  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.
