bpcusack's Parmley:J [2 articles]

Abstract

In species with large effective population sizes, highly expressed genes tend to be encoded by codons with highly abundant cognate tRNAs to maximize translation rate. However, there has been little evidence for a similar bias of synonymous codons in highly expressed human genes. Here, we ask instead whether there is evidence for the selection for codons associated with low abundance tRNAs. Rather than averaging the codon usage of complete genes, we scan the genes for windows with deviating codon usage. We ...

Abstract

BACKGROUND:In mammals, splice-regulatory domains impose marked trends on the relative abundance of certain amino acids near exon-intron boundaries. Is this a mammalian particularity or symptomatic of exonic splicing regulation across taxa? Are such trends more common in species that a priori have a harder time identifying exon ends, i.e. those with pre-mRNA rich in intronic sequence? We address these questions surveying exon composition in a sample of phylogenetically diverse genomes. RESULTS:Biased amino acid usage near exon-intron boundaries is common throughout the ...