Nature Methods
1, 233 - 239 (2004)
Published online: 18 November 2004; | doi:10.1038/nmeth719
Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomasAkira Watahiki1, 2, Kazunori Waki1, 3, Norihito Hayatsu1, 3, Toshiyuki Shiraki1, 3, Shinji Kondo3, Mari Nakamura1, 3, Daisuke Sasaki3, Takahiro Arakawa3, Jun Kawai1, 3, Matthias Harbers4, Yoshihide Hayashizaki1, 2, 3, 5
& Piero Carninci1, 31
Genome Science Laboratory, RIKEN, Wako main campus, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan. 2
Institute of Basic Medical Sciences, University of Tsukuba, 1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, Japan. 3
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. 4
K.K. Dnaform, Tsukuba Branch, 3-1 Chuo 8-chome, Ami Machi, Inashiki Gun, Ibaraki, 300-0332, Japan. 5
Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045, Japan.
Correspondence should be addressed to Matthias Harbers matthias.harbers@dnaforminc.com or Piero Carninci rgscerg@gsc.riken.jpIt is becoming increasingly clear that alternative splicing enables the complex development and homeostasis of higher organisms. To gain a better understanding of how splicing contributes to regulatory pathways, we have developed an alternative splicing library approach for the identification of alternatively spliced exons and their flanking regions by alternative splicing sequence enriched tags sequencing. Here, we have applied our approach to mouse melan-c melanocyte and B16-F10Y melanoma cell lines, in which 5,401 genes were found to be alternatively spliced. These genes include those encoding important regulatory factors such as cyclin D2, Ilk, MAPK12, MAPK14, RAB4, melastatin 1 and previously unidentified splicing events for 436 genes. Real-time PCR further identified cell line−specific exons for Tmc6, Abi1, Sorbs1, Ndel1 and Snx16. Thus, the ASL approach proved effective in identifying splicing events, which suggest that alternative splicing is important in melanoma development.
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