title: A sequence motif in the simian virus 40 (SV40) early core promoter affects alternative splicing of transcribed mRNA.
abstract: To identify new sequence elements in the promoter that affect splicing patterns of pre-mRNAs, we analyzed effects of different promoters on alternative splicing of model reporter genes. We compared the E1a alternative splicing pattern in transcripts expressed from the full-length cytomegalovirus, SV40 early, or a hybrid cytomegalovirus/SV40 early promoter and found that the hybrid promoter improved selection of the suboptimal E1a 5'SS-1. Expressing RNA from the hybrid promoter also enhanced selection of suboptimal splice sites in other alternatively spliced reporter genes, demonstrating the generality of this effect. Unlike previously defined promoter elements shown to affect alternative splicing, which were located in the enhancer/upstream activating sequences, the motif identified in this work is positioned within the core promoter; it is comprised of eight T-residues directly upstream of the SV40 early TATA box. This motif was previously implicated in DNA bending and negative regulation of transcription. Together, these results suggest that the identity of transcription complex assembled in the core promoter-dependent fashion can affect splice site selection during pre-mRNA splicing, perhaps by influencing the processivity of transcription elongation.
authors.affiliation: Rockefeller University, New York, New York 10021, USA.
authors.forename: Elisenda
authors.initials: E
authors.lastname: Gendra
authors.forename: Diana F
authors.initials: DF
authors.lastname: Colgan
authors.forename: Brendan
authors.initials: B
authors.lastname: Meany
authors.forename: Maria M
authors.initials: MM
authors.lastname: Konarska
mesh_terms: D017398:Alternative Splicing; D020816:Amino Acid Motifs; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D024042:Collagen Type I / Q000235:genetics; D000090602:Collagen Type I, alpha 1 Chain; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid; D013539:Simian virus 40 / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D024042:Collagen Type I; D000090602:Collagen Type I, alpha 1 Chain; D012333:RNA, Messenger