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Advances in DNA sequencing have revolutionized our ability to read genomes.However, even in the most well-studied of organisms, the bacterium ${\itEscherichia coli}$, for $\approx$ 65$\%$ of the promoters we remain completelyignorant of their regulation. Until we have cracked this regulatory RosettaStone, efforts to read and write genomes will remain haphazard. We introduce anew method (Reg-Seq) linking a massively-parallel reporter assay and massspectrometry to produce a base pair resolution dissection of more than 100promoters in ${\it E. coli}$ in 12 different growth conditions. First, we showthat 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. Themethod introduced here clears a path for fully characterizing the regulatorygenome of model organisms, with the potential of moving on to an array of othermicrobes of ecological and medical relevance.

Deciphering the regulatory genome of $\textit{Escherichia coli}$, one hundred promoters at a time