title: Recursive splicing in long vertebrate genes.
abstract: It is generally believed that splicing removes introns as single units from precursor messenger RNA transcripts. However, some long Drosophila melanogaster introns contain a cryptic site, known as a recursive splice site (RS-site), that enables a multi-step process of intron removal termed recursive splicing. The extent to which recursive splicing occurs in other species and its mechanistic basis have not been examined. Here we identify highly conserved RS-sites in genes expressed in the mammalian brain that encode proteins functioning in neuronal development. Moreover, the RS-sites are found in some of the longest introns across vertebrates. We find that vertebrate recursive splicing requires initial definition of an 'RS-exon' that follows the RS-site. The RS-exon is then excluded from the dominant mRNA isoform owing to competition with a reconstituted 5' splice site formed at the RS-site after the first splicing step. Conversely, the RS-exon is included when preceded by cryptic promoters or exons that fail to reconstitute an efficient 5' splice site. Most RS-exons contain a premature stop codon such that their inclusion can decrease mRNA stability. Thus, by establishing a binary splicing switch, RS-sites demarcate different mRNA isoforms emerging from long genes by coupling cryptic elements with inclusion of RS-exons.
authors.affiliation: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.|MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Sibley
authors.affiliation: University College London Genetics Institute, Gower Street, London WC1E 6BT, UK.
authors.forename: Warren
authors.initials: W
authors.lastname: Emmett
authors.affiliation: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
authors.forename: Lorea
authors.initials: L
authors.lastname: Blazquez
authors.affiliation: Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
authors.forename: Ana
authors.initials: A
authors.lastname: Faro
authors.affiliation: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
authors.forename: Nejc
authors.initials: N
authors.lastname: Haberman
authors.affiliation: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.|Institute for Clinical Neurobiology, University of Würzburg, Versbacherstr. 5, 97078, Würzburg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Briese
authors.affiliation: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.|Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia.
authors.forename: Daniah
authors.initials: D
authors.lastname: Trabzuni
authors.affiliation: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.|Department of Medical &Molecular Genetics, King's College London, Guy's Hospital, London, UK.
authors.forename: Mina
authors.initials: M
authors.lastname: Ryten
authors.affiliation: King's College London, Department of Medical & Molecular Genetics, Guy's Hospital, London SE1 9RT, UK.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Weale
authors.affiliation: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
authors.forename: John
authors.initials: J
authors.lastname: Hardy
authors.affiliation: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.|Institute of Stem Cell Research, German Research Center for Environmental Health, Helmholtz Center Munich, 85764 Neuherberg, Germany.
authors.forename: Miha
authors.initials: M
authors.lastname: Modic
authors.affiliation: Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: Tomaž
authors.initials: T
authors.lastname: Curk
authors.affiliation: Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Wilson
authors.affiliation: University College London Genetics Institute, Gower Street, London WC1E 6BT, UK.
authors.forename: Vincent
authors.initials: V
authors.lastname: Plagnol
authors.affiliation: Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.|MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
authors.forename: Jernej
authors.initials: J
authors.lastname: Ule
mesh_terms: D000818:Animals; D017487:Ankyrins / Q000235:genetics; D001483:Base Sequence; D001921:Brain / Q000166:cytology / Q000378:metabolism; D000075982:Cell Adhesion Molecule-1; D015815:Cell Adhesion Molecules / Q000235:genetics; D018388:Codon, Terminator / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D005091:Exons / Q000235:genetics; D005260:Female; D005625:Frontal Lobe / Q000166:cytology / Q000378:metabolism; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics; D007438:Introns / Q000235:genetics; D008297:Male; D011401:Promoter Regions, Genetic / Q000235:genetics; D059368:RNA Isoforms / Q000235:genetics / Q000378:metabolism; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics*; D020871:RNA Stability / Q000235:genetics; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish / Q000196:embryology / Q000235:genetics; D029961:Zebrafish Proteins / Q000235:genetics
chemical_list: C490613:ANK3 protein, human; D017487:Ankyrins; C403514:CADM1 protein, human; C556123:CADM2 protein, human; C561509:Cadm2a protein, zebrafish; D000075982:Cell Adhesion Molecule-1; D015815:Cell Adhesion Molecules; D018388:Codon, Terminator; D007136:Immunoglobulins; D059368:RNA Isoforms; D022821:RNA Splice Sites; D029961:Zebrafish Proteins