Figure 6.

Redistributed Bcd binding and precocious activation of target genes in zld⁻ embryos. (A) Relative levels of Bcd binding to basal promoter regions increase in zld⁻ compared with wild-type (wt) embryos. The percentages of peaks located within certain distances from peak summits to the nearest basal promoters are shown for different peak groups. TSSs were determined by looking for 5′ untranslated region (UTR) annotation from modENCODE submission: annotation of the developmental transcriptome of Drosophila melanogaster (ID: modENCODE_4057). P-values were calculated using a χ² test. (B) Ectopic Bcd binding correlates with up-regulated transcription. Numbers in the second column represent peaks that are associated with up-regulated genes. To identify genes associated with Bcd-binding peaks, we located coding sequences within 1 kb upstream of and downstream from the peak summit and filtered out genes with the TSS outside this region. Up-regulated genes were identified by comparing 1- to 2-h wild-type and zld⁻ microarray data from Liang et al. (2008). P-values were calculated by χ² test between the zld-only peaks and wild-type-only or shared peaks. (C–J) Expression of endogenous genes in wild-type (C,E,G) and zld⁻ (D,F,H) embryos. (I,J) lacZ expression of a dve enhancer in wild-type (I) and zld⁻ (J) embryos. (K) Bcd ChIP-qPCR of three enhancer regions. Error bars represent standard deviations from the mean. (*) P < 0.05; (**) P < 0.005.