Massively Parallel Binding Assay (MPBA) reveals limited transcription factor cooperation, challenging models of specificity
We provide the data collected using the method MPBA, allowing parallel measurement of TF binding to thousands of DNA sequence-variants within cells. The method was applied to quantify binding of dozens of transcription factors (TFs) to libraries of mutated regulatory regions, systematically screening all motif combinations. Overall design: Massively Parallel Binding Assay (MPBA), a novel method allowing parallel measurement of transcription factor (TF) binding to thousands of DNA sequence-variants within cells. In this project we apply it to quantify binding of dozens of TFs to libraries of mutated regulatory regions, systematically screening all motif combinations. In brief, we integrate a library of DNA variants into a designed plasmid and transform it into cells carrying an endogenous TF of interest fused to a Micrococcal Nuclease (MNase), which allows triggering the cleavage of TF-bound DNA upon a short calcium pulse. Sample titles are convention: TranscriptionFactor_libraryNumber_experimentNumber_biologicalRepeat_TimePoint_TechnicalRepeat. Note that each fastq file is muliplexed in two levels: (1) sample (TF,experimentNum,biologicalRepeat,TimePoint,TechnicalRepeat). (2) libraries (LibaryNum). ATAC-seq: profiles for the wild-type strain BY4741 and for a strain with double deletion of Msn2/4 genes (2 repeats for each of the tested strains).