Finding Rare Transcripts

Abstract

MOLECULAR BIOLOGY With gene identification algorithms still being refined, there is interest in finding new tools that can locate genes (and especially the product transcripts) within the human genome. Approximately 10 years ago, the use of expressed sequence tags (ESTs) was described; currently the public EST database contains nearly 4 million entries. Camargo et al. have used an approach, called ORESTES, that complements existing strategies and now describe 700,000 tags. Whereas ESTs tend to be derived from the ends of transcripts, the ORESTES protocol generates tags more frequently from the centers of transcripts, within the coding regions. Furthermore, although the probability of finding an EST corresponding to a gene is related to the level of expression of that gene, ORESTES is better at detecting genes expressed at low abundance. At least 150,000 of these tags, although clearly derived from the human genome, had no counterpart in the publicly available collections of transcripts. Although the technique is labor-intensive, requires highly purified RNA, and can generate PCR artifacts, the demonstration that a set of ORESTES markers can serve as a scaffold that can then be joined together to form a complete transcript sequence shows the promise of the approach.— BJ Proc. Natl. Acad. Sci. U.S.A. 98 , 12103 (2001).