Multifaceted effects on even-skipped transcriptional dynamics upon Kruppel dosage changes

Although fluctuations in transcription factor (TF) dosage are often well tolerated, little is known about how TF dosage modulation changes the target gene expression dynamics and results in subsequent developmental phenotypes. Using MS2/MCP-mediated quantitative live imaging in early Drosophila embryos, we characterized transcriptional dynamics of the pair-rule gene even-skipped (eve) upon changing the gap gene Kruppel (Kr) level. Decreasing Kr dosage by half leads to a transient posterior expansion of the eve stripe 2 and an anterior shift of stripe 5. Surprisingly, the most significant changes are observed in eve stripes 3 and 4, whose enhancers do not contain Kr binding sites. For both stripes, the widths of stripes are narrowed, boundaries are located more anteriorly, and the mRNA production level is reduced in Kr heterozygous embryos. We show that Kr dosage indirectly affects stripes 3 and 4 dynamics by modulating other gap gene dynamics. We quantitatively correlate moderate body segment phenotypes of Kr heterozygotes with spatiotemporal changes in eve expression. Our results indicate that nonlinear relationships between TF dosage and phenotypes underlie direct TF-DNA and indirect TF-TF interactions. Summary statementThis study analyzed the changes in transcriptional dynamics of even-skipped upon halving Kruppel dosage, and revealed how the combination of direct TF-DNA and indirect TF-TF interactions shape proper patterning.