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Chemello F, Grespi F, Zulian A, Cancellara P, Hebert-Chatelain E, Martini P, Bean C, Alessio E, Buson L, Bazzega M, Armani A, Sandri M, Ferrazza R, Laveder P, Guella G, Reggiani C, Romualdi C, Bernardi P, Scorrano L, Cagnin S, Lanfranchi G. Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle. Cell Rep 2020; 26:3784-3797.e8. [PMID: 30917329 DOI: 10.1016/j.celrep.2019.02.105] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/29/2018] [Accepted: 02/26/2019] [Indexed: 12/27/2022] Open
Abstract
Skeletal muscle is composed of different myofiber types that preferentially use glucose or lipids for ATP production. How fuel preference is regulated in these post-mitotic cells is largely unknown, making this issue a key question in the fields of muscle and whole-body metabolism. Here, we show that microRNAs (miRNAs) play a role in defining myofiber metabolic profiles. mRNA and miRNA signatures of all myofiber types obtained at the single-cell level unveiled fiber-specific regulatory networks and identified two master miRNAs that coordinately control myofiber fuel preference and mitochondrial morphology. Our work provides a complete and integrated mouse myofiber type-specific catalog of gene and miRNA expression and establishes miR-27a-3p and miR-142-3p as regulators of lipid use in skeletal muscle.
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Affiliation(s)
- Francesco Chemello
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Alessandra Zulian
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Pasqua Cancellara
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Etienne Hebert-Chatelain
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Camilla Bean
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Enrico Alessio
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Martina Bazzega
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Marco Sandri
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Ruggero Ferrazza
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Paolo Laveder
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
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Bruno* RM, Giardini G, Malacrida S, Catuzzo B, Armenia S, Ghiadoni L, Brustia R, Laveder P, Salvi P, Cauchy E, Pratali L. P6.20 ROLE OF ALTERED VASCULAR REACTIVITY IN THE PATHOPHYSIOLOGY OF ACUTE MOUNTAIN SICKNESS. Artery Res 2015. [DOI: 10.1016/j.artres.2015.10.304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Frangini M, Franzolin E, Chemello F, Laveder P, Romualdi C, Bianchi V, Rampazzo C. Synthesis of mitochondrial DNA precursors during myogenesis, an analysis in purified C2C12 myotubes. J Biol Chem 2013; 288:5624-35. [PMID: 23297407 PMCID: PMC3581417 DOI: 10.1074/jbc.m112.441147] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
During myogenesis, myoblasts fuse into multinucleated myotubes that acquire the contractile fibrils and accessory structures typical of striated skeletal muscle fibers. To support the high energy requirements of muscle contraction, myogenesis entails an increase in mitochondrial (mt) mass with stimulation of mtDNA synthesis and consumption of DNA precursors (dNTPs). Myotubes are quiescent cells and as such down-regulate dNTP production despite a high demand for dNTPs. Although myogenesis has been studied extensively, changes in dNTP metabolism have not been examined specifically. In differentiating cultures of C2C12 myoblasts and purified myotubes, we analyzed expression and activities of enzymes of dNTP biosynthesis, dNTP pools, and the expansion of mtDNA. Myotubes exibited pronounced post-mitotic modifications of dNTP synthesis with a particularly marked down-regulation of de novo thymidylate synthesis. Expression profiling revealed the same pattern of enzyme down-regulation in adult murine muscles. The mtDNA increased steadily after myoblast fusion, turning over rapidly, as revealed after treatment with ethidium bromide. We individually down-regulated p53R2 ribonucleotide reductase, thymidine kinase 2, and deoxyguanosine kinase by siRNA transfection to examine how a further reduction of these synthetic enzymes impacted myotube development. Silencing of p53R2 had little effect, but silencing of either mt kinase caused 50% mtDNA depletion and an unexpected decrease of all four dNTP pools independently of the kinase specificity. We suggest that during development of myotubes the shortage of even a single dNTP may affect all four pools through dysregulation of ribonucleotide reduction and/or dissipation of the non-limiting dNTPs during unproductive elongation of new DNA chains.
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Affiliation(s)
- Miriam Frangini
- Department of Biology, University of Padova, 35131 Padova, Italy
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Chemello F, Bean C, Cancellara P, Laveder P, Reggiani C, Lanfranchi G. Microgenomic analysis in skeletal muscle: expression signatures of individual fast and slow myofibers. PLoS One 2011; 6:e16807. [PMID: 21364935 PMCID: PMC3043066 DOI: 10.1371/journal.pone.0016807] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 12/30/2010] [Indexed: 11/18/2022] Open
Abstract
Background Skeletal muscle is a complex, versatile tissue composed of a variety of functionally diverse fiber types. Although the biochemical, structural and functional properties of myofibers have been the subject of intense investigation for the last decades, understanding molecular processes regulating fiber type diversity is still complicated by the heterogeneity of cell types present in the whole muscle organ. Methodology/Principal Findings We have produced a first catalogue of genes expressed in mouse slow-oxidative (type 1) and fast-glycolytic (type 2B) fibers through transcriptome analysis at the single fiber level (microgenomics). Individual fibers were obtained from murine soleus and EDL muscles and initially classified by myosin heavy chain isoform content. Gene expression profiling on high density DNA oligonucleotide microarrays showed that both qualitative and quantitative improvements were achieved, compared to results with standard muscle homogenate. First, myofiber profiles were virtually free from non-muscle transcriptional activity. Second, thousands of muscle-specific genes were identified, leading to a better definition of gene signatures in the two fiber types as well as the detection of metabolic and signaling pathways that are differentially activated in specific fiber types. Several regulatory proteins showed preferential expression in slow myofibers. Discriminant analysis revealed novel genes that could be useful for fiber type functional classification. Conclusions/Significance As gene expression analyses at the single fiber level significantly increased the resolution power, this innovative approach would allow a better understanding of the adaptive transcriptomic transitions occurring in myofibers under physiological and pathological conditions.
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Affiliation(s)
- Francesco Chemello
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Camilla Bean
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Pasqua Cancellara
- Department of Anatomy and Physiology, University of Padova, Padova, Italy
| | - Paolo Laveder
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Carlo Reggiani
- Department of Anatomy and Physiology, University of Padova, Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology and CRIBI Biotechnology Center, University of Padova, Padova, Italy
- * E-mail:
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Millino C, Fanin M, Vettori A, Laveder P, Mostacciuolo ML, Angelini C, Lanfranchi G. Different atrophy-hypertrophy transcription pathways in muscles affected by severe and mild spinal muscular atrophy. BMC Med 2009; 7:14. [PMID: 19351384 PMCID: PMC2676312 DOI: 10.1186/1741-7015-7-14] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 04/07/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a neurodegenerative disorder associated with mutations of the survival motor neuron gene SMN and is characterized by muscle weakness and atrophy caused by degeneration of spinal motor neurons. SMN has a role in neurons but its deficiency may have a direct effect on muscle tissue. METHODS We applied microarray and quantitative real-time PCR to study at transcriptional level the effects of a defective SMN gene in skeletal muscles affected by the two forms of SMA: the most severe type I and the mild type III. RESULTS The two forms of SMA generated distinct expression signatures: the SMA III muscle transcriptome is close to that found under normal conditions, whereas in SMA I there is strong alteration of gene expression. Genes implicated in signal transduction were up-regulated in SMA III whereas those of energy metabolism and muscle contraction were consistently down-regulated in SMA I. The expression pattern of gene networks involved in atrophy signaling was completed by qRT-PCR, showing that specific pathways are involved, namely IGF/PI3K/Akt, TNF-alpha/p38 MAPK and Ras/ERK pathways. CONCLUSION Our study suggests a different picture of atrophy pathways in each of the two forms of SMA. In particular, p38 may be the regulator of protein synthesis in SMA I. The SMA III profile appears as the result of the concurrent presence of atrophic and hypertrophic fibers. This more favorable condition might be due to the over-expression of MTOR that, given its role in the activation of protein synthesis, could lead to compensatory hypertrophy in SMA III muscle fibers.
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Affiliation(s)
- Caterina Millino
- CRIBI Biotechnology Centre, University of Padova, Padova, Italy.
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Feltrin E, Campanaro S, Diehl AD, Ehler E, Faulkner G, Fordham J, Gardin C, Harris M, Hill D, Knoell R, Laveder P, Mittempergher L, Nori A, Reggiani C, Sorrentino V, Volpe P, Zara I, Valle G, Deegan J. Muscle Research and Gene Ontology: New standards for improved data integration. BMC Med Genomics 2009; 2:6. [PMID: 19178689 PMCID: PMC2657163 DOI: 10.1186/1755-8794-2-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 01/29/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO) Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community. RESULTS The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature. CONCLUSION The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki http://wiki.geneontology.org/index.php/Muscle_Biology.
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Affiliation(s)
- Erika Feltrin
- CRIBI- Interdepartmental Biotechnology Center, University of Padua, Padua, Italy.
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Cagnin S, Biscuola M, Patuzzo C, Trabetti E, Pasquali A, Laveder P, Faggian G, Iafrancesco M, Mazzucco A, Pignatti PF, Lanfranchi G. Reconstruction and functional analysis of altered molecular pathways in human atherosclerotic arteries. BMC Genomics 2009; 10:13. [PMID: 19134193 PMCID: PMC2654039 DOI: 10.1186/1471-2164-10-13] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 01/09/2009] [Indexed: 12/24/2022] Open
Abstract
Background Atherosclerosis affects aorta, coronary, carotid, and iliac arteries most frequently than any other body vessel. There may be common molecular pathways sustaining this process. Plaque presence and diffusion is revealed by circulating factors that can mediate systemic reaction leading to plaque rupture and thrombosis. Results We used DNA microarrays and meta-analysis to study how the presence of calcified plaque modifies human coronary and carotid gene expression. We identified a series of potential human atherogenic genes that are integrated in functional networks involved in atherosclerosis. Caveolae and JAK/STAT pathways, and S100A9/S100A8 interacting proteins are certainly involved in the development of vascular disease. We found that the system of caveolae is directly connected with genes that respond to hormone receptors, and indirectly with the apoptosis pathway. Cytokines, chemokines and growth factors released in the blood flux were investigated in parallel. High levels of RANTES, IL-1ra, MIP-1alpha, MIP-1beta, IL-2, IL-4, IL-5, IL-6, IL-7, IL-17, PDGF-BB, VEGF and IFN-gamma were found in plasma of atherosclerotic patients and might also be integrated in the molecular networks underlying atherosclerotic modifications of these vessels. Conclusion The pattern of cytokine and S100A9/S100A8 up-regulation characterizes atherosclerosis as a proinflammatory disorder. Activation of the JAK/STAT pathway is confirmed by the up-regulation of IL-6, STAT1, ISGF3G and IL10RA genes in coronary and carotid plaques. The functional network constructed in our research is an evidence of the central role of STAT protein and the caveolae system to contribute to preserve the plaque. Moreover, Cav-1 is involved in SMC differentiation and dyslipidemia confirming the importance of lipid homeostasis in the atherosclerotic phenotype.
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Affiliation(s)
- Stefano Cagnin
- CRIBI Biotechnology Centre, University of Padova, Padova, Italy.
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Calura E, Cagnin S, Raffaello A, Laveder P, Lanfranchi G, Romualdi C. Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages. BMC Genomics 2008; 9:630. [PMID: 19108710 PMCID: PMC2642825 DOI: 10.1186/1471-2164-9-630] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 12/23/2008] [Indexed: 12/28/2022] Open
Abstract
Background Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of contractile proteins and reduction of fiber volume. Although in the last decade the molecular aspects underlying muscle atrophy have received increased attention, the fine mechanisms controlling muscle degeneration are still incomplete. In this study we applied meta-analysis on gene expression signatures pertaining to different types of muscle atrophy for the identification of novel key regulatory signals implicated in these degenerative processes. Results We found a general down-regulation of genes involved in energy production and carbohydrate metabolism and up-regulation of genes for protein degradation and catabolism. Six functional pathways occupy central positions in the molecular network obtained by the integration of atrophy transcriptome and molecular interaction data. They are TGF-β pathway, apoptosis, membrane trafficking/cytoskeleton organization, NFKB pathways, inflammation and reorganization of the extracellular matrix. Protein degradation pathway is evident only in the network specific for muscle short-term response to atrophy. TGF-β pathway plays a central role with proteins SMAD3/4, MYC, MAX and CDKN1A in the general network, and JUN, MYC, GNB2L1/RACK1 in the short-term muscle response network. Conclusion Our study offers a general overview of the molecular pathways and cellular processes regulating the establishment and maintenance of atrophic state in skeletal muscle, showing also how the different pathways are interconnected. This analysis identifies novel key factors that could be further investigated as potential targets for the development of therapeutic treatments. We suggest that the transcription factors SMAD3/4, GNB2L1/RACK1, MYC, MAX and JUN, whose functions have been extensively studied in tumours but only marginally in muscle, appear instead to play important roles in regulating muscle response to atrophy.
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Affiliation(s)
- Enrica Calura
- Department of Biology, University of Ferrara, Ferrara, Italy.
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Raffaello A, Laveder P, Romualdi C, Bean C, Toniolo L, Germinario E, Megighian A, Danieli-Betto D, Reggiani C, Lanfranchi G. Denervation in murine fast-twitch muscle: short-term physiological changes and temporal expression profiling. Physiol Genomics 2005; 25:60-74. [PMID: 16380408 DOI: 10.1152/physiolgenomics.00051.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Denervation deeply affects muscle structure and function, the alterations being different in slow and fast muscles. Because the effects of denervation on fast muscles are still controversial, and high-throughput studies on gene expression in denervated muscles are lacking, we studied gene expression during atrophy progression following denervation in mouse tibialis anterior (TA). The sciatic nerve was cut close to trochanter in adult CD1 mice. One, three, seven, and fourteen days after denervation, animals were killed and TA muscles were dissected out and utilized for physiological experiments and gene expression studies. Target cDNAs from TA muscles were hybridized on a dedicated cDNA microarray of muscle genes. Seventy-one genes were found differentially expressed. Microarray results were validated, and the expression of relevant genes not probed on our array was monitored by real-time quantitative PCR (RQ-PCR). Nuclear- and mitochondrial-encoded genes implicated in energy metabolism were consistently downregulated. Among genes implicated in muscle contraction (myofibrillar and sarcoplasmic reticulum), genes typical of fast fibers were downregulated, whereas those typical of slow fibers were upregulated. Electrophoresis and Western blot showed less pronounced changes in myofibrillar protein expression, partially confirming changes in gene expression. Isometric tension of skinned fibers was little affected by denervation, whereas calcium sensitivity decreased. Functional studies in mouse extensor digitorum longus muscle showed prolongation in twitch time parameters and shift to the left in force-frequency curves after denervation. We conclude that, if studied at the mRNA level, fast muscles appear not less responsive than slow muscles to the interruption of neural stimulation.
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Affiliation(s)
- Anna Raffaello
- Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative Biotechnology Center, University of Padova, Padua, Italy
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Toppo S, Cannata N, Fontana P, Romualdi C, Laveder P, Bertocco E, Lanfranchi G, Valle G. TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts. Bioinformatics 2003; 19:661-2. [PMID: 12651729 DOI: 10.1093/bioinformatics/btg045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TRAIT is a knowledgebase integrating information on transcripts with related data from genome, proteins, ortholog genes and diseases. It was initially built as a system to manage an EST-based gene discovery project on human skeletal muscle, which yielded over 4500 independent sequence clusters. Transcripts are annotated using automatic as well as manual procedures, linking known transcripts to public databases and unknown transcripts to tables of predicted features. Data are stored in a MySQL database. Complex queries are automatically built by means of a user-friendly web interface that allows the concurrent selection of many fields such as ontology, expression level, map position and protein domains. The results are parsed by the system and returned in a ranked order, in respect to the number of satisfied criteria.
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Affiliation(s)
- Stefano Toppo
- CRIBI, Università di Padova, via Ugo Bassi 58/B, Padova, 35131 Italy
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Campanaro S, Romualdi C, Fanin M, Celegato B, Pacchioni B, Trevisan S, Laveder P, De Pittà C, Pegoraro E, Hayashi YK, Valle G, Angelini C, Lanfranchi G. Gene expression profiling in dysferlinopathies using a dedicated muscle microarray. Hum Mol Genet 2002; 11:3283-98. [PMID: 12471055 DOI: 10.1093/hmg/11.26.3283] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have performed expression profiling to define the molecular changes in dysferlinopathy using a novel dedicated microarray platform made with 3'-end skeletal muscle cDNAs. Eight dysferlinopathy patients, defined by western blot, immunohistochemistry and mutation analysis, were investigated with this technology. In a first experiment RNAs from different limb-girdle muscular dystrophy type 2B patients were pooled and compared with normal muscle RNA to characterize the general transcription pattern of this muscular disorder. Then the expression profiles of patients with different clinical traits were independently obtained and hierarchical clustering was applied to discover patient-specific gene variations. MHC class I genes and genes involved in protein biosynthesis were up-regulated in relation to muscle histopathological features. Conversely, the expression of genes codifying the sarcomeric proteins titin, nebulin and telethonin was down-regulated. Neither calpain-3 nor caveolin, a sarcolemmal protein interacting with dysferlin, was consistently reduced. There was a major up-regulation of proteins interacting with calcium, namely S100 calcium-binding proteins and sarcolipin, a sarcoplasmic calcium regulator.
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Affiliation(s)
- Stefano Campanaro
- CRIBI Biotechnology Centre and Dipartimento di Biologia, Università degli Studi di Padova, Padova, Italy
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Abstract
We have developed a new strategy for producing subtracted cDNA libraries that is optimized for connective and epithelial tissues, where a few exceptionally abundant (super-prevalent) RNA species account for a large fraction of the total mRNA mass. Our method consists of a two-step subtraction of the most abundant mRNAs: the first step involves a novel use of oligo-directed RNase H digestion to lower the concentration of tissue-specific, super-prevalent RNAs. In the second step, a highly specific subtraction is achieved through hybridization with probes from a 3'-end ESTs collection. By applying this technique in skeletal muscle, we have constructed subtracted cDNA libraries that are effectively enriched for genes expressed at low levels. We further report on frequent premature termination of transcription in human muscle mitochondria and discuss the importance of this phenomenon in designing subtractive approaches. The tissue-specific collections of cDNA clones generated by our method are particularly well suited for expression profiling.
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Affiliation(s)
- Paolo Laveder
- CRIBI Biotechnology Center, Università degli Studi di Padova, via Ugo Bassi 58b, Padua I-35121, Italy
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13
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Faulkner G, Pallavicini A, Comelli A, Salamon M, Bortoletto G, Ievolella C, Trevisan S, Kojic' S, Dalla Vecchia F, Laveder P, Valle G, Lanfranchi G. FATZ, a filamin-, actinin-, and telethonin-binding protein of the Z-disc of skeletal muscle. J Biol Chem 2000; 275:41234-42. [PMID: 10984498 DOI: 10.1074/jbc.m007493200] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the identification and characterization of a novel 32-kDa protein expressed in skeletal muscle and located in the Z-disc of the sarcomere. We found that this protein binds to three other Z-disc proteins; therefore, we have named it FATZ, gamma-filamin/ABP-L, alpha-actinin and telethonin binding protein of the Z-disc. From yeast two-hybrid experiments we are able to show that the SR3-SR4 domains of alpha-actinin 2 are required to bind the COOH-terminal region of the FATZ as does gamma-filamin/ABP-L. Furthermore, by using a glutathione S-transferase overlay assay we find that FATZ also binds telethonin. The level of FATZ protein in muscle cells increases during differentiation, being clearly detectable before the onset of myosin. Although FATZ has no known interaction domains, it would appear to be involved in a complex network of interactions with other Z-band components. On the basis of the information known about its binding partners, we could envisage a central role for FATZ in the myofibrillogenesis. After screening our muscle expressed sequence tag data base and the public expressed sequence tag data bases, we were able to assemble two other muscle transcripts that show a high level of identity with FATZ in two different domains. Therefore, FATZ may be the first member of a small family of novel muscle proteins.
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Affiliation(s)
- G Faulkner
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34012 Trieste, Padova, Italy
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Abstract
A very simple hemoglobin switching was discovered in the lamprey Lampetra zanandreai. A single larval globin cDNA and two adult globin cDNAs were fully sequenced and their differential expression during lamprey development was investigated. The evolutionary positions of these new globin sequences are also discussed.
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Affiliation(s)
- G Lanfranchi
- Dipartimento di Biologia, Università degli Studi di Padova, Italy
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Nicoletti L, Laveder P, Pellizzari R, Cardazzo B, Carignani G. Comparative analysis of the region of the mitochondrial genome containing the ATPase subunit 9 gene in the two related yeast species Saccharomyces douglasii and Saccharomyces cerevisiae. Curr Genet 1994; 25:504-7. [PMID: 8082200 DOI: 10.1007/bf00351669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have determined the nucleotide sequence of a region of the mitochondrial genome of the yeast Saccharomyces douglasii which contains the ATPase subunit 9 gene and part of the intergenic sequences that surround it. The gene is 228 nucleotides long and encodes a polypeptide of 76 aa. A comparison of the coding sequence with that of S. cerevisiae reveals the presence of three silent transitions. A high level of similarity is also found between regions involved in the initiation of transcription and mRNA processing. More interestingly, a region of similarity situated outside the known regulatory regions has been identified. As the intergenic regions are generally highly divergent, the remarkable conservation of these non-coding sequences suggests that their structure may be relevant to the expression of this region of the mitochondrial DNA.
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Affiliation(s)
- L Nicoletti
- Dipartimento di Chimica Biologica, Università di Padova, Italy
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Abstract
Lampreys are very primitive vertebrates belonging to the Agnata group. Although higher vertebrates have polymeric hemoglobin molecules which are encoded by several differentially expressed genes, lampreys have monomeric hemoglobins. However, it is unclear whether one or more globin genes are present. In this paper we show that four different species of globin can be separated by electrophoresis in acetic acid-urea-Triton gels. Two of the four species are present only before metamorphosis, while the other two are present only during adult life. In order to discover whether these differences are due to post-translational modifications of a unique amino acid sequence, we extracted globin mRNAs from both larval and adult stages and translated them in vitro. We found that both larval and adult globin mRNAs produce single globin bands; however, larval and adult bands are different from each other. Our data are consistent with the idea that two different globin genes are present in lampreys and that they are differentially expressed during development.
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Affiliation(s)
- G Lanfranchi
- Dipartimento di Biologia, Università degli Studi di Padova, Italy
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