Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana

Abstract

Mutations in DNA sequences that bind transcription factors and thus modulate gene expression are a source for adaptive variations in gene expression. To understand how transcription factor binding sequences evolve in natural populations of the thale cress Arabidopsis thaliana, we integrated genomic polymorphism data for loci bound by transcription factors with in vitro data on binding affinity for these transcription factors. Specifically, we studied 19 different transcription factors, and the allele frequencies of 8,333 genomic loci bound in vivo by these transcription factors in 1,135 A. thaliana accessions. We find that transcription factor binding sequences show very low genetic diversity, suggesting that they are subject to purifying selection. High frequency alleles of such binding sequences tend to bind transcription factors strongly. Conversely, alleles that are absent from the population tend to bind them weakly. In addition, alleles with high frequencies also tend to be the endpoints of many accessible evolutionary paths leading to these alleles. We show that both high affinity and high evolutionary accessibility contribute to high allele frequency for at least some transcription factors. While binding sequences with stronger affinity are more frequent, we did not find them to be associated with higher gene expression levels. Epistatic interactions among individual mutations that alter binding affinity are pervasive, and can help explain variation in accessibility among binding sequences. In summary, combining in vitro binding affinity data with in vivo binding sequence data can help understand the forces that affect the evolution of transcription factor binding sequences in natural populations.

The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR

“…However, the molecular origins and evolution of such elements are still poorly understood. While comprehensive in vitro data on the binding of eukaryotic TFs to their binding sites have helped us understand eukaryotic genotype-phenotype maps of gene regulation 1, [11][12][13] , the topography of such landscapes remains unexplored in prokaryotes. To reduce this knowledge gap, we mapped the first comprehensive adaptive landscape of TFBS variants for bacteria.…”