Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data

Abstract

Polyadenylation is a step of mRNA processing which is crucial for its expression and stability. The major polyadenylation signal (PAS) represents a nucleotide hexamer that adheres to the AATAAA consensus sequence. Over a half of human genes have multiple cleavage and polyadenylation sites, resulting in a great diversity of transcripts differing in function, stability, and translational activity. Here, we use available whole-genome human polymorphism data together with data on interspecies divergence to study the patterns of selection acting on PAS hexamers. Common variants of PAS hexamers are depleted of single nucleotide polymorphisms (SNPs), and SNPs within PAS hexamers have a reduced derived allele frequency (DAF) and increased conservation, indicating prevalent negative selection; at the same time, the SNPs that "improve" the PAS (i.e., those leading to higher cleavage efficiency) have increased DAF, compared to those that "impair" it. SNPs are rarer at PAS of "unique" polyadenylation sites (one site per gene); among alternative polyadenylation sites, at the distal PAS and at exonic PAS. Similar trends were observed in DAFs and divergence between species of placental mammals. Thus, selection permits PAS mutations mainly at redundant and/or weakly functional PAS. Nevertheless, a fraction of the SNPs at PAS hexamers likely affect gene functions; in particular, some of the observed SNPs are associated with disease.

Keywords: 1000 genomes; AATAAA; SNP; mRNA processing; polyadenylation.

Fig. 1.

Patterns of selection in PAS hexamers. Whiskers represent standard errors of the mean. Asterisks correspond to P < 0.05 according to the Mann–Whitney’s U-test. (A) Densities of SNPs in PAS hexamers and in the control sample. (B) Mean DAF of SNPs is reduced in PAS hexamers, compared to the control sample. (C) Mean phastCons score is increased in PAS hexamers, compared to the control sample. (D) DAF depends on the effect of SNPs on the functional activity of the PAS hexamer (box width represents the number of sites SNPs in the category).

Fig. 2.

Schematic representation of functional classification of PAS hexamers. PAS hexamers are categorized according to the number and position of corresponding cleavage sites (A); number of PAS hexamers corresponding to a single cleavage site (B); localization within exon or intron (C); or localization within CDS or 3′-UTR (D). Gray boxes, coding exons; thick lines, 3′-UTR exons; angled lines, introns; arrows, cleavage sites.

Fig. 3.

Polymorphism in different functional groups of PAS hexamers. (A) SNP densities; (B) DAFs; (C) PhastCons scores. In A and B, box width represents the number of SNPs in the group. Dashed lines represent the mean value in the entire sample, and dotted lines, its standard error. Whiskers represent standard error of the mean. Asterisks identify difference of the particular group from the remaining PAS hexamers, according to Fisher’s exact test or Mann–Whitney U-test; *P < 0.05, **P < 10 ^{− 3}, ***P < 10 ^{− 10}.