Disentangling Sources of Selection on Exonic Transcriptional Enhancers

Abstract

In addition to coding for proteins, exons can also impact transcription by encoding regulatory elements such as enhancers. It has been debated whether such features confer heightened selective constraint, or evolve neutrally. We have addressed this question by developing a new approach to disentangle the sources of selection acting on exonic enhancers, in which we model the evolutionary rates of every possible substitution as a function of their effects on both protein sequence and enhancer activity. In three exonic enhancers, we found no significant association between evolutionary rates and effects on enhancer activity. This suggests that despite having biochemical activity, these exonic enhancers have no detectable selective constraint, and thus are unlikely to play a major role in protein evolution.

Keywords: cis-regulation; enhancer; evolutionary rate; exon.

Fig. 1.

Outline of our approach. For each possible substitution in an exonic enhancer, we determined the evolutionary rate across placental mammals, as inferred from the rate of substitution. We then fit a linear model to determine the relative contribution of two plausible drivers of evolutionary rate: amino acid sequence, where synonymous changes are expected to occur more commonly than nonsynonymous ones; and regulatory impact, wherein positions with high regulatory impact (such as TF binding sites) may dictate lower evolutionary rate..

Fig. 2.

Exonic enhancer evolution. (A) Phylogenetic tree of the mammalian species for which we analyzed the SORL1 exon 17 sequences. Numbers indicate the number of point mutations identified in each branch. (B) Summary of the substitution patterns for each of the three exons analyzed. Percentages for “# Sites Substituted” are relative to the total number of sites in the exon; percentages for the other columns are given relative to the total number of substitutions.