Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium ${it Escherichia coli}$, for $approx$ 65$%$ of the promoters we remain completely ignorant of their regulation. Until we have cracked this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method (Reg-Seq) linking a massively-parallel reporter assay and mass spectrometry to produce a base pair resolution dissection of more than 100 promoters in ${it E. coli}$ in 12 different growth conditions. First, we show that our method recapitulates regulatory information from known sequences. Then, we examine the regulatory architectures for more than 80 promoters in the ${it E. coli}$ genome which previously had no known regulation. In many cases, we also identify which transcription factors mediate their regulation. The method introduced here clears a path for fully characterizing the regulatory genome of model organisms, with the potential of moving on to an array of other microbes of ecological and medical relevance.
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