Single molecule analysis of combinatorial splicing.
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.
Conze
Tim
T
Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, SE-75185, Sweden. tim.conze@genpat.uu.se
Göransson
Jenny
J
Razzaghian
Hamid Reza
HR
Ericsson
Olle
O
Oberg
Daniel
D
Akusjärvi
Göran
G
Landegren
Ulf
U
Nilsson
Mats
M
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
D017500:Adenovirus E1A Proteins; D015342:DNA Probes; D022821:RNA Splice Sites