A Gradient in the Distribution of Introns in Eukaryotic Genes

Abstract

The majority of eukaryotic genes consist of exons and introns. Introns can be inserted either between codons (phase 0) or within codons, after the first nucleotide (phase 1) and after the second (phase 2). We report here that the frequency of phase 0 increases and phase 1 declines from the 5′ region to the 3′ end of genes. This trend is particularly noticeable in genomes of Homo sapiens and Arabidopsis thaliana, in which gains of novel introns in the 3′ portion of genes were probably a dominant process. Similar but more moderate gradients exist in Drosophila melanogaster and Caenorhabditis elegans genomes, where the accumulation of novel introns was not a prevailing factor. There are nine types of exons, three symmetric (0,0; 1,1; 2,2) and six asymmetric (0,1; 1,0; 1,2; 2,1; 2,0; 0,2). Assuming random distribution of different types of introns along genes, one can expect the frequencies of asymmetric exons such as 0,1 and 1,0 or 1,2 and 2,1 to be approximately equal, allowing for some variation caused by randomness. The gradient in intron distribution leads to a small but consistent and statistically significant bias: phase 1 introns are more likely at the 5′ ends and phase 0 introns are more likely at the 3′ ends of asymmetric exons. For the same reason, the frequency of 0,0 exons increases and the frequency of 1,1 exons decreases in the 3′ direction, at least in H. sapiens and A. thaliana. The number of introns per gene also affects the distribution and frequency of phase 0 and 1 introns. The gradient provides an insight into the evolution of intron-exon structures of eukaryotic genes.