An integrated approach for finding overlooked genes in yeast.
We 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 beta-galactosidase (beta-gal); non-annotated open reading frames (ORFs) translated as beta-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.
Kumar
Anuj
A
Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.
Harrison
Paul M
PM
Cheung
Kei-Hoi
KH
Lan
Ning
N
Echols
Nathaniel
N
Bertone
Paul
P
Miller
Perry
P
Gerstein
Mark B
MB
Snyder
Michael
M
D002875:Chromosomes / Q000648:ultrastructure; D000939:Epitopes / Q000378:metabolism; D005821:Genetic Techniques; D016681:Genome, Fungal; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D012313:RNA / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA; D001616:beta-Galactosidase / Q000378:metabolism
D000939:Epitopes; D012313:RNA; D001616:beta-Galactosidase