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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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Giussani M, Cardone MF, Bodega B, Ginelli E, Meneveri R. Evolutionary history of linked D4Z4 and Beta satellite clusters at the FSHD locus (4q35). Genomics 2012; 100:289-96. [PMID: 22824653 PMCID: PMC3488192 DOI: 10.1016/j.ygeno.2012.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/21/2012] [Accepted: 07/12/2012] [Indexed: 01/10/2023]
Abstract
We performed a detailed genomic investigation of the chimpanzee locus syntenic to human chromosome 4q35.2, associated to the facioscapulohumeral dystrophy. Two contigs of approximately 150 kb and 200 kb were derived from PTR chromosomes 4q35 and 3p12, respectively: both regions showed a very similar sequence organization, including D4Z4 and Beta satellite linked clusters. Starting from these findings, we derived a hypothetical evolutionary history of human 4q35, 10q26 and 3p12 chromosome regions focusing on the D4Z4–Beta satellite linked organization. The D4Z4 unit showed an open reading frame (DUX4) at both PTR 4q35 and 3p12 regions; furthermore some subregions of the Beta satellite unit showed a high degree of conservation between chimpanzee and humans. In conclusion, this paper provides evidence that at the 4q subtelomere the linkage between D4Z4 and Beta satellite arrays is a feature that appeared late during evolution and is conserved between chimpanzee and humans.
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Affiliation(s)
- Marta Giussani
- Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy.
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Ottaviani A, Schluth-Bolard C, Gilson E, Magdinier F. D4Z4 as a prototype of CTCF and lamins-dependent insulator in human cells. Nucleus 2012; 1:30-6. [PMID: 21327102 DOI: 10.4161/nucl.1.1.10799] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 11/12/2009] [Accepted: 11/16/2009] [Indexed: 12/21/2022] Open
Abstract
Using cellular models that mimic the organizations of the subtelomeric 4q35 locus found in patients affected with Facio-Scapulo-Humeral Dystrophy (FSHD) and in healthy individuals, we recently investigated the biological function of the D4Z4 macrosatellite in this subtelomeric context.We demonstrated that D4Z4 acts as a CTCF and A-type lamins dependent insulator element exhibiting both enhancer- blocking and barrier activities, and displaces a telomere towards the nuclear periphery. This peripheral positioning activity lies within a short sequence that interacts with CTCF and A-type lamins. Depletion in either of these two proteins suppresses these perinuclear activities, revealing the existence of a subtelomeric sequence that is sufficient to position an adjacent telomere to the nuclear periphery. We discuss here the biological implications of these results in the light of our current knowledge in related fields and the potential implication of other CTCF and A-type lamins insulators in the light of human pathologies.
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Affiliation(s)
- Alexandre Ottaviani
- Laboratoire de Biologie Moléculaire de la Cellule, CNRS UMR5239, Ecole Normale Supérieure de Lyon, UCBL1, Lyon, France
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Lanzuolo C. Epigenetic alterations in muscular disorders. Comp Funct Genomics 2012; 2012:256892. [PMID: 22761545 PMCID: PMC3385594 DOI: 10.1155/2012/256892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/11/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022] Open
Abstract
Epigenetic mechanisms, acting via chromatin organization, fix in time and space different transcriptional programs and contribute to the quality, stability, and heritability of cell-specific transcription programs. In the last years, great advances have been made in our understanding of mechanisms by which this occurs in normal subjects. However, only a small part of the complete picture has been revealed. Abnormal gene expression patterns are often implicated in the development of different diseases, and thus epigenetic studies from patients promise to fill an important lack of knowledge, deciphering aberrant molecular mechanisms at the basis of pathogenesis and diseases progression. The identification of epigenetic modifications that could be used as targets for therapeutic interventions could be particularly timely in the light of pharmacologically reversion of pathological perturbations, avoiding changes in DNA sequences. Here I discuss the available information on epigenetic mechanisms that, altered in neuromuscular disorders, could contribute to the progression of the disease.
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Affiliation(s)
- Chiara Lanzuolo
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Via Del Fosso di Fiorano 64, 00143 Rome, Italy
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Chien WH, Gau SSF, Wu YY, Huang YS, Fang JS, Chen YJ, Soong WT, Chiu YN, Chen CH. Identification and molecular characterization of two novel chromosomal deletions associated with autism. Clin Genet 2010; 78:449-56. [DOI: 10.1111/j.1399-0004.2010.01395.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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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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Rudd MK, Endicott RM, Friedman C, Walker M, Young JM, Osoegawa K, de Jong PJ, Green ED, Trask BJ. Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event. Genome Res 2008; 19:33-41. [PMID: 18952852 DOI: 10.1101/gr.083170.108] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Subtelomeres are concentrations of interchromosomal segmental duplications capped by telomeric repeats at the ends of chromosomes. The nature of the segments shared by different sets of human subtelomeres reflects their high rate of recent interchromosomal exchange. Here, we characterize the rearrangements incurred by the 15q subtelomere after it arose from a chromosome fission event in the common ancestor of great apes. We used FISH, sequencing of genomic clones, and PCR to map the breakpoint of this fission and track the fate of flanking sequence in human, chimpanzee, gorilla, orangutan, and macaque genomes. The ancestral locus, a cluster of olfactory receptor (OR) genes, lies internally on macaque chromosome 7. Sequence originating from this fission site is split between the terminus of 15q and the pericentromere of 14q in the great apes. Numerous structural rearrangements, including interstitial deletions and transfers of material to or from other subtelomeres, occurred subsequent to the fission, such that each species has a unique 15q structure and unique collection of ORs derived from the fission locus. The most striking rearrangement involved transfer of at least 200 kb from the fission-site region to the end of chromosome 4q, where much still resides in chimpanzee and gorilla, but not in human. This gross structural difference places the subtelomeric defect underlying facioscapulohumeral muscular dystrophy (FSHD) much closer to the telomere in human 4q than in the hybrid 4q-15q subtelomere of chimpanzee.
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Affiliation(s)
- M Katharine Rudd
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Deponti D, François S, Baesso S, Sciorati C, Innocenzi A, Broccoli V, Muscatelli F, Meneveri R, Clementi E, Cossu G, Brunelli S. Necdin mediates skeletal muscle regeneration by promoting myoblast survival and differentiation. ACTA ACUST UNITED AC 2007; 179:305-19. [PMID: 17954612 PMCID: PMC2064766 DOI: 10.1083/jcb.200701027] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Regeneration of muscle fibers that are lost during pathological muscle degeneration or after injuries is sustained by the production of new myofibers. An important cell type involved in muscle regeneration is the satellite cell. Necdin is a protein expressed in satellite cell–derived myogenic precursors during perinatal growth. However, its function in myogenesis is not known. We compare transgenic mice that overexpress necdin in skeletal muscle with both wild-type and necdin null mice. After muscle injury the necdin null mice show a considerable defect in muscle healing, whereas mice that overexpress necdin show a substantial increase in myofiber regeneration. We also find that in muscle, necdin increases myogenin expression, accelerates differentiation, and counteracts myoblast apoptosis. Collectively, these data clarify the function and mechanism of necdin in skeletal muscle and show the importance of necdin in muscle regeneration.
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Affiliation(s)
- Daniela Deponti
- Department of Histology and Medical Embryology, University of Roma-La Sapienza, 00161 Rome, Italy
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