International Mammalian Genome Society

17th International Mouse Genome Conference

9-12 November 2003, Braunschweig, Germany


POSTER 69 - DEVELOPMENT OF ALTERNATIVE SPLICING LIBRARIES REVEALS THE COMPLEXITY OF ALTERNATIVE SPLICING IN MOUSE MELANOMA AND MELANOCYTE CELLS

Watahiki A
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan and Genome Science Laboratory, RIKEN, Wako main campus, Hirosawa 2-1 Wako, Japan

Co-Authors: Shiraki T, Waki K, Kondo S, Ishizuka Y, Arakawa T, Kawai J, Hayashizaki Y, Carninci P
Institutions: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan and Genome Science Laboratory, RIKEN, Wako main campus, Hirosawa 2-1 Wako, Japan

Alternative splicing has key role in diversification of the proteome, especially of considering that the diversity of mammalian should be achieved with only about 30,000 protein coding genes. Although alternative splicing is known, we have not yet gained a comprehensive view on this phenomena. To address this problem, we have developed a new type of libraries, ASL (alternative splicing libraries) by fishing out alternatively spliced exons from two different mouse full-length cDNA libraries. Subsequent sequencing of these libraries produced a new type of sequence tag, ASSETS (Alternative Splicing Sequence TagS). ASSETS are enriched in alternative splicing exons, their upstream and downstream exon sequences and identify splicing junctions. In this time, we prepared the ASL from melanocyte and melanoma cell lines starting from full-length cDNA libraries and found close to 600 different alternatively spliced genes, of which more than 1/3 are cassette type alternative splicing.

Since ASL is derived from full length cDNA libraries, we can promptly obtain full-length isoform clones from the original libraries by combination of RIKEN mouse full-length cDNA encyclopedia system for the analysis of their functional profile. We demonstrate the system by characterizing some full-length cDNA clones for the Aph2 gene, which shows alternative splicing of the zinc-finger DHHC motif, which could have influence of its apoptotic function.


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