Using Massively Parallel Reporter Assays to Dissect the Molecular Mechanisms of Transcriptional Regulation of Bacterial Promoters.

Organisms across all domains of life must make regulatory decisions in response to changing environments. The decision about when and where to turn on transcription in bacteria is mainly controlled through the binding of transcription factors to promoter regions of the DNA. However, even for the organism Escherichia coli, whose regulation is arguably best understood, we still have no indication if or how more than half of the genes are regulated. Here we use a RNA-seq based massively-parallel reporter assays and information-theoretic modeling to dissect the mechanism of regulation for a group of both well studied and unannotated bacterial promoters. We quantitatively compare the RNA-seq based massively-parallel reporter assay to a previously used fluorescent reporter based methodology. We recover nucleotide-resolution models of transcription factor to DNA binding energy and demonstrate that we can scale up the method to cover all promoters in E. coli.