Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
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.
Watahiki
Akira
A
Genome Science Laboratory, RIKEN, Wako main campus, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan.
Waki
Kazunori
K
Hayatsu
Norihito
N
Shiraki
Toshiyuki
T
Kondo
Shinji
S
Nakamura
Mari
M
Sasaki
Daisuke
D
Arakawa
Takahiro
T
Kawai
Jun
J
Harbers
Matthias
M
Hayashizaki
Yoshihide
Y
Carninci
Piero
P
D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D014408:Biomarkers, Tumor / Q000235:genetics*; D045744:Cell Line, Tumor; D003001:Cloning, Molecular / Q000379:methods*; D005091:Exons / Q000235:genetics*; D008544:Melanocytes / Q000502:physiology; D008545:Melanoma / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D019151:Peptide Library; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
D014408:Biomarkers, Tumor; D019151:Peptide Library; D012333:RNA, Messenger