Nature Biotechnology
20, 58 - 63 (2002)
doi:10.1038/nbt0102-58
An integrated approach for finding overlooked genes in yeastAnuj Kumar1, Paul M. Harrison2, Kei-Hoi Cheung3, Ning Lan2, Nathaniel Echols2, Paul Bertone2, Perry Miller3, Mark B. Gerstein2
& Michael Snyder1, 21
Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103. 2
Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, New Haven, CT 06520-8114. 3
Center for Medical Informatics, Department of Anesthesiology, Yale University School of Medicine, New Haven, CT 06510.
Correspondence should be addressed to Michael Snyder michael.snyder@yale.eduWe report here the discovery of 137 previously unappreciated genes in yeast through a widely applicable and highly scalable approach integrating methods of gene-trapping, microarray-based expression analysis, and genome-wide homology searching. Our approach is a multistep process in which expressed sequences are first trapped using a modified transposon that produces protein fusions to  -galactosidase (-gal); non-annotated open reading frames (ORFs) translated as -gal chimeras are selected as a candidate pool of potential genes. To verify expression of these sequences, labeled RNA is hybridized against a microarray of oligonucleotides designed to detect gene transcripts in a strand-specific manner. In complement to this experimental method, novel genes are also identified in silico by homology to previously annotated proteins. As these methods are capable of identifying both short ORFs and antisense ORFs, our approach provides an effective supplement to current gene-finding schemes. In total, the genes discovered using this approach constitute 2% of the yeast genome and represent a wealth of overlooked biology.
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