title: Succession of splicing regulatory elements determines cryptic 5΄ss functionality.
abstract: A critical step in exon definition is the recognition of a proper splice donor (5΄ss) by the 5' end of U1 snRNA. In the selection of appropriate 5΄ss, cis-acting splicing regulatory elements (SREs) are indispensable. As a model for 5΄ss recognition, we investigated cryptic 5΄ss selection within the human fibrinogen Bβ-chain gene (FGB) exon 7, where we identified several exonic SREs that simultaneously acted on up- and downstream cryptic 5΄ss. In the FGB exon 7 model system, 5΄ss selection iteratively proceeded along an alternating sequence of U1 snRNA binding sites and interleaved SREs which in principle supported different 3' exon ends. Like in a relay race, SREs either suppressed a potential 5΄ss and passed the splicing baton on or splicing actually occurred. From RNA-Seq data, we systematically selected 19 genes containing exons with silent U1 snRNA binding sites competing with nearby highly used 5΄ss. Extensive SRE analysis by different algorithms found authentic 5΄ss significantly more supported by SREs than silent U1 snRNA binding sites, indicating that our concept may permit generalization to a model for 5΄ss selection and 3' exon end definition.
authors.affiliation: Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Anna-Lena
authors.initials: AL
authors.lastname: Brillen
authors.affiliation: Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Schöneweis
authors.affiliation: Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Lara
authors.initials: L
authors.lastname: Walotka
authors.affiliation: Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Linda
authors.initials: L
authors.lastname: Hartmann
authors.affiliation: Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Lisa
authors.initials: L
authors.lastname: Müller
authors.affiliation: Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Ptok
authors.affiliation: Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Kaisers
authors.affiliation: Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Gereon
authors.initials: G
authors.lastname: Poschmann
authors.affiliation: Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.|Institute for Molecular Medicine, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Kai
authors.initials: K
authors.lastname: Stühler
authors.affiliation: International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, 34149 Trieste, Italy.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Buratti
authors.affiliation: Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, 40225.
authors.forename: Stephan
authors.initials: S
authors.lastname: Theiss
authors.affiliation: Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Heiner
authors.initials: H
authors.lastname: Schaal
mesh_terms: D005091:Exons; D005340:Fibrinogen / Q000235:genetics*; D006367:HeLa Cells; D006801:Humans; D009154:Mutation; D022821:RNA Splice Sites; D012342:RNA, Small Nuclear / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D000068103:Serine-Arginine Splicing Factors / Q000378:metabolism
chemical_list: C000592498:FGB protein, human; D022821:RNA Splice Sites; D012342:RNA, Small Nuclear; D038621:Regulatory Sequences, Ribonucleic Acid; C405483:U1 small nuclear RNA; D000068103:Serine-Arginine Splicing Factors; D005340:Fibrinogen