title: Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle.
abstract: We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3' splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.
authors.affiliation: Université Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402, Montpellier, F-34000, France.|Inserm U827, Montpellier, F-34000, France.
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Bougé
authors.affiliation: Université Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402, Montpellier, F-34000, France.|Inserm U827, Montpellier, F-34000, France.
authors.forename: Eva
authors.initials: E
authors.lastname: Murauer
authors.affiliation: CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Beyne
authors.affiliation: Université Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402, Montpellier, F-34000, France.|Inserm U827, Montpellier, F-34000, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Miro
authors.affiliation: CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France.
authors.forename: Jessica
authors.initials: J
authors.lastname: Varilh
authors.affiliation: Université Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402, Montpellier, F-34000, France.|Inserm U827, Montpellier, F-34000, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Taulan
authors.affiliation: Université Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402, Montpellier, F-34000, France.|CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Koenig
authors.affiliation: Université Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402, Montpellier, F-34000, France.|Inserm U827, Montpellier, F-34000, France.|CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Claustres
authors.affiliation: Université Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402, Montpellier, F-34000, France.|Inserm U827, Montpellier, F-34000, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Tuffery-Giraud
mesh_terms: D000328:Adult; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D016189:Dystrophin / Q000235:genetics*; D005091:Exons; D020869:Gene Expression Profiling; D064368:Healthy Volunteers; D006801:Humans; D008297:Male; D018482:Muscle, Skeletal / Q000502:physiology*; D012326:RNA Splicing; D017423:Sequence Analysis, RNA; D055815:Young Adult
chemical_list: C484258:DMD protein, human; D018076:DNA, Complementary; D016189:Dystrophin