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Martínez-Vieyra I, Pacheco-Tapia G, Reyes-López C, Méndez-Méndez JV, Cerecedo D. Role of α-Dystrobrevin in the differentiation process of HL-60 cells. Exp Cell Res 2018; 370:591-600. [PMID: 30026031 DOI: 10.1016/j.yexcr.2018.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/28/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
The α-Dystrobrevin gene encodes at least five different protein isoforms, expressed in diverse tissues. The α-Dystrobrevin-1 isoform (α-Db-1) is a member of the cytoplasmic dystrophin-associated protein complex, which has a C-terminal extension comprising at least three tyrosine residues susceptible to phosphorylation in vivo. We previously described α-Db in stem-progenitor cells and blood neutrophils as playing a scaffolding role and, in association with kinesin and microtubules, α-Db promotes platelet-granule trafficking. Additionally, the microtubules must establish a balanced interaction with the lamina A/C network for appropriate nuclear morphology. Considering that the most outstanding feature during neutrophil differentiation is nuclei lobulation, we hypothesized that α-Db might possess a pivotal function during the neutrophil differentiation process. Western Blot (WB) and confocal microscope assays evidenced a differential pattern expression and a subcellular redistribution of α-Db in neutrophils derived from HL-60 cells. At the end of the differentiation process, we detected an important diminution in the expression of tubulin, kinesin, and α-Db-1. Knockdown of α-Db prevented nuclei lobulation, increased Lamin A/C and syne1 expression and augmented the roughness of derived neutrophil membrane and disturbed filopodia assembly. Our results suggest that HL-60 cells undergo extensive cytoskeletal reorganization including α-Db in order to possess lobulated nuclei when they further differentiate into neutrophils.
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Affiliation(s)
- Ivette Martínez-Vieyra
- Laboratorio de Hematobiología, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Giselle Pacheco-Tapia
- Laboratorio de Hematobiología, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - César Reyes-López
- Laboratorio de Bioquímica Estructural, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Juan Vicente Méndez-Méndez
- Centro de Nanociencias y Micro y Nanotecnología, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Doris Cerecedo
- Laboratorio de Hematobiología, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico.
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Rangrez AY, Bernt A, Poyanmehr R, Harazin V, Boomgaarden I, Kuhn C, Rohrbeck A, Frank D, Frey N. Dysbindin is a potent inducer of RhoA-SRF-mediated cardiomyocyte hypertrophy. ACTA ACUST UNITED AC 2014; 203:643-56. [PMID: 24385487 PMCID: PMC3840930 DOI: 10.1083/jcb.201303052] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dysbindin activates RhoA–SRF and MEK1–ERK1 signaling pathways in cardiomyocytes to promote cardiac hypertrophy. Dysbindin is an established schizophrenia susceptibility gene thoroughly studied in the context of the brain. We have previously shown through a yeast two-hybrid screen that it is also a cardiac binding partner of the intercalated disc protein Myozap. Because Dysbindin is highly expressed in the heart, we aimed here at deciphering its cardiac function. Using a serum response factor (SRF) response element reporter-driven luciferase assay, we identified a robust activation of SRF signaling by Dysbindin overexpression that was associated with significant up-regulation of SRF gene targets, such as Acta1 and Actc1. Concurrently, we identified RhoA as a novel binding partner of Dysbindin. Further phenotypic and mechanistic characterization revealed that Dysbindin induced cardiac hypertrophy via RhoA–SRF and MEK1–ERK1 signaling pathways. In conclusion, we show a novel cardiac role of Dysbindin in the activation of RhoA–SRF and MEK1–ERK1 signaling pathways and in the induction of cardiac hypertrophy. Future in vivo studies should examine the significance of Dysbindin in cardiomyopathy.
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Affiliation(s)
- Ashraf Yusuf Rangrez
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, D-24105 Kiel, Germany
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3
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Dystrobrevin controls neurotransmitter release and muscle Ca(2+) transients by localizing BK channels in Caenorhabditis elegans. J Neurosci 2012; 31:17338-47. [PMID: 22131396 DOI: 10.1523/jneurosci.3638-11.2011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Dystrobrevin is a major component of a dystrophin-associated protein complex. It is widely expressed in mammalian tissues, including the nervous system, in which it is localized to the presynaptic nerve terminal with unknown function. In a genetic screen for suppressors of a lethargic phenotype caused by a gain-of-function isoform of SLO-1 in Caenorhabditis elegans, we isolated multiple loss-of-function (lf) mutants of the dystrobrevin gene dyb-1.dyb-1(lf) phenocopied slo-1(lf), causing increased neurotransmitter release at the neuromuscular junction, increased frequency of Ca(2+) transients in body-wall muscle, and abnormal locomotion behavior. Neuron- and muscle-specific rescue experiments suggest that DYB-1 is required for SLO-1 function in both neurons and muscle cells. DYB-1 colocalized with SLO-1 at presynaptic sites in neurons and dense body regions in muscle cells, and dyb-1(lf) caused SLO-1 mislocalization in both types of cells without altering SLO-1 protein level. The neuronal phenotypes of dyb-1(lf) were partially rescued by mouse α-dystrobrevin-1. These observations revealed novel functions of the BK channel in regulating muscle Ca(2+) transients and of dystrobrevin in controlling neurotransmitter release and muscle Ca(2+) transients by localizing the BK channel.
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Nakamori M, Takahashi MP. The role of α-dystrobrevin in striated muscle. Int J Mol Sci 2011; 12:1660-71. [PMID: 21673914 PMCID: PMC3111625 DOI: 10.3390/ijms12031660] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 01/29/2011] [Accepted: 02/23/2011] [Indexed: 12/29/2022] Open
Abstract
Muscular dystrophies are a group of diseases that primarily affect striated muscle and are characterized by the progressive loss of muscle strength and integrity. Major forms of muscular dystrophies are caused by the abnormalities of the dystrophin glycoprotein complex (DGC) that plays crucial roles as a structural unit and scaffolds for signaling molecules at the sarcolemma. α-Dystrobrevin is a component of the DGC and directly associates with dystrophin. α-Dystrobrevin also binds to intermediate filaments as well as syntrophin, a modular adaptor protein thought to be involved in signaling. Although no muscular dystrophy has been associated within mutations of the α-dystrobrevin gene, emerging findings suggest potential significance of α-dystrobrevin in striated muscle. This review addresses the functional role of α-dystrobrevin in muscle as well as its possible implication for muscular dystrophy.
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Affiliation(s)
- Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2, D-4, Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail:
- Department of Neurology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 645 URMC, Rochester, NY 14642, USA
| | - Masanori P. Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2, D-4, Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-6-6879-3571; Fax: +81-6-6879-3579
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5
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Abstract
Mutations in the gene encoding tripartite motif protein 32 (TRIM32) cause two seemingly diverse diseases: limb-girdle muscular dystrophy type 2H (LGMD2H) or sarcotubular myopathy (STM) and Bardet–Biedl syndrome type 11(BBS11). Although TRIM32 is involved in protein ubiquitination, its substrates and the molecular consequences of disease-causing mutations are poorly understood. In this paper, we show that TRIM32 is a widely expressed ubiquitin ligase that is localized to the Z-line in skeletal muscle. Using the yeast two-hybrid system, we found that TRIM32 binds and ubiquitinates dysbindin, a protein implicated in the genetic aetiology of schizophrenia, augmenting its degradation. Small-interfering RNA-mediated knock-down of TRIM32 in myoblasts resulted in elevated levels of dysbindin. Importantly, the LGMD2H/STM-associated TRIM32 mutations, D487N and R394H impair ubiquitin ligase activity towards dysbindin and were mislocalized in heterologous cells. These mutants were able to self-associate and also co-immunoprecipitated with wild-type TRIM32 in transfected cells. Furthermore, the D487N mutant could bind to both dysbindin and its E2 enzyme but was defective in monoubiquitination. In contrast, the BBS11 mutant P130S did not show any biochemical differences compared with the wild-type protein. Our data identify TRIM32 as a regulator of dysbindin and demonstrate that the LGMD2H/STM mutations may impair substrate ubiquitination.
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Affiliation(s)
- Matthew Locke
- Department of Psychological Medicine, Cardiff University, Cardiff, UK
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6
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Pawlikowski BT, Maimone MM. alpha-Dystrobrevin isoforms differ in their colocalization with and stabilization of agrin-induced acetylcholine receptor clusters. Neuroscience 2008; 154:582-94. [PMID: 18468804 DOI: 10.1016/j.neuroscience.2008.01.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 12/21/2007] [Accepted: 01/12/2008] [Indexed: 11/19/2022]
Abstract
In skeletal muscle, alpha-dystrobrevin (alphaDB) is expressed throughout the sarcolemma with high concentrations at the neuromuscular junction. Mice lacking alphaDB display a mild muscular dystrophy and perturbations at the neuromuscular junction that include disruptions to acetylcholine receptor (AChR) cluster stability and patterning. In adult skeletal muscle, three alternatively spliced isoforms (alphaDB1, alphaDB2, alphaDB3) are expressed, while two other splice variants (alphaDB1(-) and alphaDB2(-)) are expressed only during early development. alphaDB is clearly important in AChR stabilization; however, the degree to which individual alphaDB isoforms and their specific functional domains contribute to AChR cluster stability is not fully understood. To investigate this, we established a primary muscle cell culture system from alphaDB knockout mice and stably expressed individual alphaDB isoforms using retroviral infection. A comparison between wild-type and alphaDB knockout muscle cells showed that in the absence of alphaDB, fewer AChR clusters formed in response to agrin treatment, and these AChR clusters were very unstable. Retroviral expression studies revealed that the largest isoforms (alphaDB1, alphaDB1(-), alphaDB2, alphaDB2(-)) colocalized with agrin-induced AChR clusters and rescued the AChR cluster formation defects back to wild-type levels, while only the first three isoforms fully rescued AChR cluster stability back to wild-type levels. alphaDB2(-) conferred an intermediate level of stability to the AChR clusters. In contrast, alphaDB3 showed no specific colocalization with AChR clusters and little effect on AChR cluster formation or stabilization. Twice as much syntrophin was found associated with alphaDB2 compared with alphaDB2(-) in myotubes suggesting that increased recruitment of syntrophin by alphaDB may enhance the stability of AChR clusters. Taken together, these data demonstrate that different alphaDB isoforms have different functional capabilities in the formation and maintenance of AChR clusters in muscle cells, and that these differences are likely due to the presence of different functional domains in each isoform.
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MESH Headings
- Agrin/pharmacology
- Animals
- Cells, Cultured
- DNA, Complementary/biosynthesis
- DNA, Complementary/genetics
- Dystrophin-Associated Proteins/genetics
- Dystrophin-Associated Proteins/metabolism
- Genetic Vectors
- Isomerism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Microscopy, Confocal
- Muscle, Skeletal/cytology
- Muscle, Skeletal/metabolism
- Myoblasts/drug effects
- Myoblasts/enzymology
- Plasmids/genetics
- Receptors, Cholinergic/drug effects
- Receptors, Cholinergic/metabolism
- Retroviridae/genetics
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Affiliation(s)
- B T Pawlikowski
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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7
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Ervasti JM, Sonnemann KJ. Biology of the striated muscle dystrophin-glycoprotein complex. INTERNATIONAL REVIEW OF CYTOLOGY 2008; 265:191-225. [PMID: 18275889 DOI: 10.1016/s0074-7696(07)65005-0] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Since its first description in 1990, the dystrophin-glycoprotein complex has emerged as a critical nexus for human muscular dystrophies arising from defects in a variety of distinct genes. Studies in mammals widely support a primary role for the dystrophin-glycoprotein complex in mechanical stabilization of the plasma membrane in striated muscle and provide hints for secondary functions in organizing molecules involved in cellular signaling. Studies in model organisms confirm the importance of the dystrophin-glycoprotein complex for muscle cell viability and have provided new leads toward a full understanding of its secondary roles in muscle biology.
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Affiliation(s)
- James M Ervasti
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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8
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Rees MLJ, Lien CF, Górecki DC. Dystrobrevins in muscle and non-muscle tissues. Neuromuscul Disord 2007; 17:123-34. [PMID: 17251025 DOI: 10.1016/j.nmd.2006.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 10/26/2006] [Accepted: 11/20/2006] [Indexed: 01/23/2023]
Abstract
The alpha- and beta-dystrobrevins belong to the family of dystrophin-related and dystrophin-associated proteins. As constituents of the dystrophin-associated protein complex, alpha-dystrobrevin was believed to have a role predominantly in muscles and beta-dystrobrevin in non-muscle tissues. Recent reports described novel localisations and molecular characteristics of alpha-dystrobrevin isoforms in non-muscle tissues (developing and adult). While single and double knockout studies have revealed distinct functions of dystrobrevin in some tissues, these also suggested a strong compensatory mechanism, where dystrobrevins displaying overlapping tissue expression pattern and structure/function similarity can substitute each other. No human disease has been unequivocally associated within mutations of dystrobrevin genes. However, some significant exceptions to these overlapping expression patterns, mainly in the brain, suggest that dystrobrevin mutations might underlie some specific motor, behavioural or cognitive defects. Dystrobrevin binding partner DTNBP1 (dysbindin) is a probable susceptibility gene for schizophrenia and bipolar affective disorder in some populations. As dysbindin abnormality is linked to Hermansky-Pudlak syndrome, dystrobrevins and/or their binding partners may also be required for proper function of other non-muscle tissues.
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Affiliation(s)
- Melissa L J Rees
- Department of Molecular Medicine, Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
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9
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Lien CF, Hazai D, Yeung D, Tan J, Füchtbauer EM, Jancsik V, Górecki DC. Expression of alpha-dystrobrevin in blood-tissue barriers: sub-cellular localisation and molecular characterisation in normal and dystrophic mice. Cell Tissue Res 2006; 327:67-82. [PMID: 16868787 DOI: 10.1007/s00441-006-0241-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 05/09/2006] [Indexed: 11/30/2022]
Abstract
The alpha- and beta-dystrobrevins (DBs) belong to a family of dystrophin-related and dystrophin-associated proteins that are members of the dystrophin-associated protein complex (DAPC). This complex provides a link between the cytoskeleton and the extracellular matrix or other cells. However, specific functions of the two dystrobrevins remain largely unknown, with alpha-DB being believed to have a role mainly in skeletal muscle. Here, we describe previously unknown expression patterns and the localisation and molecular characteristics of alpha-DB isoforms in non-muscle mouse tissues. We demonstrate a highly specific sub-cellular distribution of alpha-DB in organs forming blood-tissue barriers. We show alpha-DB expression and localisation in testicular Sertoli cells, stomach and respiratory epithelia and provide electron-microscopic evidence for its immunolocalisation in these cells and in the central nervous system. Moreover, we present the molecular characterisation of alpha-DB transcript in these tissues and provide evidence for a distinct heterogeneity of associations between alpha-DB and dystrophins and utrophin in normal and dystrophic non-muscle tissues. Together, our results indicate that alpha-DB, in addition to its role in skeletal muscle, may also be required for the proper function of specific non-muscle tissues and that disruption of DAPC might lead to tissue-blood barrier abnormalities.
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Affiliation(s)
- Chun Fu Lien
- Molecular Medicine, Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, St. Michael's Building, White Swan Road, Portsmouth, UK
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10
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Macpherson PCD, Cieslak D, Goldman D. Myogenin-dependent nAChR clustering in aneural myotubes. Mol Cell Neurosci 2006; 31:649-60. [PMID: 16443371 DOI: 10.1016/j.mcn.2005.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 12/07/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022] Open
Abstract
During development of the neuromuscular junction, nerve-derived agrin and the cell substrate laminin stimulate postsynaptic nAChR clustering. This clustering is dependent on activation of the tyrosine kinase, MuSK, which signals receptor clustering via a rapsyn-dependent mechanism. Myogenin is a muscle-specific transcription factor that controls myoblast differentiation and nAChR gene expression. Here, we used RNA interference to investigate if myogenin is also necessary for nAChR clustering. We find that myogenin expression is essential for robust nAChR clustering and cannot be compensated by the muscle regulatory factors MyoD, myf5, and MRF4. In addition, we show that clustering cannot be rescued in myogenin-depleted myotubes by simply overexpressing the essential clustering molecules MuSK, rapsyn, and nAChRs. These data suggest that myogenin controls the expression of molecules crucial to nAChR clustering in addition to its role in regulating nAChR gene expression.
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Affiliation(s)
- Peter C D Macpherson
- Molecular and Behavioral Neurosciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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11
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Turk R, Sterrenburg E, de Meijer EJ, van Ommen GJB, den Dunnen JT, 't Hoen PAC. Muscle regeneration in dystrophin-deficient mdx mice studied by gene expression profiling. BMC Genomics 2005; 6:98. [PMID: 16011810 PMCID: PMC1190170 DOI: 10.1186/1471-2164-6-98] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Accepted: 07/13/2005] [Indexed: 01/19/2023] Open
Abstract
Background Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characterize the molecular processes associated with regeneration, we compared gene expression levels in hindlimb muscle tissue of mdx and control mice at 9 timepoints, ranging from 1–20 weeks of age. Results Out of 7776 genes, 1735 were differentially expressed between mdx and control muscle at at least one timepoint (p < 0.05 after Bonferroni correction). We found that genes coding for components of the dystrophin-associated glycoprotein complex are generally downregulated in the mdx mouse. Based on functional characteristics such as membrane localization, signal transduction, and transcriptional activation, 166 differentially expressed genes with possible functions in regeneration were analyzed in more detail. The majority of these genes peak at the age of 8 weeks, where the regeneration activity is maximal. The following pathways are activated, as shown by upregulation of multiple members per signalling pathway: the Notch-Delta pathway that plays a role in the activation of satellite cells, and the Bmp15 and Neuregulin 3 signalling pathways that may regulate proliferation and differentiation of satellite cells. In DMD patients, only few of the identified regeneration-associated genes were found activated, indicating less efficient regeneration processes in humans. Conclusion Based on the observed expression profiles, we describe a model for muscle regeneration in mdx mice, which may provide new leads for development of DMD therapies based on the improvement of muscle regeneration efficacy.
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Affiliation(s)
- R Turk
- Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
- Department of Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa, 400 Eckstein Medical Research Building, Iowa City, IA52240-1101, U.S.A
| | - E Sterrenburg
- Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
| | - EJ de Meijer
- Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
| | - G-JB van Ommen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
| | - JT den Dunnen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
- Leiden Genome Technology Center, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
| | - PAC 't Hoen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
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12
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Association of ?-Dystrobrevin with Reorganizing Tight Junctions. J Membr Biol 2005; 203:21-30. [DOI: 10.1007/s00232-004-0728-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Accepted: 12/06/2004] [Indexed: 10/25/2022]
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13
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Trinklein ND, Aldred SJF, Saldanha AJ, Myers RM. Identification and functional analysis of human transcriptional promoters. Genome Res 2003; 13:308-12. [PMID: 12566409 PMCID: PMC420378 DOI: 10.1101/gr.794803] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genomic and full-length cDNA sequences provide opportunities for understanding human gene structure and transcriptional regulatory elements. The simplest regulatory elements to identify are promoters, as their positions are dictated by the location of transcription start sites. We aligned full-length cDNA clones from the Mammalian Gene Collection to the human genome rough draft sequence to estimate the start sites of more than 10,000 human transcripts. We selected genomic sequence just upstream from the 5' end of these cDNA sequences and designated these as putative promoters. We assayed the functions of 152 of these DNA fragments, chosen at random from the entire set, in a luciferase-based transfection assay in four human cultured cell types. Ninety-one percent of these DNA fragments showed significant transcriptional activity in at least one of the cell lines, whereas 89% showed activity in at least two of the lines. We analyzed the distributions of strengths of these promoter fragments in the different cell types and identified likely alternative promoters in a large fraction of the genes. These data indicate that this approach is an effective method for predicting human promoters and provide the first set of functional data collected in parallel for a large set of human promoters.
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Affiliation(s)
- Nathan D Trinklein
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
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14
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Zhu Y, King BL, Parvizi B, Brunk BP, Stoeckert CJ, Quackenbush J, Richardson J, Bult CJ. Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database. Genome Biol 2003; 4:R16. [PMID: 12620126 PMCID: PMC151306 DOI: 10.1186/gb-2003-4-2-r16] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2002] [Revised: 11/27/2002] [Accepted: 12/19/2002] [Indexed: 12/27/2022] Open
Abstract
Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced when the sequences they contain are integrated with such biological information as genomic location, gene function, gene expression and phenotypic variation. We present the analysis and results of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse Genome Informatics (MGI) database.
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Affiliation(s)
- Yunxia Zhu
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA.
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15
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Blake DJ. Dystrobrevin dynamics in muscle-cell signalling: a possible target for therapeutic intervention in Duchenne muscular dystrophy? Neuromuscul Disord 2002; 12 Suppl 1:S110-7. [PMID: 12206805 DOI: 10.1016/s0960-8966(02)00091-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The dystrophin-protein complex forms one of the connections between the extracellular matrix and the cytoskeleton of muscle. This link is disrupted in patients with Duchenne and Becker muscular dystrophies. Dystrobrevin is a component of the dystrophin-protein complex that binds to the C-terminus of dystrophin and also to syntrophin. As its name suggests, dystrobrevin is a relative of dystrophin participating in similar intermolecular interactions. Dystrobrevin-deficient mice have a form of muscular dystrophy that leaves the sarcolemma and dystrophin-protein complex intact but affects an as yet unidentified signalling pathway in muscle. Given that the up-regulation of several genes has a beneficial effect on the muscle in some dystrophic mouse models, alpha-dystrobrevin has a number of properties that might be protective in muscular dystrophy. This article discusses the function of dystrobrevin in muscle and reviews its suitability as a therapeutic target for treating patients with Duchenne and Becker muscular dystrophies.
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Affiliation(s)
- Derek J Blake
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
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16
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Blake DJ, Weir A, Newey SE, Davies KE. Function and genetics of dystrophin and dystrophin-related proteins in muscle. Physiol Rev 2002; 82:291-329. [PMID: 11917091 DOI: 10.1152/physrev.00028.2001] [Citation(s) in RCA: 813] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The X-linked muscle-wasting disease Duchenne muscular dystrophy is caused by mutations in the gene encoding dystrophin. There is currently no effective treatment for the disease; however, the complex molecular pathology of this disorder is now being unravelled. Dystrophin is located at the muscle sarcolemma in a membrane-spanning protein complex that connects the cytoskeleton to the basal lamina. Mutations in many components of the dystrophin protein complex cause other forms of autosomally inherited muscular dystrophy, indicating the importance of this complex in normal muscle function. Although the precise function of dystrophin is unknown, the lack of protein causes membrane destabilization and the activation of multiple pathophysiological processes, many of which converge on alterations in intracellular calcium handling. Dystrophin is also the prototype of a family of dystrophin-related proteins, many of which are found in muscle. This family includes utrophin and alpha-dystrobrevin, which are involved in the maintenance of the neuromuscular junction architecture and in muscle homeostasis. New insights into the pathophysiology of dystrophic muscle, the identification of compensating proteins, and the discovery of new binding partners are paving the way for novel therapeutic strategies to treat this fatal muscle disease. This review discusses the role of the dystrophin complex and protein family in muscle and describes the physiological processes that are affected in Duchenne muscular dystrophy.
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Affiliation(s)
- Derek J Blake
- Medical Research Council, Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Abdulrazzak H, Noro N, Simons JP, Goldspink G, Barnard EA, Górecki DC. Structural diversity despite strong evolutionary conservation in the 5'-untranslated region of the P-type dystrophin transcript. Mol Cell Neurosci 2001; 17:500-13. [PMID: 11273645 DOI: 10.1006/mcne.2000.0950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Analysis of the 5'-flanking regions of the Purkinje (P-) dystrophin genes and mRNAs in different species revealed strong sequence conservation but functional diversity. Multiple transcription initiation sites were identified in cerebella and muscles, tissues expressing P-dystrophin. The predominant initiation site was conserved, with another muscle-specific site located upstream. Despite sequence homology, significant tissue- and species-specific structural diversity in the P-type 5'-ends exists, including alternative splicing within the 5'-untranslated region combined with alternative splicing of intron 1. One amino terminus is conserved in mammals and, to a lesser extent, in chicken. However, alternative usage of ATG codons may result in a choice of N-termini or translation of short upstream ORFs in different species. Promoter activity of a fragment upstream of the cap site was shown by transient expression in myoblasts and in vivo following intramuscular injection. It is tissue- and developmentally regulated. Analysis of promoter deletions suggests the existence of negative regulatory elements in the proximal region.
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Affiliation(s)
- H Abdulrazzak
- Department of Anatomy and Developmental Biology, Division of Basic Medical Sciences, Royal Free and University College Medical School, London, NW3 2PF, United Kingdom
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Newey SE, Gramolini AO, Wu J, Holzfeind P, Jasmin BJ, Davies KE, Blake DJ. A novel mechanism for modulating synaptic gene expression: differential localization of alpha-dystrobrevin transcripts in skeletal muscle. Mol Cell Neurosci 2001; 17:127-40. [PMID: 11161474 DOI: 10.1006/mcne.2000.0918] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Alpha-dystrobrevin is a dystrophin-related and -associated protein that is involved in synapse maturation and is required for normal muscle function. There are three protein isoforms in skeletal muscle, alpha-dystrobrevin-1, -2, and -3 that are encoded by the single alpha-dystrobrevin gene. To understand the role of these proteins in muscle we have investigated the localisation and transcript distribution of the different alpha-dystrobrevin isoforms. Alpha-dystrobrevin-1 and -2 are concentrated at the neuromuscular junction and are both recruited into agrin-induced acetylcholine receptor clusters in cultured myotubes. We also demonstrate that all alpha-dystrobrevin mRNAs are transcribed from a single promoter in skeletal muscle. However, only transcripts encoding alpha-dystrobrevin-1 are preferentially accumulated at postsynaptic sites. These data suggest that the synaptic accumulation of alpha-dystrobrevin-1 mRNA occurs posttranscriptionally, identifying a novel mechanism for synaptic gene expression. Taken together, these results indicate that different isoforms possess distinct roles in synapse formation and possibly in the pathogenesis of muscular dystrophy.
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Affiliation(s)
- S E Newey
- Department of Human Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford, OX1 3QX, United Kingdom
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Mehler MF. Brain dystrophin, neurogenetics and mental retardation. BRAIN RESEARCH. BRAIN RESEARCH REVIEWS 2000; 32:277-307. [PMID: 10751678 DOI: 10.1016/s0165-0173(99)00090-9] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Duchenne muscular dystrophy (DMD) and the allelic disorder Becker muscular dystrophy (BMD) are common X-linked recessive neuromuscular disorders that are associated with a spectrum of genetically based developmental cognitive and behavioral disabilities. Seven promoters scattered throughout the huge DMD/BMD gene locus normally code for distinct isoforms of the gene product, dystrophin, that exhibit nervous system developmental, regional and cell-type specificity. Dystrophin is a complex plasmalemmal-cytoskeletal linker protein that possesses multiple functional domains, autosomal and X-linked homologs and associated binding proteins that form multiunit signaling complexes whose composition is unique to each cellular and developmental context. Through additional interactions with a variety of proteins of the extracellular matrix, plasma membrane, cytoskeleton and distinct intracellular compartments, brain dystrophin acquires the capability to participate in the modulatory actions of a large number of cellular signaling pathways. During neural development, dystrophin is expressed within the neural tube and selected areas of the embryonic and postnatal neuraxis, and may regulate distinct aspects of neurogenesis, neuronal migration and cellular differentiation. By contrast, in the mature brain, dystrophin is preferentially expressed by specific regional neuronal subpopulations within proximal somadendritic microdomains associated with synaptic terminal membranes. Increasing experimental evidence suggests that in adult life, dystrophin normally modulates synaptic terminal integrity, distinct forms of synaptic plasticity and regional cellular signal integration. At a systems level, dystrophin may regulate essential components of an integrated sensorimotor attentional network. Dystrophin deficiency in DMD/BMD patients and in the mdx mouse model appears to impair intracellular calcium homeostasis and to disrupt multiple protein-protein interactions that normally promote information transfer and signal integration from the extracellular environment to the nucleus within regulated microdomains. In DMD/BMD, the individual profiles of cognitive and behavioral deficits, mental retardation and other phenotypic variations appear to depend on complex profiles of transcriptional regulation associated with individual dystrophin mutations that result in the corresponding presence or absence of individual brain dystrophin isoforms that normally exhibit developmental, regional and cell-type-specific expression and functional regulation. This composite experimental model will allow fine-level mapping of cognitive-neurogenetic associations that encompass the interrelationships between molecular, cellular and systems levels of signal integration, and will further our understanding of complex gene-environmental interactions and the pathogenetic basis of developmental disorders associated with mental retardation.
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Affiliation(s)
- M F Mehler
- Departments of Neurology, Neuroscience and Psychiatry, the Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Cantón FR, Quail PH. Both phyA and phyB mediate light-imposed repression of PHYA gene expression in Arabidopsis. PLANT PHYSIOLOGY 1999; 121:1207-16. [PMID: 10594107 PMCID: PMC59487 DOI: 10.1104/pp.121.4.1207] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/1999] [Accepted: 08/10/1999] [Indexed: 05/18/2023]
Abstract
The negatively photoregulated PHYA gene has a complex promoter structure in Arabidopsis, with three active transcription start sites. To identify the photoreceptors responsible for regulation of this gene, and to assess the relative roles of the three transcription start sites, we analyzed the changes in PHYA transcript levels in wild-type and photoreceptor mutant seedlings under various irradiation conditions. Continuous far-red or red light exposures each induced a significant decline in transcript levels in wild-type etiolated seedlings. Analysis of mutants specifically lacking either phyA or phyB protein demonstrated that these phytochromes are required for the negative regulation induced by far-red and red light, respectively. Ribonuclease protection experiments showed further that this negative regulation is confined almost exclusively to the shortest, most abundant PHYA transcript, and occurs predominantly in shoots. By contrast, both of the other minor transcripts in shoots, and all three transcripts in roots, exhibit near constitutive expression. This complex expression pattern indicates that the PHYA gene is subject to regulation by multiple signals, including environmental, developmental, and organ-specific signals.
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Affiliation(s)
- F R Cantón
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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Enigk RE, Maimone MM. Differential expression and developmental regulation of a novel alpha-dystrobrevin isoform in muscle. Gene 1999; 238:479-88. [PMID: 10570976 DOI: 10.1016/s0378-1119(99)00358-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Alpha-dystrobrevin is a dystrophin-related protein expressed primarily in skeletal muscle, heart, lung and brain. In skeletal muscle, alpha-dystrobrevin is a component of the dystrophin-associated glycoprotein complex and is localized to the sarcolemma, presumably through interactions with dystrophin and utrophin. Alternative splicing of the alpha-dystrobrevin gene generates multiple isoforms which have been grouped into three major classes: alpha-DB1, alpha-DB2, and alpha-DB3. Various isoforms have been shown to interact with a variety of proteins; however, the physiological function of the alpha-dystrobrevins remains unknown. In the present study, we have cloned a novel alpha-dystrobrevin cDNA encoding a protein (referred to as alpha-DB2b) with a unique 11 amino acid C-terminal tail. Using RT PCR with primers specific to the new isoform, we have characterized its expression in skeletal muscle, heart, and brain, and in differentiating C2C12 muscle cells. We show that alpha-DB2b is expressed in skeletal muscle, heart and brain, and that exons 12 and 13 are alternatively spliced in alpha-DB2b to generate at least three splice variants. The major alpha-DB2b splice variant expressed in adult skeletal muscle and heart contains exons 12 and 13, while in adult brain, two alpha-DB2b splice variants are expressed at similar levels. This is consistent with the preferential expression of exons 12 and 13 in other alpha-dystrobrevin isoforms in skeletal muscle and heart. Similarly, in alpha-DB1 the first 21 nucleotides of exon 18 are preferentially expressed in skeletal muscle and heart relative to brain. We also show that the expression of alternatively spliced alpha-DB2b is developmentally regulated in muscle; during differentiation of C2C12 cells, alpha-DB2b expression switches from an isoform lacking exons 12 and 13 to one containing them. We demonstrate similar developmental upregulation of exons 12, 13, and 18 in alpha-DB1 and of exons 12 and 13 in alpha-DB2a. Finally, we show that alpha-DB2b protein is expressed in adult skeletal muscle, suggesting that it has a functional role in adult muscle. Together, these data suggest that alternatively spliced variants of the new alpha-dystrobrevin isoform, alpha-DB2b, are differentially expressed in various tissues and developmentally regulated during muscle cell differentiation in a fashion similar to that previously described for alpha-dystrobrevin isoforms.
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Affiliation(s)
- R E Enigk
- Department of Anatomy and Cell Biology, State University of New York Health Science Center, Syracuse 13210, USA
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