Regulated functional alternative splicing in Drosophila

Université Montpellier 2, UMR 5535, Institut de Génétique Moléculaire de Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier cedex 05, France.
Nucleic Acids Research (Impact Factor: 9.11). 09/2011; 40(1):1-10. DOI: 10.1093/nar/gkr648
Source: PubMed


Alternative splicing expands the coding capacity of metazoan genes, and it was largely genetic studies in the fruit-fly Drosophila melanogaster that established the principle that regulated alternative splicing results in tissue- and stage-specific protein isoforms with different functions in development. Alternative splicing is particularly prominent in germ cells, muscle and the central nervous system where it modulates the expression of various proteins including cell-surface molecules and transcription factors. Studies in flies have given us numerous insights into alternative splicing in terms of upstream regulation, the exquisite diversity of their forms and the key differential cellular functions of alternatively spliced gene products. The current inundation of transcriptome sequencing data from Drosophila provides an unprecedented opportunity to gain a comprehensive view of alternative splicing.

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Available from: Jamal Tazi, Oct 05, 2015
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    • "Alternative ''cassette'' exon splicing is thought to represent the most frequent type of AS in animals in which splice sites in primary transcripts are differentially utilized to produce different protein isoforms, often in a developmental or tissue-specific manner. The multilevel splicing cascade that regulates sex determination and sex-specific development in Drosophila is the best-characterized system of AS during cell differentiation (Lalli et al. 2003; Salz and Erickson 2010; Venables et al. 2012). In this system, the primary determinant of sex is the ratio of X chromosomes to sets of autosomes (X:A), which leads to a cascade of sexspecific differential mRNA splicing events initiated by the splicing factor SXL. Thus, SXL acts as a binary switch that determines whether a fruit fly will develop as a male or a female. "
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    ABSTRACT: Apicomplexan parasites including Toxoplasma gondii and Plasmodium species have complex life cycles that include multiple hosts and differentiation through several morphologically distinct stages requiring marked changes in gene expression. This review highlights emerging evidence implicating regulation of mRNA splicing as a mechanism to prime these parasites for rapid gene expression upon differentiation. We summarize the most important insights in alternative splicing including its role in regulating gene expression by decreasing mRNA abundance via 'Regulated Unproductive Splicing and Translation'. As a related but less well-understood mechanism, we discuss also our recent work suggesting a role for intron retention for precluding translation of stage specific isoforms of T. gondii glycolytic enzymes. We additionally provide new evidence that intron retention might be a widespread mechanism during parasite differentiation. Supporting this notion, recent genome-wide analysis of Toxoplasma and Plasmodium suggests intron retention is more pervasive than heretofore thought. These findings parallel recent emergence of intron retention being more prevalent in mammals than previously believed, thereby adding to the established roles in plants, fungi and unicellular eukaryotes. Deeper mechanistic studies of intron retention will provide important insight into its role in regulating gene expression in apicomplexan parasites and more general in eukaryotic organisms.
    Current Genetics 07/2015; DOI:10.1007/s00294-015-0506-x · 2.68 Impact Factor
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    • "This makes Drosophila particularly well-suited to modeling and studying muscular disorders (García-López et al., 2008; Lloyd and Taylor, 2010; Mosqueira et al., 2010; Timmerman and Sanyal, 2012). Regarding alternative splicing, although important functional conservation occurs between Drosophila and mammals (Venables et al., 2012), dissimilarities have also been described (Mount et al., 1992; Irion, 2012). Results obtained here from the DM1 spliceosensor flies suggested, in this specific condition, that there were only slight alternative splicing machinery differences, hence, still allowing for robust disease mirroring. "
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    ABSTRACT: Alternative splicing of pre-messenger RNAs is an important mechanism to achieve correct cellular function in higher eukaryotes. It is known that a growing number of human genetic diseases involve important splicing defects directly connected to pathologic signs. In myotonic dystrophy type 1 (DM1) it is proposed that several clinical manifestations are consequence of tissue-specific missplicing of numerous genes, triggered by a RNA gain-of-function and resultant deregulation of specific RNA-binding factors, being remarkable the nuclear sequestration of muscleblind-like family factors (MBNL1-3). Thus, identification of chemical modulators of splicing events is thought to have beneficial impacts towards the development of first valid therapy for DM1 patients. For this purpose, we generated and validated transgenic flies, which contained a luciferase reporter-based system coupled to the expression of MBNL1-reliant splicing events deregulated in DM1 patients on a relevant disease tissue (spliceosensor flies). We then developed an innovative 96-well plate screening platform to carry out in vivo high throughput pharmacological screening (HTS) with the spliceosensor model. After a large-scale evaluation (>16,000 chemical entities) several reliable splicing modulators (hits) were identified. Hit validation steps recognized separate DM1-linked therapeutic traits for some of them, which corroborated the feasibility of the approach described herein for revealing promising drug candidates by indirect improving of DM1 missplicing. The powerful Drosophila-based tool for innovative chemical screening is suitable for its use with other disease models displaying abnormal alternative splicing coupled to a luminescent reporter-based system as final read-out, thus offering widespread uses in drug discovery.
    Disease Models and Mechanisms 09/2014; 7(11). DOI:10.1242/dmm.016592 · 4.97 Impact Factor
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    • "First, the central nervous system of many species is highly complex in architecture and is a rich source of alternative transcripts [17]. Additionally, the Drosophila sex determination hierarchy is a classical model of regulated alternative splicing [18]. Three members of this hierarchy, Sex-lethal (Sxl), transformer (tra), and male specific lethal 2 (msl-2) encode broadly expressed alternatively spliced mRNAs. "
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    ABSTRACT: The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splice-junction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools.
    BMC Bioinformatics 11/2013; 14(1):320. DOI:10.1186/1471-2105-14-320 · 2.58 Impact Factor
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