TECH BRIEF | Researchers Map Worm ORFeome
Courtesy of Marc Vidal
Citing the need to verify genome annotations and to provide a resource for functional genomics, Marc Vidal of the Dana-Farber Cancer Institute and an international team of researchers have tackled what they call the "ORFeome," the complete set of protein-encoding open-reading frames (ORFs) in the Caenorhabditis elegans genome (Nat Genet, advance online publication, DOI:10.1038/ng1140, April 7, 2003).
Using annotation data, the team designed 19,477 primer pairs to precisely amplify each worm coding sequence (excluding untranslated segments), attempted amplification from a highly representative cDNA library, and cloned the resulting 11,984 ORFs into Invitrogen's Gateway system to make ORFeome 1.1.
The team used this collection to verify 4,365 predicted but experimentally unconfirmed ORFs; assess the prevalence of alternative splicing variants and the accuracy of intron-exon boundary predictions (nearly one-third were incorrect); and demonstrate its utility in "interactome" mapping and...