Skip to main content

Advertisement

SpringerLink
Log in

Normal and altered pre-mRNA processing in the DMD gene

  • Review
  • Published:
Human Genetics Aims and scope Submit manuscript

Abstract

Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression controlled by multiple post- and co-transcriptional mechanisms. The large Duchenne muscular dystrophy gene encoding the protein dystrophin provides a striking example of the complexity of human pre-mRNAs. In this review, we summarize the current state of knowledge about canonical and non-canonical splicing in the DMD pre-mRNA, with a focus on mechanisms that take place in the full-length transcript isoform expressed in human skeletal muscle. In particular, we highlight recent work demonstrating that multi-step events are required for long DMD intron removal. The role of temporary intron retention in the occurrence of alternative splicing events is also discussed. Even though the proportion of splicing mutations is lower than reported in other genes, a great diversity of splicing defects linked to point mutations, but also large genomic rearrangements are observed in the DMD gene. We provide an overview of the molecular mechanisms underlying aberrant splicing in patients with Duchenne or Becker muscular dystrophy, and we also detail how alternative splicing can serve as a disease modifier in patients by changing the outcome of the primary defect.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Aartsma-Rus A, Van Deutekom JC, Fokkema IF, Van Ommen GJ, Den Dunnen JT (2006) Entries in the leiden duchenne muscular dystrophy mutation database: an overview of mutation types and paradoxical cases that confirm the reading-frame rule. Muscle Nerve 34:135–144

    Article  CAS  PubMed  Google Scholar 

  • Akerman M, Fregoso OI, Das S, Ruse C, Jensen MA, Pappin DJ, Zhang MQ, Krainer AR (2015) Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biol 16:119

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Alpert T, Herzel L, Neugebauer KM (2016) Perfect timing: splicing and transcription rates in living cells. Wiley Interdiscip Rev RNA. doi:10.1002/wrna.1401

    PubMed  Google Scholar 

  • Arechavala-Gomeza V, Kinali M, Feng L, Guglieri M, Edge G, Main M, Hunt D, Lehovsky J, Straub V, Bushby K, Sewry CA, Morgan JE, Muntoni F (2010) Revertant fibres and dystrophin traces in Duchenne muscular dystrophy: implication for clinical trials. Neuromuscul Disord 20:295–301

    Article  PubMed  Google Scholar 

  • Ashwal-Fluss R, Meyer M, Pamudurti NR, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S (2014) circRNA biogenesis competes with pre-mRNA splicing. Mol Cell 56:55–66

    Article  CAS  PubMed  Google Scholar 

  • Austin RC, Howard PL, D’Souza VN, Klamut HJ, Ray PN (1995) Cloning and characterization of alternatively spliced isoforms of Dp71. Hum Mol Genet 4:1475–1483

    Article  CAS  PubMed  Google Scholar 

  • Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ (2010) Deciphering the splicing code. Nature 465:53–59

    Article  CAS  PubMed  Google Scholar 

  • Barrett LW, Fletcher S, Barreo RA, Bellgard MI, Flanigan KM et al (2014) Targeted suppression of a dystrophin pseudo-exon using antisense oligonucleotides. J Genet Syndr Gene Ther 5:235. doi:10.4172/2157-7412

    Google Scholar 

  • Barrett SP, Wang PL, Salzman J (2015) Circular RNA biogenesis can proceed through an exon-containing lariat precursor. Elife 4:e07540

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Beggs AH, Hoffman EP, Snyder JR, Arahata K, Specht L, Shapiro F, Angelini C, Sugita H, Kunkel LM (1991) Exploring the molecular basis for variability among patients with Becker muscular dystrophy: dystrophin gene and protein studies. Am J Hum Genet 49:54–67

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bies RD, Phelps SF, Cortez MD, Roberts R, Caskey CT, Chamberlain JS (1992) Human and murine dystrophin mRNA transcripts are differentially expressed during skeletal muscle, heart, and brain development. Nucleic Acids Res 20:1725–1731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bladen CL, Salgado D, Monges S, Foncuberta ME, Kekou K, Kosma K, Dawkins H et al (2011) The TREAT-NMD DMD global database: analysis of more than 7000 Duchenne muscular dystrophy mutations. Hum Mutat 36:395–402

    Article  CAS  Google Scholar 

  • Bland CS, Wang ET, Vu A, David MP, Castle JC, Johnson JM, Burge CB, Cooper TA (2010) Global regulation of alternative splicing during myogenic differentiation. Nucleic Acids Res 38:7651–7664

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bougé AL, Murauer E, Beyne E, Miro J, Varilh J, Taulan M, Koenig M, Claustres M, Tuffery-Giraud S (2017) Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle. Sci Rep 7:39094

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bovolenta M, Neri M, Fini S, Fabris M, Trabanelli C, Venturoli A, Martoni E et al (2008) A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies. BMC Genomics 9:572

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bovolenta M, Erriquez D, Valli E, Brioschi S, Scotton C, Neri M, Falzarano MS, Gherardi S, Fabris M, Rimessi P, Gualandi F, Perini G, Ferlini A (2012) The DMD locus harbours multiple long non-coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. PLoS One 7:e45328

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ (2014) Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res 24:1774–1786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bruun GH, Doktor TK, Borch-Jensen J, Masuda A, Krainer AR, Ohno K, Andresen BS (2016) Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol 14:54

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Burd CG, Dreyfuss G (1994) RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J 13:1197–1204

    CAS  PubMed  PubMed Central  Google Scholar 

  • Burset M, Seledtsov IA, Solovyev VV (2001) SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic Acids Res 29:255–259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cagliani R, Sironi M, Ciafaloni E, Bardoni A, Fortunato F, Prelle A, Serafini M, Bresolin N, Comi GP (2004) An intragenic deletion/inversion event in the DMD gene determines a novel exon creation and results in a BMD phenotype. Hum Genet 115:13–18

    Article  CAS  PubMed  Google Scholar 

  • Carrillo Oesterreich F, Herzel L, Straube K, Hujer K, Howard J, Neugebauer KM (2016) Splicing of nascent RNA coincides with intron exit from RNA polymerase II. Cell 165:372–381

    Article  CAS  Google Scholar 

  • Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, Cooper TA, Johnson JM (2008) Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 40:1416–1425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen LL (2016) The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol 17:205–211

    Article  CAS  PubMed  Google Scholar 

  • Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA, Goodall GJ (2015) The RNA binding protein quaking regulates formation of circRNAs. Cell 160:1125–1134

    Article  CAS  PubMed  Google Scholar 

  • Constantin B (2014) Dystrophin complex functions as a scaffold for signalling proteins. Biochim Biophys Acta 1838:635–642

    Article  CAS  PubMed  Google Scholar 

  • Cooper TA, Wan L, Dreyfuss G (2009) RNA and disease. Cell 136:777–793

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Conti L, Baralle M, Buratti E (2013) Exon and intron definition in pre-mRNA splicing. Wiley Interdiscip Rev RNA 4:49–60

    Article  PubMed  CAS  Google Scholar 

  • Deburgrave N, Daoud F, Llense S, Barbot JC, Récan D, Peccate C, Burghes AH, Béroud C, Garcia L, Kaplan JC, Chelly J, Leturcq F (2007) Protein- and mRNA-based phenotype-genotype correlations in DMD/BMD with point mutations and molecular basis for BMD with nonsense and frameshift mutations in the DMD gene. Hum Mutat 28:183–195

    Article  CAS  PubMed  Google Scholar 

  • Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C (2009) Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37:e67

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dhir A, Buratti E (2010) Alternative splicing: role of pseudoexons in human disease and potential therapeutic strategies. FEBS J 277:841–855

    Article  CAS  PubMed  Google Scholar 

  • Disset A, Bourgeois CF, Benmalek N, Claustres M, Stevenin J, Tuffery-Giraud S (2006) An exon skipping-associated nonsense mutation in the dystrophin gene uncovers a complex interplay between multiple antagonistic splicing elements. Hum Mol Genet 15:999–1013

    Article  CAS  PubMed  Google Scholar 

  • Duff MO, Olson S, Wei X, Garrett SC, Osman A, Bolisetty M, Plocik A, Celniker SE, Graveley BR (2015) Genome-wide identification of zero nucleotide recursive splicing in Drosophila. Nature 521:376–379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dwi Pramono ZA, Takeshima Y, Surono A, Ishida T, Matsuo M (2000) A novel cryptic exon in intron 2 of the human dystrophin gene evolved from an intron by acquiring consensus sequences for splicing at different stages of anthropoid evolution. Biochem Biophys Res Commun 267:321–328

    Article  CAS  PubMed  Google Scholar 

  • Dwianingsih EK, Malueka RG, Nishida A, Itoh K, Lee T, Yagi M, Iijima K, Takeshima Y, Matsuo M (2014) A novel splicing silencer generated by DMD exon 45 deletion junction could explain upstream exon 44 skipping that modifies dystrophinopathy. J Hum Genet 59:423–429

    Article  CAS  PubMed  Google Scholar 

  • Ervasti JM (2007) Dystrophin, its interactions with other proteins, and implications for muscular dystrophy. Biochim Biophys Acta 1772:108–117

    Article  CAS  PubMed  Google Scholar 

  • Fajkusová L, Lukás Z, Tvrdíková M, Kuhrová V, Hájek J, Fajkus J (2001) Novel dystrophin mutations revealed by analysis of dystrophin mRNA: alternative splicing suppresses the phenotypic effect of a nonsense mutation. Neuromuscul Disord 11:133–138

    Article  PubMed  Google Scholar 

  • Falzarano MS, Scotton C, Passarelli C, Ferlini A (2015) Duchenne muscular dystrophy: from diagnosis to therapy. Molecules 20:18168–18184

    Article  CAS  PubMed  Google Scholar 

  • Feener CA, Koenig M, Kunkel LM (1989) Alternative splicing of human dystrophin mRNA generates isoforms at the carboxy terminus. Nature 338:509–511

    Article  CAS  PubMed  Google Scholar 

  • Ferlini A, Galié N, Merlini L, Sewry C, Branzi A, Muntoni F (1998) A novel Alu-like element rearranged in the dystrophin gene causes a splicing mutation in a family with X-linked dilated cardiomyopathy. Am J Hum Genet 63:436–446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Flanigan KM, Dunn DM, von Niederhausern A, Soltanzadeh P, Gappmaier E et al (2009) Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large cohort. Hum Mutat 30:1657–1666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Flanigan KM, Dunn DM, von Niederhausern A, Soltanzadeh P, Howard MT, SampsonJB Swoboda KJ, Bromberg MB, Mendell JR, Taylor LE et al (2011) Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene. Hum Mutat 32:299–308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fu XD, Ares M Jr (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15:689–701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gaidatzis D, Burger L, Florescu M, Stadler MB (2015) Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol 33:722–729

    Article  CAS  PubMed  Google Scholar 

  • Gazzoli I, Pulyakhina I, Verwey NE, Ariyurek Y, Laros JF, ‘t Hoen PA, Aartsma-Rus A (2016) Non-sequential and multi-step splicing of the dystrophin transcript. RNA Biol 13:290–305

    Article  PubMed  Google Scholar 

  • Gelfman S, Ast G (2013) When epigenetics meets alternative splicing: the roles of DNA methylation and GC architecture. Epigenomics 5:351–353

    Article  CAS  PubMed  Google Scholar 

  • Ginjaar IB, Kneppers AL, Meulen JD, Anderson LV, Bremmer-Bout M, van Deutekom JC, Weegenaar J, den Dunnen JT, Bakker E (2000) Dystrophin nonsense mutation induces different levels of exon 29 skipping and leads to variable phenotypes within one BMDfamily. Eur J Hum Genet 8:793–796

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez I, Munita R, Agirre E, Dittmer TA, Gysling K, Misteli T, Luco RF (2015) A lncRNA regulates alternative splicing via establishment of a splicing-specific chromatin signature. Nat Struct Mol Biol 22:370–376

    CAS  PubMed  Google Scholar 

  • Goyenvalle A, Leumann C, Garcia L (2016) Therapeutic Potential of Tricyclo-DNA antisense oligonucleotides. J Neuromuscul Dis 3:157–167

    Article  PubMed  PubMed Central  Google Scholar 

  • Greer K, Mizzi K, Rice E, Kuster L, Barrero RA, Bellgard MI, Lynch BJ, Foley AR, Rathallaigh OE, Wilton SD, Fletcher S (2015) Pseudoexon activation increases phenotype severity in a Becker muscular dystrophy patient. Mol Genet Genomic Med 3:320–326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gualandi F, Trabanelli C, Rimessi P, Calzolari E, Toffolatti L, Patarnello T, Kunz G, Muntoni F, Ferlini A (2003a) Multiple exon skipping and RNA circularisation contribute to the severe phenotypic expression of exon 5 dystrophin deletion. J Med Genet 40:e100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gualandi F, Rimessi P, Cardazzo B, Toffolatti L, Dunckley MG, Calzolari E, Patarnello T, Muntoni F, Ferlini A (2003b) Genomic definition of a pure intronic dystrophin deletion responsible for an XLDC splicing mutation: in vitro mimicking and antisense modulation of the splicing abnormality. Gene 311:25–33

    Article  CAS  PubMed  Google Scholar 

  • Guiraud S, Chen H, Burns DT, Davies KE (2015) Advances in genetic therapeutic strategies for Duchenne muscular dystrophy. Exp Physiol 100:1458–1467

    Article  PubMed  PubMed Central  Google Scholar 

  • Gurvich OL, Tuohy TM, Howard MT, Finkel RS, Medne L, Anderson CB, Weiss RB, Wilton SD, Flanigan KM (2008) DMD pseudoexon mutations: splicing efficiency, phenotype, and potential therapy. Ann Neurol 63:81–89

    Article  CAS  PubMed  Google Scholar 

  • Hall MP, Nagel RJ, Fagg WS, Shiue L, Cline MS, Perriman RJ, Donohue JP, Ares M Jr (2013) Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. RNA 19:627–638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hallegger M, Llorian M, Smith CW (2010) Alternative splicing: global insights. FEBS J 277:856–866

    Article  CAS  PubMed  Google Scholar 

  • Heyn P, Kalinka AT, Tomancak P, Neugebauer KM (2015) Introns and gene expression: cellular constraints, transcriptional regulation, and evolutionary consequences. BioEssays 37:148–154

    Article  CAS  PubMed  Google Scholar 

  • Hoffman EP, Brown RH, Kunkel LM (1987) Dystrophin: the protein product of the Duchenne muscular dystrophy locus. Cell 51:919–928

    Article  CAS  PubMed  Google Scholar 

  • Howard JM, Sanford JR (2015) The RNAissance family: SR proteins as multifaceted regulators of gene expression. Wiley Interdiscip Rev RNA 6:93–110

    Article  CAS  PubMed  Google Scholar 

  • Hubé F, Francastel C (2015) Mammalian introns: when the junk generates molecular diversity. Int J Mol Sci 16:4429–4452

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, Ares M Jr, Yeo GW (2012) Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep 1:167–178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ishibashi K, Takeshima Y, Yagi M, Nishiyama A, Matsuo M (2006) Novel cryptic exons identified in introns 2 and 3 of the human dystrophin gene with duplication of exons 8–11. Kobe J Med Sci 52:61–75

    CAS  PubMed  Google Scholar 

  • Ishmukhametova A, Khau Van Kien P, Méchin D, Thorel D, Vincent MC, Rivier F, Coubes C, Humbertclaude V, Claustres M, Tuffery-Giraud S (2012) Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene. Eur J Hum Genet 20:1096–1100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ivanov A, Memczak S, Wyler E, Torti F, Porath HT, Orejuela MR, Piechotta M, Levanon EY, Landthaler M, Dieterich C, Rajewsky N (2015) Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep 10:170–177

    Article  CAS  PubMed  Google Scholar 

  • Jeck WR, Sharpless NE (2014) Detecting and characterizing circular RNAs. Nat Biotechnol 32:453–461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Juan-Mateu J, González-Quereda L, Rodríguez MJ, Verdura E, Lázaro K, Jou C et al (2013) Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes. PLoS One 8:e59916

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Juan-Mateu J, Gonzalez-Quereda L, Rodriguez MJ, Baena M, Verdura E, Nascimento A, Ortez C, Baiget M, Gallano P (2015) DMD mutations in 576 dystrophinopathy families: a step forward in genotype-phenotype correlations. PLoS One 10:e0135189

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kameyama T, Suzuki H, Mayeda A (2012) Re-splicing of mature mRNA in cancer cells promotes activation of distant weak alternative splice sites. Nucleic Acids Res 40:7896–7906

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S (2013) Function of alternative splicing. Gene 514:1–30

    Article  CAS  PubMed  Google Scholar 

  • Kelly S, Greenman C, Cook PR, Papantonis A (2015) Exon skipping is correlated with exon circularization. J Mol Biol 427:2414–2417

    Article  CAS  PubMed  Google Scholar 

  • Keren H, Lev-Maor G, Ast G (2010) Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 11:345–355

    Article  CAS  PubMed  Google Scholar 

  • Kerr TP, Sewry CA, Robb SA, Roberts RG (2001) Long mutant dystrophins and variable phenotypes: evasion of nonsense-mediated decay? Hum Genet 109:402–407

    Article  CAS  PubMed  Google Scholar 

  • Kesari A, Neel R, Wagoner L, Harmon B, Spurney C, Hoffman EP (2009) Somatic mosaicism for Duchenne dystrophy: evidence for genetic normalization mitigating muscle symptoms. Am J Med Genet A 149A:1499–1503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khelifi MM, Ishmukhametova A, Khau Van Kien P, Thorel D, Méchin D, Perelman S, Pouget J, Claustres M, Tuffery-Giraud S (2011) Pure Intronic rearrangements leading to aberrant pseudoexon inclusion in dystrophinopathy: a new class of mutations? Hum Mutat 32:467–475

    Article  CAS  PubMed  Google Scholar 

  • Koenig M, Hoffman EP, Bertelson CJ, Monaco AP, Feener C, Kunkel LM (1987) Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals. Cell 50:509–517

    Article  CAS  PubMed  Google Scholar 

  • Koenig M, Monaco AP, Kunkel LM (1988) The complete sequence of dystrophin predicts a rod-shaped cytoskeletal protein. Cell 53:219–228

    Article  CAS  PubMed  Google Scholar 

  • Koren E, Lev-Maor G, Ast G (2007) The emergence of alternative 3′ and 5′ splice site exons from constitutive exons. PLoS Comput Biol 3:e95

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz MJ (2013) Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 14:153–165

    Article  CAS  PubMed  Google Scholar 

  • Lasda E, Parker R (2014) Circular RNAs: diversity of form and function. RNA 20:1829–1842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li YI, Sanchez-Pulido L, Haerty W, Ponting CP (2015) RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts. Genome Res 25:1–13

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG (2011) Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci U S A 108:11093–11098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Llorian M, Smith CW (2011) Decoding muscle alternative splicing. Curr Opin Genet Dev 21:380–387

    Article  CAS  PubMed  Google Scholar 

  • Lorain S, Peccate C, Le Hir M, Griffith G, Philippi S, Précigout G, Mamchaoui K, Jollet A, Voit T, Garcia L (2013) Dystrophin rescue by trans-splicing: a strategy for DMD genotypes not eligible for exon skipping approaches. Nucleic Acids Res 41:8391–8402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu QL, Morris GE, Wilton SD, Ly T, Artem’yeva OV, Strong P, Partridge TA (2000) Massive idiosyncratic exon skipping corrects the nonsense mutation in dystrophic mouse muscle and produces functional revertant fibers by clonal expansion. J Cell Biol 148(5):985–996

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luco RF, Misteli T (2011) More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation. Curr Opin Genet Dev 21:366–372

    Article  CAS  PubMed  Google Scholar 

  • Luo HR, Moreau GA, Levin N, Moore MJ (1999) The human Prp8 protein is a component of both U2- and U12-dependent spliceosomes. RNA 5:893–908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Madden HR, Fletcher S, Davis MR, Wilton SD (2009) Characterization of a complex Duchenne muscular dystrophy-causing dystrophin gene inversion and restoration of the reading frame by induced exon skipping. Hum Mutat 30:22–28

    Article  CAS  PubMed  Google Scholar 

  • Malueka RG, Takaoka Y, Yagi M, Awano H, Lee T, Dwianingsih EK, Nishida A, Takeshima Y, Matsuo M (2012) Categorization of 77 dystrophin exons into 5 groups by a decision tree using indexes of splicing regulatory factors as decision markers. BMC Genet 13:23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martone J, Briganti F, Legnini I, Morlando M, Picillo E, Sthandier O, Politano L, Bozzoni I (2016) The lack of the Celf2a splicing factor converts a Duchenne genotype into a Becker phenotype. Nat Commun 7:10488

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matlin AJ, Clark F, Smith CW (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6:386–398

    Article  CAS  PubMed  Google Scholar 

  • Matsuo M, Masumura T, Nakajima T, Kitoh Y, Takumi T, Nishio H et al (1990) A very small frame-shifting deletion within exon 19 of the Duchenne muscular dystrophy gene. Biochem Biophys Res Commun 170:963–967

    Article  CAS  PubMed  Google Scholar 

  • Milasin J, Muntoni F, Severini GM, Bartoloni L, Vatta M, Krajinovic M, Mateddu A, Angelini C, Camerini F, Falaschi A, Mestroni L, Giacca M (1996) A point mutation in the 5′ splice site of the dystrophin gene first intron responsible for X-linked dilated cardiomyopathy. Hum Mol Genet 5:73–79

    Article  CAS  PubMed  Google Scholar 

  • Miro J, Laaref AM, Rofidal V, Lagrafeuille R, Hem S, Thorel D, Méchin D, Mamchaoui K, Mouly V, Claustres M, Tuffery-Giraud S (2015) FUBP1: a new protagonist in splicing regulation of the DMD gene. Nucleic Acids Res 43:2378–2389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Monaco AP, Bertelson CJ, Liechti-Gallati S, Moser H, Kunkel LM (1988) An explanation for the phenotypic differences between patients bearing partial deletions of the DMD locus. Genomics 2:90–95

    Article  CAS  PubMed  Google Scholar 

  • Muntoni F, Torelli S, Ferlini A (2003) Dystrophin and mutations: one gene, several proteins, multiple phenotypes. Lancet Neurol 2:731–740

    Article  CAS  PubMed  Google Scholar 

  • Neri M, Torelli S, Brown S, Ugo I, Sabatelli P, Merlini L, Spitali P, Rimessi P, Gualandi F, Sewry C, Ferlini A, Muntoni F (2007) Dystrophin levels as low as 30% are sufficient to avoid muscular dystrophy in the human. Neuromuscul Disord 17:913–918

    Article  PubMed  Google Scholar 

  • Newey SE, Benson MA, Ponting CP, Davies KE, Blake DJ (2000) Alternative splicing of dystrobrevin regulates the stoichiometry of syntrophin binding to the dystrophin protein complex. Curr Biol 10:1295–1298

    Article  CAS  PubMed  Google Scholar 

  • Niks EH, Aartsma-Rus A (2017) Exon skipping: a first in class strategy for Duchenne muscular dystrophy. Expert Opin Biol Ther 17:225–236

    Article  CAS  PubMed  Google Scholar 

  • Nishida A, Kataoka N, Takeshima Y, Yagi M, Awano H, Ota M, Itoh K, Hagiwara M, Matsuo M (2011) Chemical treatment enhances skipping of a mutated exon in the dystrophin gene. Nat Commun 2:308

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nishida A, Minegishi M, Takeuchi A, Awano H, Niba ET, Matsuo M (2015a) Neuronal SH-SY5Y cells use the C-dystrophin promoter coupled with exon 78 skipping and display multiple patterns of alternative splicing including two intronic insertion events. Hum Genet 134:993–1001

    Article  CAS  PubMed  Google Scholar 

  • Nishida A, Minegishi M, Takeuchi A, Niba ET, Awano H, Lee T, Iijima K, Takeshima Y, Matsuo M (2015b) Tissue- and case-specific retention of intron 40 in mature dystrophin mRNA. J Hum Genet 60:327–333

    Article  CAS  PubMed  Google Scholar 

  • Nishida A, Oda A, Takeuchi A, Lee T, Awano H, Hashimoto N, Takeshima Y, Matsuo M (2016) Staurosporine allows dystrophin expression by skipping of nonsense-encoding exon. Brain Dev 38:738–745

    Article  PubMed  Google Scholar 

  • Nishiyama A, Takeshima Y, Zhang Z, Habara Y, Tran THT, Yagi M, Matsuo M (2008) Dystrophin nonsense mutations can generate alternative rescue transcripts in lymphocytes. Ann Hum Genet 72:717–724

    Article  CAS  PubMed  Google Scholar 

  • Norwood FL, Sutherland-Smith AJ, Keep NH, Kendrick-Jones J (2000) The structure of the N-terminal actin-binding domain of human dystrophin and how mutations in this domain may cause Duchenne or Becker muscular dystrophy. Structure 8:481–491

    Article  CAS  PubMed  Google Scholar 

  • Nudel U, Robzyk K, Yaffe D (1988) Expression of the putative Duchenne muscular dystrophy gene in differentiated myogenic cell cultures and in the brain. Nature 331:635–638

    Article  CAS  PubMed  Google Scholar 

  • Oshima J, Magner DB, Lee JA, Breman AM, Schmitt ES, White LD, Crowe CA, Merrill M, Jayakar P, Rajadhyaksha A, Eng CM, del Gaudio D (2009) Regional genomic instability predisposes to complex dystrophin gene rearrangements. Hum Genet 126:411–423

    Article  PubMed  Google Scholar 

  • Pandit S, Zhou Y, Shiue L, Coutinho-Mansfield G, Li H, Qiu J, Huang J, Yeo GW, Ares M Jr, Fu XD (2013) Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell 50:223–235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pandya-Jones A, Black DL (2009) Co-transcriptional splicing of constitutive and alternative exons. RNA 15:1896–1908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perry MM, Muntoni F (2016) Noncoding RNAs and Duchenne muscular dystrophy. Epigenomics 8:1527–1537

    Article  CAS  PubMed  Google Scholar 

  • Prior TW, Bartolo C, Papp AC, Snyder PJ, Sedra MS, Burghes AH, Kissel JT, Luquette MH, Tsao CY, Mendell JR (1997) Dystrophin expression in a Duchenne muscular dystrophy patient with a frame shift deletion. Neurology 48:486–488

    Article  CAS  PubMed  Google Scholar 

  • Raj B, Blencowe BJ (2015) Alternative splicing in the mammalian nervous system: recent insights into mechanisms and functional roles. Neuron 87:14–27

    Article  CAS  PubMed  Google Scholar 

  • Rapaport D, Lederfein D, Den Dunnen JT, Grootscholten PM, Van Ommen GJB, Fuchs O, Nudel U, Yaffe D (1992) Characterization and cell type distribution of a novel, major transcript of the Duchenne muscular dystrophy gene. Differentiation 49:187–193

    Article  CAS  PubMed  Google Scholar 

  • Rau F, Lainé J, Ramanoudjame L, Ferry A, Arandel L, Delalande O, Jollet A et al (2015) Abnormal splicing switch of DMD’s penultimate exon compromises muscle fibre maintenance in myotonic dystrophy. Nat Commun 6:7205

    Article  PubMed  PubMed Central  Google Scholar 

  • Reiss J, Rininsland F (1994) An explanation for the constitutive exon 9 cassette splicing of the DMD gene. Hum Mol Genet 3:295–298

    Article  CAS  PubMed  Google Scholar 

  • Roberts RG, Bentley DR, Bobrow M (1993) Infidelity in the structure of ectopic transcripts: a novel exon in lymphocyte dystrophin transcripts. Hum Mutat 2:293–299

    Article  CAS  PubMed  Google Scholar 

  • Romano M, Buratti E, Baralle D (2013) Role of pseudoexons and pseudointrons in human cancer. Int J Cell Biol 2013:810572

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sadoulet-Puccio HM, Kunkel LM (1996) Dystrophin and its isoforms. Brain Pathol 6:25–35

    Article  CAS  PubMed  Google Scholar 

  • Sakuma M, Iida K, Hagiwara M (2015) Deciphering targeting rules of splicing modulator compounds: case of TG003. BMC Mol Biol 16:16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Santos R, Gonçalves A, Oliveira J, Vieira E, Vieira JP, Evangelista T, Moreno T, Santos M, Fineza I, Bronze-da-Rocha E (2014) New variants, challenges and pitfalls in DMD genotyping: implications in diagnosis, prognosis and therapy. J Hum Genet 59:454–464

    Article  CAS  PubMed  Google Scholar 

  • Shiga N, Takeshima Y, Sakamoto H, Inoue K, Yokota Y, Yokoyama M, Matsuo M (1997) Disruption of the splicing enhancer sequence within exon 27 of the dystrophin gene by a nonsense mutation induces partial skipping of the exon and is responsible for Becker muscular dystrophy. J Clin Invest 100:2204–2210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sibley CR, Emmett W, Blazquez L, Faro A, Haberman N, Briese M, Trabzuni D, Ryten M, Weale ME, Hardy J, Modic M, Curk T, Wilson SW, Plagnol V, Ule J (2015) Recursive splicing in long vertebrate genes. Nature 521:371–375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sibley CR, Blazquez L, Ule J (2016) Lessons from non-canonical splicing. Nat Rev Genet 17:407–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh J, Padgett RA (2009) Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 16:1128–1133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sironi M, Cagliani R, Pozzoli U, Bardoni A, Comi GP, Giorda R, Bresolin N (2002) The dystrophin gene is alternatively spliced throughout its coding sequence. FEBS Lett 517:163–166

    Article  CAS  PubMed  Google Scholar 

  • Sironi M, Cagliani R, Comi GP, Pozzoli U, Bardoni A, Giorda R, Bresolin N (2003) Trans-acting factors may cause dystrophin splicing misregulation in BMD skeletal muscles. FEBS Lett 537:30–34

    Article  CAS  PubMed  Google Scholar 

  • Sterne-Weiler T, Howard J, Mort M, Cooper DN, Sanford JR (2011) Loss of exon identity is a common mechanism of human inherited disease. Genome Res 21:1563–1571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suminaga R, Takeshima Y, Adachi K, Yagi M, Nakamura H, Matsuo M (2002) A novel cryptic exon in intron 3 of the dystrophin gene was incorporated into dystrophin mRNA with a single nucleotide deletion in exon 5. J Hum Genet 47:196–201

    Article  CAS  PubMed  Google Scholar 

  • Sun H, Chasin LA (2000) Multiple splicing defects in an intronic false exon. Mol Cell Biol 20:6125–6414

    Google Scholar 

  • Surono A, Takeshima Y, Wibawa T, Pramono ZA, Matsuo M (1997) Six novel transcripts that remove a huge intron ranging from 250 to 800 kb are produced by alternative splicing of the 5′ region of the dystrophin gene in human skeletal muscle. Biochem Biophys Res Commun 239:895–899

    Article  CAS  PubMed  Google Scholar 

  • Surono A, Takeshima Y, Wibawa T, Ikezawa M, Nonaka I, Matsuo M (1999) Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing. Hum Mol Genet 8:493–500

    Article  CAS  PubMed  Google Scholar 

  • Suzuki H, Kameyama T, Ohe K, Tsukahara T, Mayeda A (2013) Nested introns in an intron: evidence of multi-step splicing in a large intron of the human dystrophin pre-mRNA. FEBS Lett 587(6):555–561

    Article  CAS  PubMed  Google Scholar 

  • Suzuki H, Aoki Y, Kameyama T, Saito T, Masuda S, Tanihata J, Nagata T, Mayeda A, Takeda S, Tsukahara T (2016) Endogenous multiple exon skipping and back-splicing at the DMD mutation hotspot. Int J Mol Sci 17:10

    Google Scholar 

  • Takeshima Y, Yagi M, Okizuka Y, Awano H, Zhang Z, Yamauchi Y, Nishio H, Matsuo M (2010) Mutation spectrum of the dystrophin gene in 442 Duchenne/Becker muscular dystrophy cases from one Japanese referral center. J Hum Genet 55:379–388

    Article  CAS  PubMed  Google Scholar 

  • Tennyson CN, Klamut HJ, Worton RG (1995) The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat Genet 9:184–190

    Article  CAS  PubMed  Google Scholar 

  • Tennyson CN, Shi Q, Worton RG (1996) Stability of the human dystrophin transcript in muscle. Nucleic Acids Res 24:3059–3064

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thanaraj TA, Clark F (2001) Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. Nucleic Acids Res 29:2581–2593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 22:1616–1625

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Torelli S, Muntoni F (1996) Alternative splicing of dystrophin exon 4 in normal human muscle. Hum Genet 97:521–523

    Article  CAS  PubMed  Google Scholar 

  • Trabelsi M, Beugnet C, Deburgrave N, Commere V, Orhant L, Leturcq F, Chelly J (2014) When a mid-intronic variation of DMD gene creates an ESE site. Neuromuscul Disord 24:1111–1117

    Article  PubMed  Google Scholar 

  • Tran VK, Zhang Z, Yagi M, Nishiyama A, Habara Y, Takeshima Y, Matsuo M (2005) A novel cryptic exon identified in the 3′ region of intron 2 of the human dystrophin gene. J Hum Genet 50:425–433

    Article  CAS  PubMed  Google Scholar 

  • Tran VK, Takeshima Y, Zhang Z, Yagi M, Nishiyama A, Habara Y, Matsuo M (2006) Splicing analysis disclosed a determinant single nucleotide for exon skipping caused by a novel intraexonic four-nucleotide deletion in the dystrophin gene. J Med Genet 43:924–930

    Article  CAS  PubMed  Google Scholar 

  • Tuffery-Giraud S, Saquet C, Chambert S, Claustres M (2003) Pseudoexon activation in the DMD gene as a novel mechanism for Becker muscular dystrophy. Hum Mutat 21:608–614

    Article  CAS  PubMed  Google Scholar 

  • Tuffery-Giraud S, Saquet C, Thorel D, Disset A, Rivier F, Malcolm S, Claustres M (2005) Mutation spectrum leading to an attenuated phenotype in dystrophinopathies. Eur J Hum Genet 13:1254–1260

    Article  CAS  PubMed  Google Scholar 

  • Tuffery-Giraud S, Béroud C, Leturcq F, Ben Yaou R, Hamroun D, Michel-Calemard L et al (2009) Genotype-phenotype analysis in 2405 patients with a dystrophinopathy using the UMD-DMD database: a model of nationwide knowledgebase. Hum Mutat 30:934–945

    Article  CAS  PubMed  Google Scholar 

  • van Vliet L, de Winter CL, van Deutekom JC, van Ommen GJ, Aartsma-Rus A (2008) Assessment of the feasibility of exon 45-55 multiexon skipping for Duchenne muscular dystrophy. BMC Med Genet 9:105

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vorechovsky I (2010) Transposable elements in disease-associated cryptic exons. Hum Genet 127:135–154

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Burge CB (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14:802–813

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang GS, Cooper TA (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 8:749–761

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wein N, Vulin A, Falzarano MS, Szigyarto CA, Maiti B, Findlay A, Heller KN et al (2014) Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. Nat Med 20:992–1000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Werfel S, Nothjunge S, Schwarzmayr T, Strom TM, Meitinger T, Engelhardt S (2016) Characterization of circular RNAs in human, mouse and rat hearts. J Mol Cell Cardiol 98:103–107

    Article  CAS  PubMed  Google Scholar 

  • Wilton SD, Veedu RN, Fletcher S (2015) The emperor’s new dystrophin: finding sense in the noise. Trends Mol Med 21:417–426

    Article  CAS  PubMed  Google Scholar 

  • Wong JJ, Au AY, Ritchie W, Rasko JE (2016) Intron retention in mRNA: No longer nonsense: known and putative roles of intron retention in normal and disease biology. BioEssays 38:41–49

    Article  PubMed  Google Scholar 

  • Wu Q, Krainer AR (1999) AT-AC Pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes. Mol Cell Biol 19:3225–3236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao X, Wang Z, Jang M, Burge CB (2007) Coevolutionary networks of splicing cis-regulatory elements. Proc Natl Acad Sci USA 104:18583–18588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yeo G, Burge CB (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11:377–394

    Article  CAS  PubMed  Google Scholar 

  • Zaphiropoulos PG (1996) Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. Proc Natl Acad Sci USA 93:6536–6541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Habara Y, Nishiyama A, Oyazato Y, Yagi M, Takeshima Y, Matsuo M (2007) Identification of seven novel cryptic exons embedded in the dystrophin gene and characterization of 14 cryptic dystrophin exons. J Hum Genet 52:607–617

    Article  CAS  PubMed  Google Scholar 

  • Zhang C, Li WH, Krainer AR, Zhang MQ (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci USA. 105:5797–5802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu J, Mayeda A, Krainer AR (2001) Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. Mol Cell 8:1351–1361

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We acknowledge constant support from the Association Française contre les myopathies (AFM) and Université de Montpellier (UM).

Author information

Authors and Affiliations

  1. Laboratoire de Génétique de Maladies Rares (LGMR, EA7402), University of Montpellier, Institut Universitaire de Recherche Clinique (IURC), 641 av du Doyen G. Giraud, Montpellier, Cedex 5, 34093, France

    Sylvie Tuffery-Giraud, Julie Miro, Michel Koenig & Mireille Claustres

  2. Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France

    Michel Koenig & Mireille Claustres

Authors
  1. Sylvie Tuffery-Giraud
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Julie Miro
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michel Koenig
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mireille Claustres
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sylvie Tuffery-Giraud.

Ethics declarations

Conflict of interest

S. Tuffery-Giraud has received a speaker honorarium from Company PTC Therapeutics, and has been an ad hoc consultant for this company. Remuneration for these activities is paid to University of Montpellier.

Additional information

Michel Koenig and Mireille Claustres are last co-authors.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 65 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tuffery-Giraud, S., Miro, J., Koenig, M. et al. Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 136, 1155–1172 (2017). https://doi.org/10.1007/s00439-017-1820-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00439-017-1820-9

Search

Navigation