Natural selection in Transcription Factor (TF)-DNA interaction motifs – A comparative and population genomics perspective

Natural selection heavily influences the evolutionary trajectories of species by impacting their genotype to phenotype transitions. On the molecular level, these transitions are shaped by the regulatory sequences (RSs). In this study, we employed a combination of population and comparative genomics to investigate how natural selection affects specific RS classes involved in the regulatory transcription factor (TF)-DNA interactions. These interactions consist of two motifs, namely: TF-binding domains (TF-BDs) and TF-binding sites (TF-BSs). Using publicly available annotation data for Homo sapiens, Arabidopsis thaliana and Drosophila melanogaster, we first constructed the species-specific lists of the TF-BD regions. On applying some of the commonly used summary statistics, we found signals of purifying selection acting on TF-BDs, consistent with their functional importance. Next, using the biochemical assay-based annotations, we identified potential TF-BS regions and used variants within them as nonsynonymous equivalent. Interestingly, we also observed that non-coding TF-BS regions showed similar levels of constraint to that of coding regions for populations with large Ne. Signals of positive selection were limited. Nevertheless, McDonald–Kreitman estimates revealed that, in both fruit-fly and thale-cress, α for TF-BDs was consistently higher than for adjacent non-binding domains, whereas no such difference was apparent in humans. Taken together, our comparative analysis shows that the efficiency of negative—and to a lesser extent positive—selection on TF-DNA interface elements scales with effective population size. The dataset and analysis pipeline provide a baseline for future studies of regulatory evolution across coding and non-coding regions.