U12 intron positions are more strongly conserved between animals and plants than U2 intron positions

Abstract

We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. The U12 introns, especially, conserved ones are concentrated in 5'-portions of plant and animal genes, where the U12 to U2 conversions occurs preferentially in the 3'-portions of genes. These results are compatible with the hypothesis that the high level of conservation of U12 intron positions and their persistence in genomes despite the unidirectional U12 to U2 conversion are explained by the role of the slowly excised U12 introns in down-regulation of gene expression.

Figure 1

Distribution of the positions of U12 and U2 introns across the length of the coding sequences in Arabidopsis (A) and human (B) genes. For each intron, the distance from the 5' end of the coding sequence (after removal of intron sequences) was calculated and divided by the total length of the coding sequence. The resulting fractions were partitioned into 10 equal length bins. For comparing the distribution of intron in the 5' and 3' halves of genes, the total numbers of introns in bins 1–5 and in bins 6–10 were compared. The statistical significance of the difference between these numbers was determined using the two-sided binomial test, with the sum of these numbers treated as the total number of trials and the number of distribution in bins 1–5 as the number of successes, with prior probability of 0.5. (A) 139,982 U2 and 182 U12 intron positions in Arabidopsis genes were analyzed. Among the U2 introns, 69,819 and 70,163 introns were contained in the 5' and 3'portions of genes, respectively (P = 0.3593). For U12 introns, 114 and 68 introns were contained in 5' and 3' portions of genes, respectively (P= 8.04 × 10^-4). (B) 230,339 U12 and 570 U12 intron positions in human genes were analyzed. Among the U2 introns, 119,949 and 110,390 introns were contained in the 5' and 3' region, respectively (P= 2.2 × 10^-16). Among the U12 introns, 318 and 252 introns were present in the 5' and 3' region, respectively (P= 6.4 × 10^-3).