Title: Pho4 TF Mutant Data Repository
Abstract:\
Transcription factors (TFs) bind regulatory DNA to control gene expression, and mutations to either TFs or DNA can alter binding affinities to rewire regulatory networks and drive phenotypic variation. While studies have profiled energetic effects of DNA mutations extensively, we lack similar information for TF variants. Here, we present STAMMP (Simultaneous Transcription Factor Affinity Measurements via Microfluidic Protein Arrays), a high-throughput microfluidic platform enabling quantitative characterization of hundreds of TF variants simultaneously. Measured affinities for ~210 mutants of a model yeast TF (Pho4) interacting with 9 oligonucleotides (>1,800 Kds) reveal that many combinations of mutations to poorly conserved TF residues and nucleotides flanking the core binding site alter but preserve physiological binding, providing a mechanism for mutations in cis and trans to rewire networks without insurmountable evolutionary penalties. Moreover, biochemical double-mutant cycles across the TF-DNA interface reveal molecular mechanisms driving recognition, linking sequence to function.
Folders and brief description:
1) Information for aggregate analyses: contains data across all replicates for all Pho4 mutants, files separated by oligonucleotide identity; also contains data for supplemental analyses as appropriate
2) Information for raw curves: Data for generating raw binding curves, as well as raw PDFs of curves
3) Information for specificity analysis: contains spreadsheets of pairwise comparisons of Pho4 mutants for 2 oligonucleotide sequences of interest.
All folders contain respective ReadMe files for navigation.
bioRxiv: https://doi.org/10.1101/2020.06.22.165571
Final publication: https://doi.org/10.1016/j.cels.2020.11.012
If data is used, please cite Aditham, AK, et al. High-Throughput Affinity Measurements
of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants. Cell Systems, 2020.
Date created: 2020-Jun-22
Date updated: 2020-Dec-19
