1 Department of Bioinformatics and Molecular Biology, Genentech, Inc, South San Francisco, California 94080, USA. Background: Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes.Which genes are the most and least readthrough-permissive?
We found that genes containing UGA, the most readthrough-permissive stop codon, followed by C, the most readthrough-permissive nt +4, had the highest readthrough efficiency relative to the overall median. UGA followed by G, the least readthrough-permissive nt +4, reduced readthrough efficiency but not to the level of overall median (Fig 6A).Do readthrough-promoting stop codons and nucleotides occur at a genome-wide level?
To summarize, we showed that readthrough-promoting stop codon and nucleotides at positions +4 to +9 previously determined in reporter assays also occur at a genome-wide level, with some combinations of stop codon and nt +4 identities selected for or against each other.What is the most readthrough-permissive stop codon?
Consistent with the notion that UGA is the most readthrough-permissive stop codon and UAA is the strongest terminator , genes with UAA as stop codons had significantly lower readthrough efficiencies while genes with UGA had significantly higher readthrough efficiencies compared to the sample median in all samples except for rli1-dcells.