Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases.
Chromosomal rearrangements resulting in gene fusions are frequently involved in carcinogenesis. Here, we describe a semiautomatic procedure for identifying fusion gene transcripts by using publicly available mRNA and EST databases. With this procedure, we have identified 96 transcript sequences that are derived from 60 known fusion genes. Also, 47 or more additional sequences appear to be derived from 20 or more previously unknown putative fusion genes. We have experimentally verified the presence of a previously unknown IRA1/RGS17 fusion in the breast cancer cell line MCF7. The fusion gene encodes the full-length RGS17 protein, a regulator of G protein-coupled signaling, under the control of the IRA1 gene promoter. This study demonstrates that databases of ESTs can be used to discover fusion genes resulting from structural rearrangement of chromosomes.
Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA.
Yoonsoo
Y
Hahn
Tapan Kumar
TK
Bera
Kristen
K
Gehlhaus
Ilan R
IR
Kirsch
Ira H
IH
Pastan
Byungkook
B
Lee
D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D019992:Databases as Topic; D020224:Expressed Sequence Tags; D005260:Female; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction
C470219:BCAS3-BCAS4 fusion protein, human; D015514:Oncogene Proteins, Fusion; D012333:RNA, Messenger