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Abbas A, Hammad AS, Al-Shafai M. The role of genetic and epigenetic GNAS alterations in the development of early-onset obesity. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108487. [PMID: 38103632 DOI: 10.1016/j.mrrev.2023.108487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND GNAS (guanine nucleotide-binding protein, alpha stimulating) is an imprinted gene that encodes Gsα, the α subunit of the heterotrimeric stimulatory G protein. This subunit mediates the signalling of a diverse array of G protein-coupled receptors (GPCRs), including the melanocortin 4 receptor (MC4R) that serves a pivotal role in regulating food intake, energy homoeostasis, and body weight. Genetic or epigenetic alterations in GNAS are known to cause pseudohypoparathyroidism in its different subtypes and have been recently associated with isolated, early-onset, severe obesity. Given the diverse biological functions that Gsα serves, multiple molecular mechanisms involving various GPCRs, such as MC4R, β2- and β3-adrenoceptors, and corticotropin-releasing hormone receptor, have been implicated in the pathophysiology of severe, early-onset obesity that results from genetic or epigenetic GNAS changes. SCOPE OF REVIEW This review examines the structure and function of GNAS and provides an overview of the disorders that are caused by defects in this gene and may feature early-onset obesity. Moreover, it elucidates the potential molecular mechanisms underlying Gsα deficiency-induced early-onset obesity, highlighting some of their implications for the diagnosis, management, and treatment of this complex condition. MAJOR CONCLUSIONS Gsα deficiency is an underappreciated cause of early-onset, severe obesity. Therefore, screening children with unexplained, severe obesity for GNAS defects is recommended, to enhance the molecular diagnosis and management of this condition.
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Affiliation(s)
- Alaa Abbas
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Ayat S Hammad
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar.
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Garnier A, Bork NI, Jacquet E, Zipfel S, Muñoz-Guijosa C, Baczkó I, Reichenspurner H, Donzeau-Gouge P, Maier LS, Dobrev D, Girdauskas E, Nikolaev VO, Fischmeister R, Molina CE. Mapping genetic changes in the cAMP-signaling cascade in human atria. J Mol Cell Cardiol 2021; 155:10-20. [PMID: 33631188 DOI: 10.1016/j.yjmcc.2021.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 11/15/2022]
Abstract
AIM To obtain a quantitative expression profile of the main genes involved in the cAMP-signaling cascade in human control atria and in different cardiac pathologies. METHODS AND RESULTS Expression of 48 target genes playing a relevant role in the cAMP-signaling cascade was assessed by RT-qPCR. 113 samples were obtained from right atrial appendages (RAA) of patients in sinus rhythm (SR) with or without atrium dilation, paroxysmal atrial fibrillation (AF), persistent AF or heart failure (HF); and left atrial appendages (LAA) from patients in SR or with AF. Our results show that right and left atrial appendages in donor hearts or from SR patients have similar expression values except for AC7 and PDE2A. Despite the enormous chamber-dependent variability in the gene-expression changes between pathologies, several distinguishable patterns could be identified. PDE8A, PI3Kγ and EPAC2 were upregulated in AF. Different phosphodiesterase (PDE) families showed specific pathology-dependent changes. CONCLUSION By comparing mRNA-expression patterns of the cAMP-signaling cascade related genes in right and left atrial appendages of human hearts and across different pathologies, we show that 1) gene expression is not significantly affected by cardioplegic solution content, 2) it is appropriate to use SR atrial samples as controls, and 3) many genes in the cAMP-signaling cascade are affected in AF and HF but only few of them appear to be chamber (right or left) specific. TOPIC Genetic changes in human diseased atria. TRANSLATIONAL PERSPECTIVE The cyclic AMP signaling pathway is important for atrial function. However, expression patterns of the genes involved in the atria of healthy and diseased hearts are still unclear. We give here a general overview of how different pathologies affect the expression of key genes in the cAMP signaling pathway in human right and left atria appendages. Our study may help identifying new genes of interest as potential therapeutic targets or clinical biomarkers for these pathologies and could serve as a guide in future gene therapy studies.
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Affiliation(s)
- Anne Garnier
- Université Paris-Saclay, Inserm, UMR-S 1180, Châtenay-Malabry, France
| | - Nadja I Bork
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Germany; German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| | - Eric Jacquet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette, France
| | - Svante Zipfel
- Dept. of Cardiovascular Surgery, University Heart Center Hamburg, Germany
| | | | - Istvan Baczkó
- Dept. Pharmacology and Pharmacotherapy, Univ. of Szeged, Hungary
| | | | | | - Lars S Maier
- Dept. Internal Medicine II, University Heart Center, University Hospital Regensburg, Germany
| | - Dobromir Dobrev
- Institute of Pharmacology, West-German Heart and Vascular Center, Faculty of Medicine, University Duisburg-, Essen, Germany
| | - Evaldas Girdauskas
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany; Dept. of Cardiovascular Surgery, University Heart Center Hamburg, Germany
| | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Germany; German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| | | | - Cristina E Molina
- Université Paris-Saclay, Inserm, UMR-S 1180, Châtenay-Malabry, France; Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Germany; German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
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Möhlendick B, Schmid KW, Siffert W. The GNAS SNP c.393C>T (rs7121) as a marker for disease progression and survival in cancer. Pharmacogenomics 2019; 20:553-562. [PMID: 31124412 DOI: 10.2217/pgs-2018-0199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G-protein receptor signaling plays a key role in multiple signal transduction pathways. Aberrant activity of the stimulatory Gsα subunit has been frequently associated with cancer. GNAS sequence alterations and conformational changes of Gsα can both enhance or diminish its function and change downstream effects of G-protein receptor signaling. In this review and meta-analysis, we focus on the synonymous SNP rs7121 (FokI, c.393C>T), which is associated with either tumor progression or prolonged survival in cancer patients (overall hazard ratio = 2.256; p < 0.001). We finally point out the relevance of GNAS rs7121 as a promising biomarker and a prediction tool for therapy response and the need of further experiments to implement it into routine clinical diagnostics.
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Affiliation(s)
- Birte Möhlendick
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Kurt W Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Winfried Siffert
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany
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Klenke S, Siffert W, Frey UH. A novel aspect of GNAS imprinting: higher maternal expression of Gαs in human lymphoblasts, peripheral blood mononuclear cells, mammary adipose tissue, and heart. Mol Cell Endocrinol 2011; 341:63-70. [PMID: 21664251 DOI: 10.1016/j.mce.2011.05.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 05/11/2011] [Accepted: 05/11/2011] [Indexed: 10/25/2022]
Abstract
The human GNAS gene is imprinted in a tissue-specific manner, being expressed primarily from the maternal allele in pituitary, thyroid, renal proximal tubules, and gonads, but is supposed to be biallelically expressed with an equal allelic expression in most other tissues. We analysed allelic expression of Gαs using Pyrosequencing. By genotyping the GNAS T393C polymorphism we quantified mRNA transcripts in lymphoblasts (Ly, n=11), peripheral blood mononuclear cells (PBMC, n=18), mammary adipose tissue (MAT, n=23) and heart tissue (HT, n=44). Allelic expression analysis revealed an unequal allelic expression (ratio maternal/total×100±SEM: 55.7±1% (95% CI 53.4-58.1%) in Ly, 56.1±0.8 (95% CI 54.5-57.7%) in PBMC, 54.5±0.8% (95% CI 53-56.1%) in MAT and 54.1±0.6% (95% CI 53-55.3%) in HT). Maternal ratio differed significantly from the mean (p<0.0001). This phenomenon may be a general feature existing in all tissues.
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Affiliation(s)
- Stefanie Klenke
- Institut für Pharmakogenetik, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, 45122 Essen, Germany
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Riminucci M, Robey PG, Saggio I, Bianco P. Skeletal progenitors and the GNAS gene: fibrous dysplasia of bone read through stem cells. J Mol Endocrinol 2010; 45:355-64. [PMID: 20841428 PMCID: PMC3384548 DOI: 10.1677/jme-10-0097] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Activating mutations of the GNAS gene, which causes fibrous dysplasia of bone (FD), lead to remarkable changes in the properties of skeletal progenitors, and it is these changes that mediate the pathological effect of this gene on bone. Mutated skeletal stem cells lose the ability to differentiate into adipocytes, and to maintain in situ, and transfer heterotopically, the hematopoietic microenvironment, leading to abnormal bone marrow histology in FD. They overexpress molecular effectors of osteoclastogenesis, thus promoting inappropriate bone resorption leading to fragility of FD bone. They express the phosphate-regulating hormone FGF-23 at normal levels, whose excess in the serum of FD patients correlates with the mass of osteogenic cells within FD lesions, leading to osteomalacia and deformity of the FD bone, and revealing that bone is an endocrine organ regulating renal handling of phosphate. Mechanisms of allelic selection and stem cell selection occur in mutated skeletal stem cells and contribute to the inherent diversity and evolution over time in FD. The definition of the etiological role of GNAS mutations marks the watershed between many decades of descriptive observation and the definition of cellular and molecular mechanisms that would explain and hopefully allow for a cure for the disease. Placing stem cells at center stage has permitted substantial advances in one decade, and promises more for the one to come.
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Affiliation(s)
- Mara Riminucci
- Department of Molecular Medicine, La Sapienza University, 00161 Rome, Italy
- Biomedical Science Park San Raffaele, 00128 Rome, Italy
| | - Pamela Gehron Robey
- Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Isabella Saggio
- Biomedical Science Park San Raffaele, 00128 Rome, Italy
- Department of Genetics and Molecular Biology, Sapienza University of Rome, and Institute for Molecular Biology and Pathology, National Research Council (CNR) Rome, Italy
| | - Paolo Bianco
- Department of Molecular Medicine, La Sapienza University, 00161 Rome, Italy
- Biomedical Science Park San Raffaele, 00128 Rome, Italy
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Schindler S, Heiner M, Platzer M, Szafranski K. Comparison of methods for quantification of subtle splice variants. Electrophoresis 2010; 30:3674-81. [PMID: 19862747 DOI: 10.1002/elps.200900292] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alternative splicing is capable of generating multiple mRNA variants from a single gene and is hence a key mediator of molecular diversity generated at the transcript level. Consequently, delivering quantitative information on the fractions of splice variants is essential for the understanding of their biological roles. Here we compare techniques for subtle splice variant quantification that are able to resolve length differences as small as one nucleotide: PAGE with ethidium-bromide densitometry, pyrosequencing, and CE-LIF. We give comprehensive descriptions of assay designs and calibration procedures and present an evaluation of these methods in terms of accuracy, reproducibility and applicability. We also examined template concentrations and reverse transcription-coupled PCR conditions as potential cause of biased results as they were observed for extreme low template concentrations and/or PCR amplicons with size differences of 195 nt. As proof of concept, we determine the splice ratios of variants differing by 3 and 12 nt in five human tissues. We demonstrate that CE-LIF is the most precise and also the most labor- and time-efficient method.
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Zhou W, Calciano MA, Jordan H, Brenner M, Johnson S, Wu D, Lei L, Pallares D, Beurdeley P, Rouet F, Gill PS, Bracco L, Soucaille C, Einstein R. High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity. BMC Genet 2009; 10:63. [PMID: 19804644 PMCID: PMC2768739 DOI: 10.1186/1471-2156-10-63] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 10/05/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Commercially available microarrays have been used in many settings to generate expression profiles for a variety of applications, including target selection for disease detection, classification, profiling for pharmacogenomic response to therapeutics, and potential disease staging. However, many commercially available microarray platforms fail to capture transcript diversity produced by alternative splicing, a major mechanism for driving proteomic diversity through transcript heterogeneity. RESULTS The human Genome-Wide SpliceArray(TM) (GWSA), a novel microarray platform, utilizes an existing probe design concept to monitor such transcript diversity on a genome scale. The human GWSA allows the detection of alternatively spliced events within the human genome through the use of exon body and exon junction probes to provide a direct measure of each transcript, through simple calculations derived from expression data. This report focuses on the performance and validation of the array when measured against standards recently published by the Microarray Quality Control (MAQC) Project. The array was shown to be highly quantitative, and displayed greater than 85% correlation with the HG-U133 Plus 2.0 array at the gene level while providing more extensive coverage of each gene. Almost 60% of splice events among genes demonstrating differential expression of greater than 3 fold also contained extensive splicing alterations. Importantly, almost 10% of splice events within the gene set displaying constant overall expression values had evidence of transcript diversity. Two examples illustrate the types of events identified: LIM domain 7 showed no differential expression at the gene level, but demonstrated deregulation of an exon skip event, while erythrocyte membrane protein band 4.1 -like 3 was differentially expressed and also displayed deregulation of a skipped exon isoform. CONCLUSION Significant changes were detected independent of transcriptional activity, indicating that the controls for transcript generation and transcription are distinct, and require novel tools in order to detect changes in specific transcript quantity. Our results demonstrate that the SpliceArray(TM) design will provide researchers with a robust platform to detect and quantify specific changes not only in overall gene expression, but also at the individual transcript level.
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Affiliation(s)
- Weiyin Zhou
- ExonHit Therapeutics Inc, 217 Perry Parkway, Bldg 5, Gaithersburg, MD, 20877 USA.
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Méreau A, Anquetil V, Cibois M, Noiret M, Primot A, Vallée A, Paillard L. Analysis of splicing patterns by pyrosequencing. Nucleic Acids Res 2009; 37:e126. [PMID: 19671523 PMCID: PMC2770645 DOI: 10.1093/nar/gkp626] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Several different mRNAs can be produced from a given pre-mRNA by regulated alternative splicing, or as the result of deregulations that may lead to pathological states. Analysing splicing patterns is therefore of importance to describe and understand developmental programs, cellular responses to internal or external cues, or human diseases. We describe here a method, Pyrosequencing Analysis of Splicing Patterns (PASP), that combines RT–PCR and pyrosequencing of PCR products. We demonstrated that: (i) Ratios of two pure RNAs mixed in various proportions were accurately measured by PASP; (ii) PASP can be adapted to virtually any splicing event, including mutually exclusive exons, complex patterns of exon skipping or inclusion, and alternative 3′ terminal exons; (iii) In extracts from different organs, the proportions of RNA isoforms measured by PASP reflected those measured by other methods. The PASP method is therefore reliable for analysing splicing patterns. All steps are done in 96-wells microplates, without gel electrophoresis, opening the way to high-throughput comparisons of RNA from several sources.
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Affiliation(s)
- Agnès Méreau
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, IFR 140, CNRS, UMR6061, Equipe Expression Génétique et Développement, Université Européenne de Bretagne, F-35000 Rennes, France
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9
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Amelogenin sex determination by pyrosequencing of short PCR products. Int J Legal Med 2008; 122:333-5. [DOI: 10.1007/s00414-008-0228-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 02/22/2008] [Indexed: 10/25/2022]
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Szafranski K, Schindler S, Taudien S, Hiller M, Huse K, Jahn N, Schreiber S, Backofen R, Platzer M. Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns. Genome Biol 2008; 8:R154. [PMID: 17672918 PMCID: PMC2374985 DOI: 10.1186/gb-2007-8-8-r154] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 06/14/2007] [Accepted: 08/01/2007] [Indexed: 01/25/2023] Open
Abstract
TG dinucleotides functioning as alternative 3' splice sites were identified and experimentally verified in 36 human genes. Background Despite some degeneracy of sequence signals that govern splicing of eukaryotic pre-mRNAs, it is an accepted rule that U2-dependent introns exhibit the 3' terminal dinucleotide AG. Intrigued by anecdotal evidence for functional non-AG 3' splice sites, we carried out a human genome-wide screen. Results We identified TG dinucleotides functioning as alternative 3' splice sites in 36 human genes. The TG-derived splice variants were experimentally validated with a success rate of 92%. Interestingly, ratios of alternative splice variants are tissue-specific for several introns. TG splice sites and their flanking intron sequences are substantially conserved between orthologous vertebrate genes, even between human and frog, indicating functional relevance. Remarkably, TG splice sites are exclusively found as alternative 3' splice sites, never as the sole 3' splice site for an intron, and we observed a distance constraint for TG-AG splice site tandems. Conclusion Since TGs splice sites are exclusively found as alternative 3' splice sites, the U2 spliceosome apparently accomplishes perfect specificity for 3' AGs at an early splicing step, but may choose 3' TGs during later steps. Given the tiny fraction of TG 3' splice sites compared to the vast amount of non-viable TGs, cis-acting sequence signals must significantly contribute to splice site definition. Thus, we consider TG-AG 3' splice site tandems as promising subjects for studies on the mechanisms of 3' splice site selection.
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Affiliation(s)
- Karol Szafranski
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany
| | - Stefanie Schindler
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany
| | - Stefan Taudien
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany
| | - Michael Hiller
- Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee, 79110 Freiburg, Germany
| | - Klaus Huse
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany
| | - Niels Jahn
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University Kiel, Schittenhelmstr., 24105 Kiel, Germany
| | - Rolf Backofen
- Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee, 79110 Freiburg, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany
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Rukov JL, Irimia M, Mørk S, Lund VK, Vinther J, Arctander P. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae. Mol Biol Evol 2007; 24:909-17. [PMID: 17272679 DOI: 10.1093/molbev/msm023] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative splicing (AS) is an important contributor to proteome diversity and is regarded as an explanatory factor for the relatively low number of human genes compared with less complex animals. To assess the evolutionary conservation of AS and its developmental regulation, we have investigated the qualitative and quantitative expression of 21 orthologous alternative splice events through the development of 2 nematode species separated by 85-110 Myr of evolutionary time. We demonstrate that most of these alternative splice events present in Caenorhabditis elegans are conserved in Caenorhabditis briggsae. Moreover, we find that relative isoform expression levels vary significantly during development for 78% of the AS events and that this quantitative variation is highly conserved between the 2 species. Our results suggest that AS is generally tightly regulated through development and that the regulatory mechanisms controlling AS are to a large extent conserved during the evolution of Caenorhabditis. This strong conservation indicates that both major and minor splice forms have important functional roles and that the relative quantities in which they are expressed are crucial. Our results therefore suggest that the quantitative regulation of isoform expression levels is an intrinsic part of most AS events. Moreover, our results indicate that AS contributes little to transcript variation in Caenorhabditis genes and that gene duplication may be the major evolutionary mechanism for the origin of novel transcripts in these 2 species.
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Affiliation(s)
- Jakob Lewin Rukov
- Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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Bracco L, Throo E, Cochet O, Einstein R, Maurier F. Methods and platforms for the quantification of splice variants' expression. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2007; 44:1-25. [PMID: 17076262 DOI: 10.1007/978-3-540-34449-0_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The relatively limited number of human protein encoding genes highlights the importance of the diversity generated at the level of the mRNA transcripts. As alternative RNA splicing plays a key role in mediating this diversity, it becomes critical to develop the tools and platforms that will deliver quantitative information on the specific expression levels associated with splice isoforms. This chapter describes the constraints generated by this global transcriptome analysis and the state-of-the-art techniques and products available to the scientific community.
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Affiliation(s)
- Laurent Bracco
- ExonHit Therapeutics, 65 Boulevard Masséna, F-75013 Paris
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Royo JL, Pascual MH, Salinas A, Tello FJ, Rivero MDC, Herrero EF, Real LM, Ruiz A. Pyrosequencing protocol requiring a unique biotinylated primer. Clin Chem Lab Med 2006; 44:435-41. [PMID: 16599838 DOI: 10.1515/cclm.2006.072] [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: 11/15/2022]
Abstract
BACKGROUND DNA sequencing has markedly changed the nature of biomedical research. Large-scale sequencing projects have generated several millions of potential polymorphisms widespread in the human genome requiring validation and incorporation into screening panels. As a consequence, high-throughput analysis of these variants in different populations of interest is now the cornerstone of structural genomics. Pyrosequencing is a versatile technique allowing an easy 96-well typing format. However, every polymorphism requires a specific labeled primer to generate a single-stranded DNA fragment containing the region of interest. METHODS We describe how with an adjusted primer stoichiometry we can standardize the labeling of every amplicon with a single biotinylated universal primer (BM13S). RESULTS We circumvent the need for specific biotinylated primers for each single-nucleotide polymorphism (SNP) under study. As an example, we assessed this novel protocol by genotyping three SNPs mapping calpain-10, caveolin-1 and CYP19A1. CONCLUSION The present approach represents an alternative to standard pyrosequencing protocols, since it requires a single biotinylated primer that is suitable for each SNP under study.
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Affiliation(s)
- Jose Luis Royo
- Departamento de Genomica Estructural, Neocodex SL, Sevilla, Spain.
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