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Evolution of binding preferences among whole-genome duplicated transcription factors


Gera, Tamar; Jonas, Felix; More, Roye; Barkai, Naama (2022), Evolution of binding preferences among whole-genome duplicated transcription factors, Dryad, Dataset,


Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge is known for only a few studied cases. To provide a genome-scale view, we considered the 35% of budding yeast TFs, classified as whole-genome duplication (WGD)-retained paralogs. Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed that ancestral preferences are unevenly split between duplicates, while new targets are acquired preferentially by the least conserved paralog (biased sub/neo-functionalization). Dimer-forming paralogs evolved mostly one-sided dependency, while other paralogs interacted through low-magnitude DNA-binding competition that minimized paralog interference. We discuss the implications of our findings for the evolutionary design of transcriptional networks.


Next-generation Sequencing (NGS) data processed with MATLAB.

Usage Notes

This dataset is meant to be used with the scripts provided in the associated GitHub repo: