Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas

Akira Watahiki, Kazunori Waki, Norihito Hayatsu, Toshiyuki Shiraki, Shinji Kondo, Mari Nakamura, Daisuke Sasaki, Takahiro Arakawa, Jun Kawai, Matthias Harbers, Yoshihide Nakamura, Piero Carninci

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

It 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.

Original languageEnglish
Pages (from-to)233-239
Number of pages7
JournalNature Methods
Volume1
Issue number3
DOIs
Publication statusPublished - 2004 Dec
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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    Watahiki, A., Waki, K., Hayatsu, N., Shiraki, T., Kondo, S., Nakamura, M., Sasaki, D., Arakawa, T., Kawai, J., Harbers, M., Nakamura, Y., & Carninci, P. (2004). Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nature Methods, 1(3), 233-239. https://doi.org/10.1038/nmeth719