Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing

The Drosophila melanogaster gene Dscam can generate thousands of different ectodomains via mutual exclusive splicing of three large exon clusters. The isoform diversity plays a profound role in both neuronal wiring and pathogen recognition. However, it remained unexplored how many isoforms are indeed expressed, whether the splicing choice between the clusters is independent and why the diversity encoded in the gene locus seems to be beyond necessity. To address these questions, we developed IsomSeq, a novel multiple segment sequencing method that allows to directly quantify the alternatively spliced exon combination of Dscam isoforms within an entire cellular and organismal transcriptome. Overall design: We sequenced the dscam repertoire of adult brain, S2 cell line, and 5 different developmental stages (embryo, L1, L2, L3, pupa)