compared to proteins pulled down by a control probe, p<0.05) and ChIP-qPCR in patients' myoblasts (65-fold enrichment, p<0.01). Interestingly, the interaction was only observed in FSHD myoblasts but not in the control myoblasts. Upon further treatment of FSHD myoblasts with PARP1 inhibitors, we showed that treatment with a PARP1 inhibitor, 3-aminobenzamide (0.5 mM), for 24 h had a suppression of DUX4 (2.6 fold, p<0.05) and ZSCAN4, a gene previously shown to be upregulated by DUX4, (1.6 fold, p<0.01) in FSHD myoblasts. Treatment with fisetin (0.5 mM), a polyphenol compound with PARP1 inhibitory property, for 24 h also suppressed the expression of DUX4 (44.8 fold, p<0.01) and ZSCAN4 (2.2 fold, p<0.05) in the FSHD myoblasts. We further showed that DNA methyltransferase 1 (DNMT1), a gene regulated by PARP1 was also enriched at the DUX4 promoter in RD cells through immunoblotting (2-fold, p<0.01) and immortalized FSHD myoblasts (42-fold, p<0.01) but not control myoblasts through ChIP qPCR. CONCLUSION Our results showed that PARP1 and DNMT1 interacted with DUX4 promoter and may be involved in modulating DUX4 expression in FSHD.
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Affiliation(s)
- Vishakha Sharma
- Department of Molecular Medicine, George Washington University, Washington DC, USA
| | - Sachchida Nand Pandey
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Hunain Khawaja
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Kristy J Brown
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Yetrib Hathout
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
- Department of Integrative Systems Biology, George Washington University, Washington DC, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
- Department of Integrative Systems Biology, George Washington University, Washington DC, USA
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13
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3D genomics imposes evolution of the domain model of eukaryotic genome organization. Chromosoma 2016; 126:59-69. [DOI: 10.1007/s00412-016-0604-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/11/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
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14
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Jones TI, Parilla M, Jones PL. Transgenic Drosophila for Investigating DUX4 and FRG1, Two Genes Associated with Facioscapulohumeral Muscular Dystrophy (FSHD). PLoS One 2016; 11:e0150938. [PMID: 26942723 PMCID: PMC4778869 DOI: 10.1371/journal.pone.0150938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is typically an adult onset dominant myopathy. Epigenetic changes in the chromosome 4q35 region linked to both forms of FSHD lead to a relaxation of repression and increased somatic expression of DUX4-fl (DUX4-full length), the pathogenic alternative splicing isoform of the DUX4 gene. DUX4-fl encodes a transcription factor expressed in healthy testis and pluripotent stem cells; however, in FSHD, increased levels of DUX4-fl in myogenic cells lead to aberrant regulation of target genes. DUX4-fl has proven difficult to study in vivo; thus, little is known about its normal and pathogenic roles. The endogenous expression of DUX4-fl in FSHD-derived human muscle and myogenic cells is extremely low, exogenous expression of DUX4-fl in somatic cells rapidly induces cytotoxicity, and, due in part to the lack of conservation beyond primate lineages, viable animal models based on DUX4-fl have been difficult to generate. By contrast, the FRG1 (FSHD region gene 1), which is linked to FSHD, is evolutionarily conserved from invertebrates to humans, and has been studied in several model organisms. FRG1 expression is critical for the development of musculature and vasculature, and overexpression of FRG1 produces a myopathic phenotype, yet the normal and pathological functions of FRG1 are not well understood. Interestingly, DUX4 and FRG1 were recently linked when the latter was identified as a direct transcriptional target of DUX4-FL. To better understand the pathways affected in FSHD by DUX4-fl and FRG1, we generated transgenic lines of Drosophila expressing either gene under control of the UAS/GAL4 binary system. Utilizing these lines, we generated screenable phenotypes recapitulating certain known consequences of DUX4-fl or FRG1 overexpression. These transgenic Drosophila lines provide resources to dissect the pathways affected by DUX4-fl or FRG1 in a genetically tractable organism and may provide insight into both muscle development and pathogenic mechanisms in FSHD.
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Affiliation(s)
- Takako I. Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
- The Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Megan Parilla
- The Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Peter L. Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
- The Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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15
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Bou Saada Y, Dib C, Dmitriev P, Hamade A, Carnac G, Laoudj-Chenivesse D, Lipinski M, Vassetzky YS. Facioscapulohumeral dystrophy myoblasts efficiently repair moderate levels of oxidative DNA damage. Histochem Cell Biol 2016; 145:475-83. [PMID: 26860865 DOI: 10.1007/s00418-016-1410-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2016] [Indexed: 10/22/2022]
Abstract
Facioscapulohumeral dystrophy (FSHD) is a progressive muscular dystrophy linked to a deletion of a subset of D4Z4 macrosatellite repeats accompanied by a chromatin relaxation of the D4Z4 array on chromosome 4q. In vitro, FSHD primary myoblasts show altered expression of oxidative-related genes and are more susceptible to oxidative stress. Double homeobox 4 (DUX4) gene, encoded within each D4Z4 unit, is normally transcriptionally silenced but is found aberrantly expressed in skeletal muscles of FSHD patients. Its expression leads to a deregulation of DUX4 target genes including those implicated in redox balance. Here, we assessed DNA repair efficiency of oxidative DNA damage in FSHD myoblasts and DUX4-transfected myoblasts. We have shown that the DNA repair activity is altered neither in FSHD myoblasts nor in immortalized human myoblasts transiently expressing DUX4. DNA damage caused by moderate doses of an oxidant is efficiently repaired while FSHD myoblasts exposed for 24 h to high levels of oxidative stress accumulated more DNA damage than normal myoblasts, suggesting that FSHD myoblasts remain more vulnerable to oxidative stress at high doses of oxidants.
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Affiliation(s)
- Yara Bou Saada
- UMR 8126, CNRS, Univ. Paris-Sud, Institut de Cancérologie Gustave-Roussy, Université Paris Saclay, 94805, Villejuif, France
| | - Carla Dib
- UMR 8126, CNRS, Univ. Paris-Sud, Institut de Cancérologie Gustave-Roussy, Université Paris Saclay, 94805, Villejuif, France
| | - Petr Dmitriev
- UMR 8126, CNRS, Univ. Paris-Sud, Institut de Cancérologie Gustave-Roussy, Université Paris Saclay, 94805, Villejuif, France
| | - Aline Hamade
- ER030-EDST, Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
| | - Gilles Carnac
- INSERM U-1046, 371 Avenue du Doyen Gaston Giraud, 34295, Montpellier, France
| | | | - Marc Lipinski
- UMR 8126, CNRS, Univ. Paris-Sud, Institut de Cancérologie Gustave-Roussy, Université Paris Saclay, 94805, Villejuif, France
| | - Yegor S Vassetzky
- UMR 8126, CNRS, Univ. Paris-Sud, Institut de Cancérologie Gustave-Roussy, Université Paris Saclay, 94805, Villejuif, France. .,Koltzov Institute of Developmental Biology, Moscow, 117334, Russia.
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16
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Dib C, Saada YB, Dmitriev P, Richon C, Dessen P, Laoudj-Chenivesse D, Carnac G, Lipinski M, Vassetzky YS. Correction of the FSHD myoblast differentiation defect by fusion with healthy myoblasts. J Cell Physiol 2015. [DOI: 10.1002/jcp.25110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carla Dib
- UMR 8126, University of Paris-Sud, CNRS; Institut de Cancérologie Gustave-Roussy; F-94805 Villejuif France
| | - Yara Bou Saada
- UMR 8126, University of Paris-Sud, CNRS; Institut de Cancérologie Gustave-Roussy; F-94805 Villejuif France
| | - Petr Dmitriev
- UMR 8126, University of Paris-Sud, CNRS; Institut de Cancérologie Gustave-Roussy; F-94805 Villejuif France
| | - Catherine Richon
- Functional Genomics Unit; Institut de Cancérologie Gustave-Roussy; F-94805 Villejuif France
| | - Philippe Dessen
- Functional Genomics Unit; Institut de Cancérologie Gustave-Roussy; F-94805 Villejuif France
| | | | - Gilles Carnac
- INSERM U-1046; 371 Avenue du Doyen Gaston Giraud; F-34295 Montpellier France
| | - Marc Lipinski
- UMR 8126, University of Paris-Sud, CNRS; Institut de Cancérologie Gustave-Roussy; F-94805 Villejuif France
| | - Yegor S. Vassetzky
- UMR 8126, University of Paris-Sud, CNRS; Institut de Cancérologie Gustave-Roussy; F-94805 Villejuif France
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17
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Kim E, Rich J, Karoutas A, Tarlykov P, Cochet E, Malysheva D, Mamchaoui K, Ogryzko V, Pirozhkova I. ZNF555 protein binds to transcriptional activator site of 4qA allele and ANT1: potential implication in Facioscapulohumeral dystrophy. Nucleic Acids Res 2015; 43:8227-42. [PMID: 26184877 PMCID: PMC4787827 DOI: 10.1093/nar/gkv721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 06/27/2015] [Indexed: 01/18/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is an epi/genetic satellite disease associated with at least two satellite sequences in 4q35: (i) D4Z4 macrosatellite and (ii) β-satellite repeats (BSR), a prevalent part of the 4qA allele. Most of the recent FSHD studies have been focused on a DUX4 transcript inside D4Z4 and its tandem contraction in FSHD patients. However, the D4Z4-contraction alone is not pathological, which would also require the 4qA allele. Since little is known about BSR, we investigated the 4qA BSR functional role in the transcriptional control of the FSHD region 4q35. We have shown that an individual BSR possesses enhancer activity leading to activation of the Adenine Nucleotide Translocator 1 gene (ANT1), a major FSHD candidate gene. We have identified ZNF555, a previously uncharacterized protein, as a putative transcriptional factor highly expressed in human primary myoblasts that interacts with the BSR enhancer site and impacts the ANT1 promoter activity in FSHD myoblasts. The discovery of the functional role of the 4qA allele and ZNF555 in the transcriptional control of ANT1 advances our understanding of FSHD pathogenesis and provides potential therapeutic targets.
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Affiliation(s)
- Elena Kim
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Jeremy Rich
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Adam Karoutas
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Pavel Tarlykov
- National Center for Biotechnology, Astana 010000, Kazakhstan
| | - Emilie Cochet
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France Proteomic Platform, IRCIV Gustave Roussy, Villejuif 94408, France
| | - Daria Malysheva
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Kamel Mamchaoui
- Thérapie des maladies du muscle strié, Institut de Myologie, UM76-Pierre et Marie CURIE University/U974-INSERM/UMR7215-CNRS, Paris 75013, France
| | - Vasily Ogryzko
- Proteomic Platform, IRCIV Gustave Roussy, Villejuif 94408, France INSERM, CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Iryna Pirozhkova
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
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18
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Erokhin M, Vassetzky Y, Georgiev P, Chetverina D. Eukaryotic enhancers: common features, regulation, and participation in diseases. Cell Mol Life Sci 2015; 72:2361-75. [PMID: 25715743 PMCID: PMC11114076 DOI: 10.1007/s00018-015-1871-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/07/2015] [Accepted: 02/20/2015] [Indexed: 01/01/2023]
Abstract
Enhancers are positive DNA regulatory sequences controlling temporal and tissue-specific gene expression. These elements act independently of their orientation and distance relative to the promoters of target genes. Enhancers act through a variety of transcription factors that ensure their correct match with target promoters and consequent gene activation. There is a growing body of evidence on association of enhancers with transcription factors, co-activators, histone chromatin marks, and lncRNAs. Alterations in enhancers lead to misregulation of gene expression, causing a number of human diseases. In this review, we focus on the common characteristics of enhancers required for transcription stimulation.
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Affiliation(s)
- Maksim Erokhin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
| | - Yegor Vassetzky
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
- UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, 94805 Villejuif, France
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
| | - Darya Chetverina
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
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19
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Himeda CL, Jones TI, Jones PL. Facioscapulohumeral muscular dystrophy as a model for epigenetic regulation and disease. Antioxid Redox Signal 2015; 22:1463-82. [PMID: 25336259 PMCID: PMC4432493 DOI: 10.1089/ars.2014.6090] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Aberrant epigenetic regulation is an integral aspect of many diseases and complex disorders. Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, is caused by disrupted genetic and epigenetic regulation of a macrosatellite repeat. FSHD provides a powerful model to investigate disease-relevant epigenetic modifiers and general mechanisms of epigenetic regulation that govern gene expression. RECENT ADVANCES In the context of a genetically permissive allele, the one aspect of FSHD that is consistent across all known cases is the aberrant epigenetic state of the disease locus. In addition, certain mutations in the chromatin regulator SMCHD1 (structural maintenance of chromosomes hinge-domain protein 1) are sufficient to cause FSHD2 and enhance disease severity in FSHD1. Thus, there are multiple pathways to generate the epigenetic dysregulation required for FSHD. CRITICAL ISSUES Why do some individuals with the genetic requirements for FSHD develop disease pathology, while others remain asymptomatic? Similarly, disease progression is highly variable among individuals. What are the relative contributions of genetic background and environmental factors in determining disease manifestation, progression, and severity in FSHD? What is the interplay between epigenetic factors regulating the disease locus and which, if any, are viable therapeutic targets? FUTURE DIRECTIONS Epigenetic regulation represents a potentially powerful therapeutic target for FSHD. Determining the epigenetic signatures that are predictive of disease severity and identifying the spectrum of disease modifiers in FSHD are vital to the development of effective therapies.
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Affiliation(s)
- Charis L Himeda
- The Wellstone Program and the Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School , Worcester, Massachusetts
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20
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Thijssen PE, Balog J, Yao Z, Pham TP, Tawil R, Tapscott SJ, Van der Maarel SM. DUX4 promotes transcription of FRG2 by directly activating its promoter in facioscapulohumeral muscular dystrophy. Skelet Muscle 2014; 4:19. [PMID: 25789155 PMCID: PMC4364343 DOI: 10.1186/2044-5040-4-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 10/13/2014] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The most common form of facioscapulohumeral muscular dystrophy (FSHD) is caused by a genetic contraction of the polymorphic D4Z4 macrosatellite repeat array in the subtelomeric region of chromosome 4q. In some studies, genes centromeric to the D4Z4 repeat array have been reported to be over-expressed in FSHD, including FRG1 and FRG2, presumably due to decreased long-distance repression by the shorter array through a mechanism similar to position-effect variegation. Differential regulation of FRG1 in FSHD has never been unequivocally proven, however, FRG2 has been reproducibly shown to be induced in primary FSHD-derived muscle cells when differentiated in vitro. The molecular function of FRG2 and a possible contribution to FSHD pathology remain unclear. Recent evidence has identified the mis-expression of DUX4, located within the D4Z4 repeat unit, in skeletal muscle as the cause of FSHD. DUX4 is a double homeobox transcription factor that has been shown to be toxic when expressed in muscle cells. METHODS We used a combination of expression analysis by qRT/PCR and RNA sequencing to determine the transcriptional activation of FRG2 and DUX4. We examined this in both differentiating control and FSHD derived muscle cell cultures or DUX4 transduced control cell lines. Next, we used ChIP-seq analysis and luciferase reporter assays to determine the potential DUX4 transactivation effect on the FRG2 promoter. RESULTS We show that DUX4 directly activates the expression of FRG2. Increased expression of FRG2 was observed following expression of DUX4 in myoblasts and fibroblasts derived from control individuals. Moreover, we identified DUX4 binding sites at the FRG2 promoter by chromatin immunoprecipitation followed by deep sequencing and confirmed the direct regulation of DUX4 on the FRG2 promoter by luciferase reporter assays. Activation of luciferase was dependent on both DUX4 expression and the presence of the DUX4 DNA binding motifs in the FRG2 promoter. CONCLUSION We show that the FSHD-specific upregulation of FRG2 is a direct consequence of the activity of DUX4 protein rather than representing a regional de-repression secondary to fewer D4Z4 repeats.
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Affiliation(s)
- Peter E Thijssen
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Zizhen Yao
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle WA 98109, USA
| | - Tan Phát Pham
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle WA 98109, USA
| | - Silvère M Van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
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21
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Affiliation(s)
- J. Rich
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
| | - V. V. Ogryzko
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
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22
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Tawil R, van der Maarel SM, Tapscott SJ. Facioscapulohumeral dystrophy: the path to consensus on pathophysiology. Skelet Muscle 2014; 4:12. [PMID: 24940479 PMCID: PMC4060068 DOI: 10.1186/2044-5040-4-12] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/13/2014] [Indexed: 01/07/2023] Open
Abstract
Although the pathophysiology of facioscapulohumeral dystrophy (FSHD) has been controversial over the last decades, progress in recent years has led to a model that incorporates these decades of findings and is gaining general acceptance in the FSHD research community. Here we review how the contributions from many labs over many years led to an understanding of a fundamentally new mechanism of human disease. FSHD is caused by inefficient repeat-mediated epigenetic repression of the D4Z4 macrosatellite repeat array on chromosome 4, resulting in the variegated expression of the DUX4 retrogene, encoding a double-homeobox transcription factor, in skeletal muscle. Normally expressed in the testis and epigenetically repressed in somatic tissues, DUX4 expression in skeletal muscle induces expression of many germline, stem cell, and other genes that might account for the pathophysiology of FSHD. Although some disagreements regarding the details of mechanisms remain in the field, the coalescing agreement on a central model of pathophysiology represents a pivot-point in FSHD research, transitioning the field from discovery-oriented studies to translational studies aimed at developing therapies based on a sound model of disease pathophysiology.
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Affiliation(s)
- Rabi Tawil
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Stephen J Tapscott
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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23
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Himeda CL, Debarnot C, Homma S, Beermann ML, Miller JB, Jones PL, Jones TI. Myogenic enhancers regulate expression of the facioscapulohumeral muscular dystrophy-associated DUX4 gene. Mol Cell Biol 2014; 34:1942-55. [PMID: 24636994 PMCID: PMC4019064 DOI: 10.1128/mcb.00149-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/12/2014] [Accepted: 03/11/2014] [Indexed: 11/20/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is linked to epigenetic dysregulation of the chromosome 4q35 D4Z4 macrosatellite. However, this does not account for the tissue specificity of FSHD pathology, which requires stable expression of an alternative full-length mRNA splice form of DUX4 (DUX4-fl) from the D4Z4 array in skeletal muscle. Here, we describe the identification of two enhancers, DUX4 myogenic enhancer 1 (DME1) and DME2 which activate DUX4-fl expression in skeletal myocytes but not fibroblasts. Analysis of the chromatin revealed histone modifications and RNA polymerase II occupancy consistent with DME1 and DME2 being functional enhancers. Chromosome conformation capture analysis confirmed association of DME1 and DME2 with the DUX4 promoter in vivo. The strong interaction between DME2 and the DUX4 promoter in both FSHD and unaffected primary myocytes was greatly reduced in fibroblasts, suggesting a muscle-specific interaction. Nucleosome occupancy and methylome sequencing analysis indicated that in most FSHD myocytes, both enhancers are associated with nucleosomes but have hypomethylated DNA, consistent with a permissive transcriptional state, sporadic occupancy, and the observed DUX4 expression in rare myonuclei. Our data support a model in which these myogenic enhancers associate with the DUX4 promoter in skeletal myocytes and activate transcription when epigenetically derepressed in FSHD, resulting in the pathological misexpression of DUX4-fl.
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Affiliation(s)
- Charis L. Himeda
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Céline Debarnot
- Ecole Supérieure de Biotechnologie Strasbourg, Illkirch, France
| | - Sachiko Homma
- Neuromuscular Biology and Disease Group, Departments of Neurology and Physiology Biophysics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Mary Lou Beermann
- Neuromuscular Biology and Disease Group, Departments of Neurology and Physiology Biophysics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jeffrey B. Miller
- Neuromuscular Biology and Disease Group, Departments of Neurology and Physiology Biophysics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Peter L. Jones
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Takako I. Jones
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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24
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DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix. Eur J Hum Genet 2014; 22:1117-23. [PMID: 24448543 DOI: 10.1038/ejhg.2013.306] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 12/22/2022] Open
Abstract
Mechanisms that regulate attachment of the scaffold/matrix attachment regions (S/MARs) to the nuclear matrix remain largely unknown. We have studied the effect of simple sequence length polymorphism (SSLP), DNA methylation and chromatin organization in an S/MAR implicated in facioscapulohumeral dystrophy (FSHD), a hereditary disease linked to a partial deletion of the D4Z4 repeat array on chromosome 4q. This FSHD-related nuclear matrix attachment region (FR-MAR) loses its efficiency in myoblasts from FSHD patients. Three criteria were found to be important for high-affinity interaction between the FR-MAR and the nuclear matrix: the presence of a specific SSLP haplotype in chromosomal DNA, the methylation of one specific CpG within the FR-MAR and the absence of histone H3 acetylated on lysine 9 in the relevant chromatin fragment.
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25
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G R, M Z, R T. Facioscapulohumeral Muscular Dystrophy: More Complex than it Appears. Curr Mol Med 2014; 14:1052-1068. [PMID: 25323867 PMCID: PMC4264243 DOI: 10.2174/1566524014666141010155054] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 05/20/2014] [Accepted: 07/25/2014] [Indexed: 02/07/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) has been classified as an autosomal dominant myopathy, linked to rearrangements in an array of 3.3 kb tandemly repeated DNA elements (D4Z4) located at the 4q subtelomere (4q35). For the last 20 years, the diagnosis of FSHD has been confirmed in clinical practice by the detection of one D4Z4 allele with a reduced number (≤8) of repeats at 4q35. Although wide inter- and intra-familial clinical variability was found in subjects carrying D4Z4 alleles of reduced size, this DNA testing has been considered highly sensitive and specific. However, several exceptions to this general rule have been reported. Specifically, FSHD families with asymptomatic relatives carrying D4Z4 reduced alleles, FSHD genealogies with subjects affected with other neuromuscular disorders and FSHD affected patients carrying D4Z4 alleles of normal size have been described. In order to explain these findings, it has been proposed that the reduction of D4Z4 repeats at 4q35 could be pathogenic only in certain chromosomal backgrounds, defined as "permissive" specific haplotypes. However, our most recent studies show that the current DNA signature of FSHD is a common polymorphism and that in FSHD families the risk of developing FSHD for carriers of D4Z4 reduced alleles (DRA) depends on additional factors besides the 4q35 locus. These findings highlight the necessity to re-evaluate the significance and the predictive value of DRA, not only for research but also in clinical practice. Further clinical and genetic analysis of FSHD families will be extremely important for studies aiming at dissecting the complexity of FSHD.
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Affiliation(s)
- Ricci G
- Department of Life Sciences, “Miogen” Laboratory, University of Modena and Reggio Emilia, Modena, Italy
- Department of Clinical and Experimental Medicine, Section of Neurology, University of Pisa, Pisa, Italy
| | - Zatz M
- Human Genome Research and Stem Cell Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Tupler R
- Department of Life Sciences, “Miogen” Laboratory, University of Modena and Reggio Emilia, Modena, Italy
- Program in Gene Function and Expression, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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26
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Dmitriev P, Stankevicins L, Ansseau E, Petrov A, Barat A, Dessen P, Robert T, Turki A, Lazar V, Labourer E, Belayew A, Carnac G, Laoudj-Chenivesse D, Lipinski M, Vassetzky YS. Defective regulation of microRNA target genes in myoblasts from facioscapulohumeral dystrophy patients. J Biol Chem 2013; 288:34989-5002. [PMID: 24145033 DOI: 10.1074/jbc.m113.504522] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant hereditary neuromuscular disorder linked to the deletion of an integral number of 3.3-kb-long macrosatellite repeats (D4Z4) within the subtelomeric region of chromosome 4q. Most genes identified in this region are overexpressed in FSHD myoblasts, including the double homeobox genes DUX4 and DUX4c. We have carried out a simultaneous miRNome/transcriptome analysis of FSHD and control primary myoblasts. Of 365 microRNAs (miRNAs) analyzed in this study, 29 were found to be differentially expressed between FSHD and normal myoblasts. Twenty-one microRNAs (miR-1, miR-7, miR-15a, miR-22, miR-30e, miR-32, miR-107, miR-133a, miR-133b, miR-139, miR-152, miR-206, miR-223, miR-302b, miR-331, miR-362, miR-365, miR-382, miR-496, miR-532, miR-654, and miR-660) were up-regulated, and eight were down-regulated (miR-15b, miR-20b, miR-21, miR-25, miR-100, miR-155, miR-345, and miR-594). Twelve of the miRNAs up-regulated in FHSD were also up-regulated in the cells ectopically expressing DUX4c, suggesting that this gene could regulate miRNA gene transcription. The myogenic miRNAs miR-1, miR-133a, miR-133b, and miR-206 were highly expressed in FSHD myoblasts, which nonetheless did not prematurely enter myogenic differentiation. This could be accounted for by the fact that in FSHD myoblasts, functionally important target genes, including cell cycle, DNA damage, and ubiquitination-related genes, escape myogenic microRNA-induced repression.
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Affiliation(s)
- Petr Dmitriev
- From UMR 8126, Université Paris-Sud, CNRS, Institut de Cancérologie Gustave-Roussy, F-94805 Villejuif, France
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Ji L, Xu R, Lu L, Zhang J, Yang G, Huang J, Wu C, Zheng C. TM6, a novel nuclear matrix attachment region, enhances its flanking gene expression through influencing their chromatin structure. Mol Cells 2013; 36:127-37. [PMID: 23852133 PMCID: PMC3887953 DOI: 10.1007/s10059-013-0092-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/21/2013] [Accepted: 05/28/2013] [Indexed: 01/16/2023] Open
Abstract
Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.
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Affiliation(s)
- Lusha Ji
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
- Present address: College of Life Sciences, Liaocheng University, Liaocheng, Shandong 252059,
P.R. China
| | - Rui Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Longtao Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
- Present address: Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong 261061,
P.R.China
| | - Jiedao Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018,
P.R. China
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Huidobro C, Fernandez AF, Fraga MF. The role of genetics in the establishment and maintenance of the epigenome. Cell Mol Life Sci 2013; 70:1543-73. [PMID: 23474979 PMCID: PMC11113764 DOI: 10.1007/s00018-013-1296-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/19/2022]
Abstract
Epigenetic mechanisms play an important role in gene regulation during development. DNA methylation, which is probably the most important and best-studied epigenetic mechanism, can be abnormally regulated in common pathologies, but the origin of altered DNA methylation remains unknown. Recent research suggests that these epigenetic alterations could depend, at least in part, on genetic mutations or polymorphisms in DNA methyltransferases and certain genes encoding enzymes of the one-carbon metabolism pathway. Indeed, the de novo methyltransferase 3B (DNMT3B) has been recently found to be mutated in several types of cancer and in the immunodeficiency, centromeric region instability and facial anomalies syndrome (ICF), in which these mutations could be related to the loss of global DNA methylation. In addition, mutations in glycine-N-methyltransferase (GNMT) could be associated with a higher risk of hepatocellular carcinoma and liver disease due to an unbalanced S-adenosylmethionine (SAM)/S-adenosylhomocysteine (SAH) ratio, which leads to aberrant methylation reactions. Also, genetic variants of chromatin remodeling proteins and histone tail modifiers are involved in genetic disorders like α thalassemia X-linked mental retardation syndrome, CHARGE syndrome, Cockayne syndrome, Rett syndrome, systemic lupus erythematous, Rubinstein-Taybi syndrome, Coffin-Lowry syndrome, Sotos syndrome, and facioescapulohumeral syndrome, among others. Here, we review the potential genetic alterations with a possible role on epigenetic factors and discuss their contribution to human disease.
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Affiliation(s)
- Covadonga Huidobro
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA-HUCA), University of Oviedo, Oviedo, Spain
| | - Agustin F. Fernandez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA-HUCA), University of Oviedo, Oviedo, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA-HUCA), University of Oviedo, Oviedo, Spain
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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Tassin A, Leroy B, Laoudj-Chenivesse D, Wauters A, Vanderplanck C, Le Bihan MC, Coppée F, Wattiez R, Belayew A. FSHD myotubes with different phenotypes exhibit distinct proteomes. PLoS One 2012; 7:e51865. [PMID: 23272181 PMCID: PMC3525578 DOI: 10.1371/journal.pone.0051865] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/08/2012] [Indexed: 12/12/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a progressive muscle disorder linked to a contraction of the D4Z4 repeat array in the 4q35 subtelomeric region. This deletion induces epigenetic modifications that affect the expression of several genes located in the vicinity. In each D4Z4 element, we identified the double homeobox 4 (DUX4) gene. DUX4 expresses a transcription factor that plays a major role in the development of FSHD through the initiation of a large gene dysregulation cascade that causes myogenic differentiation defects, atrophy and reduced response to oxidative stress. Because miRNAs variably affect mRNA expression, proteomic approaches are required to define the dysregulated pathways in FSHD. In this study, we optimized a differential isotope protein labeling (ICPL) method combined with shotgun proteomic analysis using a gel-free system (2DLC-MS/MS) to study FSHD myotubes. Primary CD56(+) FSHD myoblasts were found to fuse into myotubes presenting various proportions of an atrophic or a disorganized phenotype. To better understand the FSHD myogenic defect, our improved proteomic procedure was used to compare predominantly atrophic or disorganized myotubes to the same matching healthy control. FSHD atrophic myotubes presented decreased structural and contractile muscle components. This phenotype suggests the occurrence of atrophy-associated proteolysis that likely results from the DUX4-mediated gene dysregulation cascade. The skeletal muscle myosin isoforms were decreased while non-muscle myosin complexes were more abundant. In FSHD disorganized myotubes, myosin isoforms were not reduced, and increased proteins were mostly involved in microtubule network organization and myofibrillar remodeling. A common feature of both FSHD myotube phenotypes was the disturbance of several caveolar proteins, such as PTRF and MURC. Taken together, our data suggest changes in trafficking and in the membrane microdomains of FSHD myotubes. Finally, the adjustment of a nuclear fractionation compatible with mass spectrometry allowed us to highlight alterations of proteins involved in mRNA processing and stability.
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Affiliation(s)
- Alexandra Tassin
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Dalila Laoudj-Chenivesse
- INSERM U1046 Physiologie et Médecine expérimentale Cœur et Muscle, CHU A. de Villeneuve, Montpellier, France
| | - Armelle Wauters
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Céline Vanderplanck
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Marie-Catherine Le Bihan
- University Pierre et Marie Curie- Paris 6, UM 76, INSERM U974, CNRS UMR 7215, Institut de Myologie, Paris, France
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
- * E-mail:
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Cabianca DS, Casa V, Gabellini D. A novel molecular mechanism in human genetic disease: a DNA repeat-derived lncRNA. RNA Biol 2012; 9:1211-7. [PMID: 23047063 DOI: 10.4161/rna.21922] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Two thirds of the human genome is composed of repetitive sequences. Despite their prevalence, DNA repeats are largely ignored. The vast majority of our genome is transcribed to produce non protein-coding RNAs. Among these, long non protein-coding RNAs represent the most prevalent and functionally diverse class. The relevance of the non protein-coding genome to human disease has mainly been studied regarding the altered microRNA expression and function in human cancer. On the contrary, the elucidation of the involvement of long non-coding RNAs in disease is only in its infancy. We have recently found that a chromatin associated, long non protein-coding RNA regulates a Polycomb/Trithorax epigenetic switch at the basis of the repeat associated facioscapulohumeral muscular dystrophy, a common muscle disorder. Based on this, we propose that long non-coding RNAs produced by repetitive sequences contribute in shaping the epigenetic landscape in normal human physiology and in disease.
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Affiliation(s)
- Daphne S Cabianca
- Dulbecco Telethon Institute and Division of Regenerative Medicine, Stem cells, and Gene therapy, San Raffaele Scientific Institute, Milan, Italy
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31
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The epigenetics of facioscapulohumeral muscular dystrophy. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 2012; 149:819-31. [PMID: 22541069 PMCID: PMC3350859 DOI: 10.1016/j.cell.2012.03.035] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 12/21/2011] [Accepted: 03/22/2012] [Indexed: 02/05/2023]
Abstract
Repetitive sequences account for more than 50% of the human genome. Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant disease associated with reduction in the copy number of the D4Z4 repeat mapping to 4q35. By an unknown mechanism, D4Z4 deletion causes an epigenetic switch leading to de-repression of 4q35 genes. Here we show that the Polycomb group of epigenetic repressors targets D4Z4 in healthy subjects and that D4Z4 deletion is associated with reduced Polycomb silencing in FSHD patients. We identify DBE-T, a chromatin-associated noncoding RNA produced selectively in FSHD patients that coordinates de-repression of 4q35 genes. DBE-T recruits the Trithorax group protein Ash1L to the FSHD locus, driving histone H3 lysine 36 dimethylation, chromatin remodeling, and 4q35 gene transcription. This study provides insights into the biological function of repetitive sequences in regulating gene expression and shows how mutations of such elements can influence the progression of a human genetic disease.
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Affiliation(s)
- Daphne S Cabianca
- Dulbecco Telethon Institute at San Raffaele Scientific Institute, Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Milan, Italy
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Neguembor MV, Gabellini D. In junk we trust: repetitive DNA, epigenetics and facioscapulohumeral muscular dystrophy. Epigenomics 2012; 2:271-87. [PMID: 22121874 DOI: 10.2217/epi.10.8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant myopathy with a peculiar etiology. Unlike most genetic disorders, FSHD is not caused by mutations in a protein-coding gene. Instead, it is associated with contraction of the D4Z4 macrosatellite repeat array located at 4q35. Interestingly, D4Z4 deletion is not sufficient per se to cause FSHD. Moreover, the disease severity, its rate of progression and the distribution of muscle weakness display great variability even among close family relatives. Hence, additional genetic and epigenetic events appear to be required for FSHD pathogenesis. Indeed, recent findings suggest that virtually all levels of epigenetic regulation, from DNA methylation to higher order chromosomal architecture, exhibit alterations in the disease locus causing deregulation of 4q35 gene expression, ultimately leading to FSHD.
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Affiliation(s)
- Maria V Neguembor
- International PhD Program in Cellular & Molecular Biology, Vita-Salute San Raffaele University, Milan, Italy
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Pikó H, Molnár MJ, Herczegfalvi A, Mayer P, Karcagi V. [Role of associated alleles and hypomethylation status in the clinical expression of facioscapulohumeral muscular dystrophy]. Orv Hetil 2011; 152:1576-85. [PMID: 21920844 DOI: 10.1556/oh.2011.29179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
UNLABELLED Autosomal dominant facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of the D4Z4 repeat region on 4q35. In addition, epigenetic modifying factors play a role in the complex pathomechanism of the disease. AIMS Introduction of a new diagnostic panel in Hungary for the extended molecular analysis of the disease which also provides new insights into the pathomechanism. METHODS In total, DNA samples of 185 clinically diagnosed FSHD patients and 71 asymptomatic relatives were analyzed by EcoRI and BlnI restriction digestion and Southern blot technique with probe p13-E11. Further investigations of the 4q35 alleles associated with the FSHD phenotype utilized qA and qB probes and a restriction analysis of the proximal D4Z4 unit by detecting a G/C SNP and the methylation status. RESULTS From the patients analyzed 115 had the D4Z4 repeat contraction, whereas from 71 asymptomatic family members five harbored the pathogenic fragment size. In eight families, prenatal testing had to be offered with an outcome of four affected fetuses. Methylation test was performed in 31 genetically confirmed FSHD patients and hypomethylation status was detected in all cases. All the 115 confirmed patients had 4qA alleles with the G polymorphism. Translocation events between 4q35 and the homologous 10q26 regions were also detected. CONCLUSION Molecular diagnosis of FSHD became a routine approach in Hungary thus supporting the work of the clinicians, improving quality of life and genetic counseling of the affected families. The provided results from this research suggest that FSHD is associated with complex epigenetic disease mechanisms.
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Affiliation(s)
- Henriett Pikó
- Országos Környezet-egészségügyi Intézet, Molekuláris Genetikai és Diagnosztikai Osztály, Budapest
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35
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Pope BD, Tsumagari K, Battaglia D, Ryba T, Hiratani I, Ehrlich M, Gilbert DM. DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy. PLoS One 2011; 6:e27413. [PMID: 22096571 PMCID: PMC3214052 DOI: 10.1371/journal.pone.0027413] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/17/2011] [Indexed: 01/08/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35.2 from 11-100 copies to 1-10 copies. The extent to which D4Z4 contraction at 4q35.2 affects overall 4q35.2 chromatin organization remains unclear. Because DNA replication timing is highly predictive of long-range chromatin interactions, we generated genome-wide replication-timing profiles for FSHD and control myogenic precursor cells. We compared non-immortalized myoblasts from four FSHD patients and three control individuals to each other and to a variety of other human cell types. This study also represents the first genome-wide comparison of replication timing profiles in non-immortalized human cell cultures. Myoblasts from both control and FSHD individuals all shared a myoblast-specific replication profile. In contrast, male and female individuals were readily distinguished by monoallelic differences in replication timing at DXZ4 and other regions across the X chromosome affected by X inactivation. We conclude that replication timing is a robust cell-type specific feature that is unaffected by FSHD-related D4Z4 contraction.
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Affiliation(s)
- Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Koji Tsumagari
- Human Genetics Program, Department of Biochemistry, and Tulane Cancer Center, Tulane Medical School, New Orleans, Louisiana, United States of America
| | - Dana Battaglia
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Ichiro Hiratani
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Melanie Ehrlich
- Human Genetics Program, Department of Biochemistry, and Tulane Cancer Center, Tulane Medical School, New Orleans, Louisiana, United States of America
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
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Goes ACS, Cappellen D, Santos GC, Pirozhkova I, Lipinski M, Vassetzky Y, de Moura-Gallo CV. Loop domain organization of the p53 locus in normal and breast cancer cells correlates with the transcriptional status of the TP53 and the neighboring genes. J Cell Biochem 2011; 112:2072-81. [PMID: 21465532 DOI: 10.1002/jcb.23129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
P53 is a tumor suppressor protein critical for genome integrity. Although its control at the protein level is well known, the transcriptional regulation of the TP53 gene is still unclear. We have analyzed the organization of the TP53 gene domain using DNA arrays in several breast cancer and control cell lines. We have found that in the control breast epithelial cell line, HB2, the TP53 gene is positioned within a relatively small DNA domain, encompassing 50 kb, delimited by two nuclear matrix attachment sites. Interestingly, this domain structure was found to be radically different in the studied breast cancer cell lines, MCF7, T47D, MDA-MB-231, and BT474, in which the domain size was increased and TP53 transcription was decreased. We propose a model in which the organization of the TP53 gene domain correlates with the transcriptional status of TP53 and neighboring genes.
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Affiliation(s)
- Andrea C S Goes
- Unité Mixte de Recherche 8126, Signalisation, Noyaux et Innovations en Cancérologie, Centre NaTional de la Recherche Scientifique, Institut de Cancérologie Gustave-Roussy, Université Paris-Sud 11, F-94805 Villejuif Cedex, France
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Richards M, Coppée F, Thomas N, Belayew A, Upadhyaya M. Facioscapulohumeral muscular dystrophy (FSHD): an enigma unravelled? Hum Genet 2011; 131:325-40. [PMID: 21984394 DOI: 10.1007/s00439-011-1100-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/26/2011] [Indexed: 01/02/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common muscular dystrophy after the dystrophinopathies and myotonic dystrophy and is associated with a typical pattern of muscle weakness. Most patients with FSHD carry a large deletion in the polymorphic D4Z4 macrosatellite repeat array at 4q35 and present with 1-10 repeats whereas non-affected individuals possess 11-150 repeats. An almost identical repeat array is present at 10q26 and the high sequence identity between these two arrays can cause difficulties in molecular diagnosis. Each 3.3-kb D4Z4 unit contains a DUX4 (double homeobox 4) gene that, among others, is activated upon contraction of the 4q35 repeat array due to the induction of chromatin remodelling of the 4qter region. A number of 4q subtelomeric sequence variants are now recognised, although FSHD only occurs in association with three 'permissive' haplotypes, each of which is associated with a polyadenylation signal located immediately distal of the last D4Z4 unit. The resulting poly-A tail appears to stabilise DUX4 mRNAs transcribed from this most distal D4Z4 unit in FSHD muscle cells. Synthesis of both the DUX4 transcripts and protein in FSHD muscle cells induces significant cell toxicity. DUX4 is a transcription factor that may target several genes which results in a deregulation cascade which inhibits myogenesis, sensitises cells to oxidative stress and induces muscle atrophy, thus recapitulating many of the key molecular features of FSHD.
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Affiliation(s)
- Mark Richards
- School of Medicine, Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
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38
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Dmitriev P, Petrov A, Ansseau E, Stankevicins L, Charron S, Kim E, Bos TJ, Robert T, Turki A, Coppée F, Belayew A, Lazar V, Carnac G, Laoudj D, Lipinski M, Vassetzky YS. The Krüppel-like factor 15 as a molecular link between myogenic factors and a chromosome 4q transcriptional enhancer implicated in facioscapulohumeral dystrophy. J Biol Chem 2011; 286:44620-31. [PMID: 21937448 DOI: 10.1074/jbc.m111.254052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a dominant hereditary disease with a prevalence of 7 per 100,000 individuals, is associated with a partial deletion in the subtelomeric D4Z4 repeat array on chromosome 4q. The D4Z4 repeat contains a strong transcriptional enhancer that activates promoters of several FSHD-related genes. We report here that the enhancer within the D4Z4 repeat binds the Krüppel-like factor KLF15. KLF15 was found to be up-regulated during myogenic differentiation induced by serum starvation or by overexpression of the myogenic differentiation factor MYOD. When overexpressed, KLF15 activated the D4Z4 enhancer and led to overexpression of DUX4c (Double homeobox 4, centromeric) and FRG2 (FSHD region gene 2) genes, whereas its silencing caused inactivation of the D4Z4 enhancer. In immortalized human myoblasts, the D4Z4 enhancer was activated by the myogenic factor MYOD, an effect that was abolished upon KLF15 silencing or when the KLF15-binding sites within the D4Z4 enhancer were mutated, indicating that the myogenesis-related activation of the D4Z4 enhancer was mediated by KLF15. KLF15 and several myogenesis-related factors were found to be expressed at higher levels in myoblasts, myotubes, and muscle biopsies from FSHD patients than in healthy controls. We propose that KLF15 serves as a molecular link between myogenic factors and the activity of the D4Z4 enhancer, and it thus contributes to the overexpression of the DUX4c and FRG2 genes during normal myogenic differentiation and in FSHD.
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Affiliation(s)
- Petr Dmitriev
- CNRS UMR8126, Université Paris-Sud 11, Institut de Cancérologie Gustave Roussy, 94805 Villejuif, France
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Decreased proliferation kinetics of mouse myoblasts overexpressing FRG1. PLoS One 2011; 6:e19780. [PMID: 21603621 PMCID: PMC3095625 DOI: 10.1371/journal.pone.0019780] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 04/04/2011] [Indexed: 11/24/2022] Open
Abstract
Although recent publications have linked the molecular events driving facioscapulohumeral muscular dystrophy (FSHD) to expression of the double homeobox transcription factor DUX4, overexpression of FRG1 has been proposed as one alternative causal agent as mice overexpressing FRG1 present with muscular dystrophy. Here, we characterize proliferative defects in two independent myoblast lines overexpressing FRG1. Myoblasts isolated from thigh muscle of FRG1 transgenic mice, an affected dystrophic muscle, exhibit delayed proliferation as measured by decreased clone size, whereas myoblasts isolated from the unaffected diaphragm muscle proliferated normally. To confirm the observation that overexpression of FRG1 could impair myoblast proliferation, we examined C2C12 myoblasts with inducible overexpression of FRG1, finding increased doubling time and G1-phase cells in mass culture after induction of FRG1 and decreased levels of pRb phosphorylation. We propose that depressed myoblast proliferation may contribute to the pathology of mice overexpressing FRG1 and may play a part in FSHD.
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Cabianca DS, Gabellini D. The cell biology of disease: FSHD: copy number variations on the theme of muscular dystrophy. J Cell Biol 2010; 191:1049-60. [PMID: 21149563 PMCID: PMC3002039 DOI: 10.1083/jcb.201007028] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/08/2010] [Indexed: 01/17/2023] Open
Abstract
In humans, copy number variations (CNVs) are a common source of phenotypic diversity and disease susceptibility. Facioscapulohumeral muscular dystrophy (FSHD) is an important genetic disease caused by CNVs. It is an autosomal-dominant myopathy caused by a reduction in the copy number of the D4Z4 macrosatellite repeat located at chromosome 4q35. Interestingly, the reduction of D4Z4 copy number is not sufficient by itself to cause FSHD. A number of epigenetic events appear to affect the severity of the disease, its rate of progression, and the distribution of muscle weakness. Indeed, recent findings suggest that virtually all levels of epigenetic regulation, from DNA methylation to higher order chromosomal architecture, are altered at the disease locus, causing the de-regulation of 4q35 gene expression and ultimately FSHD.
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Affiliation(s)
- Daphne Selvaggia Cabianca
- International PhD Program in Cellular and Molecular Biology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Division of Regenerative Medicine, San Raffaele Scientific Institute, DIBIT 1, 2A3-49, 20132 Milan, Italy
| | - Davide Gabellini
- Division of Regenerative Medicine, San Raffaele Scientific Institute, DIBIT 1, 2A3-49, 20132 Milan, Italy
- Dulbecco Telethon Institute, 20132 Milan, Italy
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41
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Abstract
Alternative splicing of pre-mRNAs is a major contributor to proteomic diversity and to the control of gene expression in higher eukaryotic cells. For this reasons, alternative splicing is tightly regulated in different tissues and developmental stages and its disruption can lead to a wide range of human disorders. The aim of this review is to focus on the relevance of alternative splicing for muscle function and muscle disease. We begin by giving a brief overview of alternative splicing, muscle-specific gene expression and muscular dystrophy. Next, to illustrate these concepts we focus on two muscular dystrophy, myotonic muscular dystrophy and facioscapulohumeral muscular dystrophy, both associated to disruption of splicing regulation in muscle.
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Affiliation(s)
- Mariaelena Pistoni
- Division of Regenerative Medicine, San Raffaele Scientific Institute, Milan, Italy
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42
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Barat-Houari M, Nguyen K, Bernard R, Fernandez C, Vovan C, Bareil C, Khau Van Kien P, Thorel D, Tuffery-Giraud S, Vasseur F, Attarian S, Pouget J, Girardet A, Lévy N, Claustres M. New multiplex PCR-based protocol allowing indirect diagnosis of FSHD on single cells: can PGD be offered despite high risk of recombination? Eur J Hum Genet 2010; 18:533-8. [PMID: 19935833 PMCID: PMC2987324 DOI: 10.1038/ejhg.2009.207] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 10/01/2009] [Accepted: 10/14/2009] [Indexed: 01/23/2023] Open
Abstract
Molecular pathophysiology of facioscapulohumeral muscular dystrophy (FSHD) involves the heterozygous contraction of the number of tandemly repeated D4Z4 units at chromosome 4q35.2. FSHD is associated with a range of 1-10 D4Z4 units instead of 11-150 in normal controls. Several factors complicate FSHD molecular diagnosis, especially the cis-segregation of D4Z4 contraction with a 4qA allele, whereas D4Z4 shortening is silent both on alleles 4qB and 10q. Discrimination of pathogenic 4q-D4Z4 alleles from highly homologous 10q-D4Z4 arrays requires the use of the conventional Southern blot, which is not suitable at the single-cell level. Preimplantation genetic diagnosis (PGD) is a frequent request from FSHD families with several affected relatives. We aimed to develop a rapid and sensitive PCR-based multiplex approach on single cells to perform an indirect familial segregation study of pathogenic alleles. Among several available polymorphic markers at 4q35.2, the four most proximal (D4S2390, D4S1652, D4S2930 and D4S1523, <1.23 Mb) showing the highest heterozygote frequencies (67-91%) were selected. Five recombination events in the D4S2390-D4S1523 interval were observed among 144 meioses. In the D4S2390-D4Z4 interval, no recombination event occurred among 28 FSHD meioses. Instead, a particular haplotype segregated with both clinical and molecular status, allowing the characterization of an at-risk allele in each tested FSHD family (maximal LOD score 2.98 for theta=0.0). This indirect protocol can easily complement conventional techniques in prenatal diagnosis. Although our multiplex PCR-based approach technically fulfils guidelines for single-cell analysis, the relatively high recombination risk hampers its application to PGD.
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Affiliation(s)
- Mouna Barat-Houari
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France.
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43
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Rivera-Mulia JC, Aranda-Anzaldo A. Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach. DNA Res 2010; 17:23-35. [PMID: 20047947 PMCID: PMC2818189 DOI: 10.1093/dnares/dsp027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear DNA of metazoans is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). DNA is anchored to the NM by non-coding sequences known as matrix attachment regions (MARs). There are no consensus sequences for identification of MARs and not all potential MARs are actually bound to the NM constituting loop attachment regions (LARs). Fundamental processes of nuclear physiology occur at macromolecular complexes organized on the NM; thus, the topological organization of DNA loops must be important. Here, we describe a general method for determining the structural DNA loop organization in any large genomic region with a known sequence. The method exploits the topological properties of loop DNA attached to the NM and elementary topological principles such as that points in a deformable string (DNA) can be positionally mapped relative to a position-reference invariant (NM), and from such mapping, the configuration of the string in third dimension can be deduced. Therefore, it is possible to determine the specific DNA loop configuration without previous characterization of the LARs involved. We determined in hepatocytes and B-lymphocytes of the rat the DNA loop organization of a genomic region that contains four members of the albumin gene family.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, Toluca, Edo. Méx., México
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44
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Barro M, Carnac G, Flavier S, Mercier J, Vassetzky Y, Laoudj-Chenivesse D. Myoblasts from affected and non-affected FSHD muscles exhibit morphological differentiation defects. J Cell Mol Med 2010; 14:275-89. [PMID: 18505476 PMCID: PMC2910739 DOI: 10.1111/j.1582-4934.2008.00368.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is a muscular hereditary disease with a prevalence of 1 in 20,000 caused by a partial deletion of a subtelomeric repeat array on chromosome 4q. However, very little is known about the pathogenesis as well as the molecular and biochemical changes linked to the progressive muscle degeneration observed in these patients. Several studies have investigated possible pathophysiological pathways in FSHD myoblasts and mature muscle cells but some of these reports were apparently in contradiction. The discrepancy between these studies may be explained by differences between the sources of myoblasts. Therefore, we decided to thoroughly analyze affected and unaffected muscles from patients with FSHD in terms of vulnerability to oxidative stress, differentiation capacity and morphological abnormalities. We have established a panel of primary myoblast cell cultures from patients affected with FSHD and matched healthy individuals. Our results show that primary myoblasts are more susceptible to an induced oxidative stress than control myoblasts. Moreover, we demonstrate that both types of FSHD primary myoblasts differentiate into multi-nucleated myotubes, which present morphological abnormalities. Whereas control myoblasts fuse to form branched myotubes with aligned nuclei, FSHD myoblasts fuse to form either thin and branched myotubes with aligned nuclei or large myotubes with random nuclei distribution. In conclusion, we postulate that these abnormalities could be responsible for muscle weakness in patients with FSHD and provide an important marker for FSHD myoblasts.
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Abstract
PURPOSE OF REVIEW Knowledge of the pathogenetic mechanisms in facioscapulohumeral muscular dystrophy is still scattered, but has recently been advanced through novel developments on the genetic scientific front. RECENT FINDINGS The present brief review highlights some recent studies on the pathogenesis of facioscapulohumeral muscular dystrophy pointing to major involvement of muscle development pathways and possibly vascular development pathways as well, which feeds into ideas about homeobox-related transcriptional dysregulation, which was originally suggested, based on the apparent descending order of muscle weakness. SUMMARY The present findings and observations set a broad agenda for further research and possible therapeutic targets.
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Ansseau E, Laoudj-Chenivesse D, Marcowycz A, Tassin A, Vanderplanck C, Sauvage S, Barro M, Mahieu I, Leroy A, Leclercq I, Mainfroid V, Figlewicz D, Mouly V, Butler-Browne G, Belayew A, Coppée F. DUX4c is up-regulated in FSHD. It induces the MYF5 protein and human myoblast proliferation. PLoS One 2009; 4:e7482. [PMID: 19829708 PMCID: PMC2759506 DOI: 10.1371/journal.pone.0007482] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 09/17/2009] [Indexed: 12/21/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease linked to contractions of the D4Z4 repeat array in 4q35. We have previously identified a double homeobox gene (DUX4) within each D4Z4 unit that encodes a transcription factor expressed in FSHD but not control myoblasts. DUX4 and its target genes contribute to the global dysregulation of gene expression observed in FSHD. We have now characterized the homologous DUX4c gene mapped 42 kb centromeric of the D4Z4 repeat array. It encodes a 47-kDa protein with a double homeodomain identical to DUX4 but divergent in the carboxyl-terminal region. DUX4c was detected in primary myoblast extracts by Western blot with a specific antiserum, and was induced upon differentiation. The protein was increased about 2-fold in FSHD versus control myotubes but reached 2-10-fold induction in FSHD muscle biopsies. We have shown by Western blot and by a DNA-binding assay that DUX4c over-expression induced the MYF5 myogenic regulator and its DNA-binding activity. DUX4c might stabilize the MYF5 protein as we detected their interaction by co-immunoprecipitation. In keeping with the known role of Myf5 in myoblast accumulation during mouse muscle regeneration DUX4c over-expression activated proliferation of human primary myoblasts and inhibited their differentiation. Altogether, these results suggested that DUX4c could be involved in muscle regeneration and that changes in its expression could contribute to the FSHD pathology.
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Affiliation(s)
- Eugénie Ansseau
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | | | - Aline Marcowycz
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | - Céline Vanderplanck
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | - Sébastien Sauvage
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | - Marietta Barro
- INSERM ERI 25 Muscle et Pathologies, CHU A. de Villeneuve, Montpellier, France
| | - Isabelle Mahieu
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | - Axelle Leroy
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | - India Leclercq
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | | | - Denise Figlewicz
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Vincent Mouly
- Institute of Myology, Platform for human cell culture, Paris, France
| | | | - Alexandra Belayew
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
| | - Frédérique Coppée
- Laboratory of Molecular Biology, University of Mons-Hainaut, 6, Mons, Belgium
- * E-mail:
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47
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Verlaan DJ, Berlivet S, Hunninghake GM, Madore AM, Larivière M, Moussette S, Grundberg E, Kwan T, Ouimet M, Ge B, Hoberman R, Swiatek M, Dias J, Lam KC, Koka V, Harmsen E, Soto-Quiros M, Avila L, Celedón JC, Weiss ST, Dewar K, Sinnett D, Laprise C, Raby BA, Pastinen T, Naumova AK. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Am J Hum Genet 2009; 85:377-93. [PMID: 19732864 DOI: 10.1016/j.ajhg.2009.08.007] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 07/31/2009] [Accepted: 08/12/2009] [Indexed: 02/05/2023] Open
Abstract
Common SNPs in the chromosome 17q12-q21 region alter the risk for asthma, type 1 diabetes, primary biliary cirrhosis, and Crohn disease. Previous reports by us and others have linked the disease-associated genetic variants with changes in expression of GSDMB and ORMDL3 transcripts in human lymphoblastoid cell lines (LCLs). The variants also alter regulation of other transcripts, and this domain-wide cis-regulatory effect suggests a mechanism involving long-range chromatin interactions. Here, we further dissect the disease-linked haplotype and identify putative causal DNA variants via a combination of genetic and functional analyses. First, high-throughput resequencing of the region and genotyping of potential candidate variants were performed. Next, additional mapping of allelic expression differences in Yoruba HapMap LCLs allowed us to fine-map the basis of the cis-regulatory differences to a handful of candidate functional variants. Functional assays identified allele-specific differences in nucleosome distribution, an allele-specific association with the insulator protein CTCF, as well as a weak promoter activity for rs12936231. Overall, this study shows a common disease allele linked to changes in CTCF binding and nucleosome occupancy leading to altered domain-wide cis-regulation. Finally, a strong association between asthma and cis-regulatory haplotypes was observed in three independent family-based cohorts (p = 1.78 x 10(-8)). This study demonstrates the requirement of multiple parallel allele-specific tools for the investigation of noncoding disease variants and functional fine-mapping of human disease-associated haplotypes.
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48
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Bodega B, Ramirez GDC, Grasser F, Cheli S, Brunelli S, Mora M, Meneveri R, Marozzi A, Mueller S, Battaglioli E, Ginelli E. Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation. BMC Biol 2009; 7:41. [PMID: 19607661 PMCID: PMC2719609 DOI: 10.1186/1741-7007-7-41] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 07/16/2009] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder associated with the partial deletion of integral numbers of 3.3 kb D4Z4 DNA repeats within the subtelomere of chromosome 4q. A number of candidate FSHD genes, adenine nucleotide translocator 1 gene (ANT1), FSHD-related gene 1 (FRG1), FRG2 and DUX4c, upstream of the D4Z4 array (FSHD locus), and double homeobox chromosome 4 (DUX4) within the repeat itself, are upregulated in some patients, thus suggesting an underlying perturbation of the chromatin structure. Furthermore, a mouse model overexpressing FRG1 has been generated, displaying skeletal muscle defects. RESULTS In the context of myogenic differentiation, we compared the chromatin structure and tridimensional interaction of the D4Z4 array and FRG1 gene promoter, and FRG1 expression, in control and FSHD cells. The FRG1 gene was prematurely expressed during FSHD myoblast differentiation, thus suggesting that the number of D4Z4 repeats in the array may affect the correct timing of FRG1 expression. Using chromosome conformation capture (3C) technology, we revealed that the FRG1 promoter and D4Z4 array physically interacted. Furthermore, this chromatin structure underwent dynamic changes during myogenic differentiation that led to the loosening of the FRG1/4q-D4Z4 array loop in myotubes. The FRG1 promoter in both normal and FSHD myoblasts was characterized by H3K27 trimethylation and Polycomb repressor complex binding, but these repression signs were replaced by H3K4 trimethylation during differentiation. The D4Z4 sequences behaved similarly, with H3K27 trimethylation and Polycomb binding being lost upon myogenic differentiation. CONCLUSION We propose a model in which the D4Z4 array may play a critical chromatin function as an orchestrator of in cis chromatin loops, thus suggesting that this repeat may play a role in coordinating gene expression.
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Affiliation(s)
- Beatrice Bodega
- Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy.
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49
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Zeng W, de Greef JC, Chen YY, Chien R, Kong X, Gregson HC, Winokur ST, Pyle A, Robertson KD, Schmiesing JA, Kimonis VE, Balog J, Frants RR, Ball AR, Lock LF, Donovan PJ, van der Maarel SM, Yokomori K. Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet 2009; 5:e1000559. [PMID: 19593370 PMCID: PMC2700282 DOI: 10.1371/journal.pgen.1000559] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 06/12/2009] [Indexed: 12/11/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant muscular dystrophy in which no mutation of pathogenic gene(s) has been identified. Instead, the disease is, in most cases, genetically linked to a contraction in the number of 3.3 kb D4Z4 repeats on chromosome 4q. How contraction of the 4qter D4Z4 repeats causes muscular dystrophy is not understood. In addition, a smaller group of FSHD cases are not associated with D4Z4 repeat contraction (termed "phenotypic" FSHD), and their etiology remains undefined. We carried out chromatin immunoprecipitation analysis using D4Z4-specific PCR primers to examine the D4Z4 chromatin structure in normal and patient cells as well as in small interfering RNA (siRNA)-treated cells. We found that SUV39H1-mediated H3K9 trimethylation at D4Z4 seen in normal cells is lost in FSHD. Furthermore, the loss of this histone modification occurs not only at the contracted 4q D4Z4 allele, but also at the genetically intact D4Z4 alleles on both chromosomes 4q and 10q, providing the first evidence that the genetic change (contraction) of one 4qD4Z4 allele spreads its effect to other genomic regions. Importantly, this epigenetic change was also observed in the phenotypic FSHD cases with no D4Z4 contraction, but not in other types of muscular dystrophies tested. We found that HP1gamma and cohesin are co-recruited to D4Z4 in an H3K9me3-dependent and cell type-specific manner, which is disrupted in FSHD. The results indicate that cohesin plays an active role in HP1 recruitment and is involved in cell type-specific D4Z4 chromatin regulation. Taken together, we identified the loss of both histone H3K9 trimethylation and HP1gamma/cohesin binding at D4Z4 to be a faithful marker for the FSHD phenotype. Based on these results, we propose a new model in which the epigenetic change initiated at 4q D4Z4 spreads its effect to other genomic regions, which compromises muscle-specific gene regulation leading to FSHD pathogenesis.
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Affiliation(s)
- Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Jessica C. de Greef
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands
| | - Yen-Yun Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Richard Chien
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Heather C. Gregson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Sara T. Winokur
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - April Pyle
- Institute for Stem Cell Biology and Medicine, Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Keith D. Robertson
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - John A. Schmiesing
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Virginia E. Kimonis
- Division of Medical Genetics and Metabolism, Department of Pediatrics, University of California Irvine Medical Center, Orange, California, United States of America
| | - Judit Balog
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands
| | - Rune R. Frants
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands
| | - Alexander R. Ball
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Leslie F. Lock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Peter J. Donovan
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | | | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
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50
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Arashiro P, Eisenberg I, Kho AT, Cerqueira AMP, Canovas M, Silva HCA, Pavanello RCM, Verjovski-Almeida S, Kunkel LM, Zatz M. Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers. Proc Natl Acad Sci U S A 2009; 106:6220-5. [PMID: 19339494 PMCID: PMC2664154 DOI: 10.1073/pnas.0901573106] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Indexed: 01/19/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a progressive muscle disorder that has been associated with a contraction of 3.3-kb repeats on chromosome 4q35. FSHD is characterized by a wide clinical inter- and intrafamilial variability, ranging from wheelchair-bound patients to asymptomatic carriers. Our study is unique in comparing the gene expression profiles from related affected, asymptomatic carrier, and control individuals. Our results suggest that the expression of genes on chromosome 4q is altered in affected and asymptomatic individuals. Remarkably, the changes seen in asymptomatic samples are largely in products of genes encoding several chemokines, whereas the changes seen in affected samples are largely in genes governing the synthesis of GPI-linked proteins and histone acetylation. Besides this, the affected patient and related asymptomatic carrier share the 4qA161 haplotype. Thus, these polymorphisms by themselves do not explain the pathogenicity of the contracted allele. Interestingly, our results also suggest that the miRNAs might mediate the regulatory network in FSHD. Together, our results support the previous evidence that FSHD may be caused by transcriptional dysregulation of multiple genes, in cis and in trans, and suggest some factors potentially important for FSHD pathogenesis. The study of the gene expression profiles from asymptomatic carriers and related affected patients is a unique approach to try to enhance our understanding of the missing link between the contraction in D4Z4 repeats and muscle disease, while minimizing the effects of differences resulting from genetic background.
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Affiliation(s)
- Patricia Arashiro
- Human Genome Research Center, Department of Genetics and Evolutive Biology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, Brazil
| | - Iris Eisenberg
- The Howard Hughes Medical Institute, Program in Genomics, Division of Genetics
| | - Alvin T. Kho
- Informatics Program, Children's Hospital, Harvard Medical School, Boston, MA 02115
| | - Antonia M. P. Cerqueira
- Human Genome Research Center, Department of Genetics and Evolutive Biology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, Brazil
| | - Marta Canovas
- Human Genome Research Center, Department of Genetics and Evolutive Biology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, Brazil
| | - Helga C. A. Silva
- Brazilian Center of Study, Diagnosis, and Investigation of Malignant Hyperthermia, Department of Surgery, Discipline of Anaesthesia, Pain and Intensive Care, University Federal of São Paulo, 04024-002, São Paulo, Brazil; and
| | - Rita C. M. Pavanello
- Human Genome Research Center, Department of Genetics and Evolutive Biology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-900, São Paulo, Brazil
| | - Louis M. Kunkel
- The Howard Hughes Medical Institute, Program in Genomics, Division of Genetics
| | - Mayana Zatz
- Human Genome Research Center, Department of Genetics and Evolutive Biology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, Brazil
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