title: Silencer elements as possible inhibitors of pseudoexon splicing.
abstract: Human pre-mRNAs contain a definite number of exons and several pseudoexons which are located within intronic regions. We applied a computational approach to address the question of how pseudoexons are neglected in favor of exons and to possibly identify sequence elements preventing pseudoexon splicing. A search for possible splicing silencers was carried out on a pseudoexon selection that resembled exons in terms of splice site strength and exon splicing enhancer (ESE) representation; three motifs were retrieved through hexamer composition comparisons. One of these functions as a powerful silencer in transfection-based splicing assays and matches a previously identified silencer sequence with hnRNP H binding ability. The other two motifs are novel and failed to induce skipping of a constitutive exon, indicating that they might act as weak repressors or in synergy with other unidentified elements. All three motifs are enriched in pseudoexons compared with intronic regions and display higher frequencies in intronless gene-coding sequences compared with exons. We consider that a subpopulation of pseudoexons might rely on negative regulators for splicing repression; this hypothesis, if experimentally verified, might improve our understanding of exonic splicing regulatory sequences and provide the identification of a novel mutation target for human genetic diseases.
authors.affiliation: IRCCS E. Medea, Associazione La Nostra Famiglia, 23842 Bosisio Parini, LC, Italy. msironi@bp.lnf.it
authors.forename: Manuela
authors.initials: M
authors.lastname: Sironi
authors.forename: Giorgia
authors.initials: G
authors.lastname: Menozzi
authors.forename: Laura
authors.initials: L
authors.lastname: Riva
authors.forename: Rachele
authors.initials: R
authors.lastname: Cagliani
authors.forename: Giacomo P
authors.initials: GP
authors.lastname: Comi
authors.forename: Nereo
authors.initials: N
authors.lastname: Bresolin
authors.forename: Roberto
authors.initials: R
authors.lastname: Giorda
authors.forename: Uberto
authors.initials: U
authors.lastname: Pozzoli
mesh_terms: D000818:Animals; D019556:COS Cells; D002522:Chlorocebus aethiops; D019295:Computational Biology; D005091:Exons; D006801:Humans; D007438:Introns; D012326:RNA Splicing; D017423:Sequence Analysis, RNA; D037941:Silencer Elements, Transcriptional