Evolution of binding preferences among whole-genome duplicated transcription factors
Data files
Mar 22, 2022 version files 2.31 GB
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Abf2Ixr1.mat
12.74 MB
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allSGDtargets.mat
1.23 MB
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allZscoreMat.mat
13.88 MB
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bestCISBPInVitroWM.mat
14.20 KB
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ccPredictions.mat
388.16 KB
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CCpredictionsWJpred.mat
405.99 KB
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checAllver5.mat
775.79 MB
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checWTdelLactisSwap.mat
1.16 GB
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DBDdefForSwapping.mat
2.28 MB
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group_imp.mat
126.06 MB
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H3CC_henikoff.mat
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indRepeats.zip
159.51 MB
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iupred2.mat
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nmer7N0.mat
21.05 MB
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paraSeqs.mat
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promCorrSort.mat
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promoterIDXvec.mat
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promoterLengthsORF.mat
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promoterOL.mat
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README.txt
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SC_genome.mat
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SGDTargetsRegulatorsResults.mat
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summaryTable.mat
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Abstract
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.
This dataset is meant to be used with the scripts provided in the associated GitHub repo:
https://github.com/barkailab/Gera2021