title: Single molecule analysis of combinatorial splicing.
abstract: Alternative splicing creates diverse mRNA isoforms from single genes and thereby enhances complexity of transcript structure and of gene function. We describe a method called spliceotyping, which translates combinatorial mRNA splicing patterns along transcripts into a library of binary strings of nucleic acid tags that encode the exon composition of individual mRNA molecules. The exon inclusion pattern of each analyzed transcript is thus represented as binary data, and the abundance of different splice variants is registered by counts of individual molecules. The technique is illustrated in a model experiment by analyzing the splicing patterns of the adenovirus early 1A gene and the beta actin reference transcript. The method permits many genes to be analyzed in parallel and it will be valuable for elucidating the complex effects of combinatorial splicing.
authors.affiliation: Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, SE-75185, Sweden. tim.conze@genpat.uu.se
authors.forename: Tim
authors.initials: T
authors.lastname: Conze
authors.forename: Jenny
authors.initials: J
authors.lastname: Göransson
authors.forename: Hamid Reza
authors.initials: HR
authors.lastname: Razzaghian
authors.forename: Olle
authors.initials: O
authors.lastname: Ericsson
authors.forename: Daniel
authors.initials: D
authors.lastname: Oberg
authors.forename: Göran
authors.initials: G
authors.lastname: Akusjärvi
authors.forename: Ulf
authors.initials: U
authors.lastname: Landegren
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
mesh_terms: D000256:Adenoviridae / Q000235:genetics; D017500:Adenovirus E1A Proteins / Q000235:genetics; D017398:Alternative Splicing; D015342:DNA Probes; D006367:HeLa Cells; D006801:Humans; D009693:Nucleic Acid Hybridization / Q000379:methods*; D022821:RNA Splice Sites
chemical_list: D017500:Adenovirus E1A Proteins; D015342:DNA Probes; D022821:RNA Splice Sites