Opposite GC skews at the 5' and 3' ends of genes in unicellular fungi.
BACKGROUND
GC-skews have previously been linked to transcription in some eukaryotes. They have been associated with transcription start sites, with the coding strand G-biased in mammals and C-biased in fungi and invertebrates.


RESULTS
We show a consistent and highly significant pattern of GC-skew within genes of almost all unicellular fungi. The pattern of GC-skew is asymmetrical: the coding strand of genes is typically C-biased at the 5' ends but G-biased at the 3' ends, with intermediate skews at the middle of genes. Thus, the initiation, elongation, and termination phases of transcription are associated with different skews. This pattern influences the encoded proteins by generating differential usage of amino acids at the 5' and 3' ends of genes. These biases also affect fourfold-degenerate positions and extend into promoters and 3' UTRs, indicating that skews cannot be accounted by selection for protein function or translation.


CONCLUSIONS
We propose two explanations, the mutational pressure hypothesis, and the adaptive hypothesis. The mutational pressure hypothesis is that different co-factors bind to RNA pol II at different phases of transcription, producing different mutational regimes. The adaptive hypothesis is that cytidine triphosphate deficiency may lead to C-avoidance at the 3' ends of transcripts to control the flow of RNA pol II molecules and reduce their frequency of collisions.
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. malcolm.mclean5@btinternet.com
Malcolm A
MA
McLean
Itay
I
Tirosh
D001482:Base Composition; D002176:Candida albicans / Q000235:genetics; D003570:Cytidine Triphosphate / Q000378:metabolism; D005658:Fungi / Q000235:genetics*; D005800:Genes, Fungal; D012319:RNA Polymerase II / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D003570:Cytidine Triphosphate; D012319:RNA Polymerase II