Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.
BACKGROUND
Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes.


RESULTS
735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque.


CONCLUSIONS
The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells.
Oduru
Sreedhar
S
Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA. oduru.sreedhar@ttuhsc.edu
Campbell
Janee L
JL
Karri
SriTulasi
S
Hendry
William J
WJ
Khan
Shafiq A
SA
Williams
Simon C
SC
D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D002843:Chromatin / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics; D003001:Cloning, Molecular / Q000379:methods; D019295:Computational Biology / Q000379:methods; D006224:Cricetinae; D004247:DNA / Q000235:genetics*; D015723:Gene Library; D005796:Genes / Q000235:genetics*; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D016547:Kinesins / Q000235:genetics; D008297:Male; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D051381:Rats; D017422:Sequence Analysis, DNA / Q000379:methods; D023741:Takifugu / Q000235:genetics; D013737:Testis / Q000737:chemistry* / Q000378:metabolism*
D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004247:DNA; D016547:Kinesins