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Free keywords:
gene expression; modeling; motif search; mutational analysis;
promoter
Abstract:
The core promoter plays a central role in setting metazoan gene
expression levels, but how exactly it “computes” expression
remains poorly understood. To dissect its function, we carried out
a comprehensive structure–function analysis in Drosophila. First,
we performed a genome-wide bioinformatic analysis, providing an
improved picture of the sequence motifs architecture. We then
measured synthetic promoters’ activities of ~3,000 mutational
variants with and without an external stimulus (hormonal activation),
at large scale and with high accuracy using robotics and a
dual luciferase reporter assay. We observed a strong impact on
activity of the different types of mutations, including knockout of
individual sequence motifs and motif combinations, variations of
motif strength, nucleosome positioning, and flanking sequences. A
linear combination of the individual motif features largely
accounts for the combinatorial effects on core promoter activity.
These findings shed new light on the quantitative assessment of
gene expression in metazoans.
