Abstract
Differences in transcriptional regulatory networks underlie much of the phenotypic variation observed across organisms. Changes to cis-regulatory elements are widely believed to be the predominant means by which regulatory networks evolve, yet examples of regulatory network divergence due to transcription factor (TF) variation have also been observed. To systematically ascertain the extent to which TFs contribute to regulatory divergence, we analyzed the evolution of the largest class of metazoan TFs, Cys2-His2 zinc finger (C2H2-ZF) TFs, across 12 Drosophila species spanning ~45 million years of evolution. Remarkably, we uncovered that a significant fraction of all C2H2-ZF 1-to-1 orthologs in flies exhibit variations that can affect their DNA-binding specificities. In addition to loss and recruitment of C2H2-ZF domains, we found diverging DNA-contacting residues in ~44% of domains shared between D. melanogaster and the other fly species. These diverging DNA-contacting residues, found in ~70% of the D. melanogaster C2H2-ZF genes in our analysis and corresponding to ~26% of all annotated D. melanogaster TFs, show evidence of functional constraint: they tend to be conserved across phylogenetic clades and evolve slower than other diverging residues. These same variations were rarely found as polymorphisms within a population of D. melanogaster flies, indicating their rapid fixation. The predicted specificities of these dynamic domains gradually change across phylogenetic distances, suggesting stepwise evolutionary trajectories for TF divergence. Further, whereas proteins with conserved C2H2-ZF domains are enriched in developmental functions, those with varying domains exhibit no functional enrichments. Our work suggests that a subset of highly dynamic and largely unstudied TFs are a likely source of regulatory variation in Drosophila and other metazoans.
Highlights
Differences in regulatory networks have been proposed to be one of the major determinants of the phenotypic variations observed across organisms [1]
Our work suggests that a subset of highly dynamic and largely unstudied transcription factors (TFs) are a likely source of regulatory variation in Drosophila and other metazoans
Cys2-His2 zinc finger (C2H2-ZF) domains are known to primarily work in tandem to specify DNA motifs [50] (S1B Fig.), and so we include only those C2H2-ZF genes with 2+ C2H2-ZF domains in our analysis; we refer to these genes as poly-ZF
Summary
Differences in regulatory networks have been proposed to be one of the major determinants of the phenotypic variations observed across organisms [1]. Case studies of specific biological systems have revealed instances of regulatory divergence stemming from TF variation. These variations include gene loss as well as gene duplication where the subsequent paralogs exhibit gain and loss of effector domains, changes in interactions with other regulatory proteins, or novel TF binding potential [10,11,12,13,14,15]. A large-scale experimental study ascertaining the extent to which TF variation may contribute to overall regulatory network evolution is still lacking; it would require determining DNA-binding specificities or genomic occupancies for numerous TFs across a diverse set of organisms.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
