Despite the increasing number of genomes that have been “fully” sequenced, researchers still struggle to determine conclusively how many genes are hidden within the jungle of genetic sequence. Now (Nature Biotechnology, Vol. 20, No. 1, 01 Jan 02), Michael Snyder and colleagues have developed an integrated approach to address this problem that should be easy to scale up for use in organisms with larger genomes. In the process, they have detected over a hundred yeast genes that had previously been overlooked.
To achieve this, the authors applied a multistep approach. First, gene sequences that were “active,” and might therefore potentially code for proteins, were detected by tagging with a foreign DNA sequence (termed a Tn3 transposon) that also encoded beta-galactosidase, an enzyme that is detectable using a colored stain. Staining allowed yeast colonies containing the tagged DNA to be identified; their DNA was then sequenced, and any sequences that did not match those of known genes were selected as potential new genes. Next, to (1) check that the “new” sequences did indeed code for genes and (2) find their location on the DNA double helix’s two strands (the sense, or coding, and antisense strands), RNA from the tagged genes was screened against microarrays of short DNA oligonucleotides. Independently, the “new” sequences were also screened against databases of genes from the genomes of other organisms to look for matches that could provide clues to the sequences' function.
Using this scheme, the researchers identified 137 new genes. Around 75% were shorter than the minimal length (around 300 bases) previously thought for a valid gene meaning that they would have been excluded from consideration under criteria previously used to identify genes in DNA sequence. Unexpectedly, 15 of the new genes were located within other known genes, but on the antisense strand opposite these known genes on the DNA double helix.
The researchers believe that this approach complements other gene-detection techniques, enabling gene hunters to identify elusive genes. In the four years since the yeast genome was released in 1997, functional and comparative genomics studies have identified only 65 additional genes. In their single paper, Snyder and colleagues describe over twice that number—around 2% of those previously known to exist in yeast.
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