CBP Occupancy in Drosophila Embryos Figure 5. CBP occupancy at Dorsal-target genes in the mesoderm does not always correlate with changes in Dorsal occupancy or gene expression. A and F) In situ hybridization with digoxigenin-labeled twist (twi) and snail (sna) RNA probes in 2–4 hour old wild-type (wt) and mutant embryos that alter the Dorsal protein gradient, resulting in conversion of the entire embryo into dorsal ectoderm, neuroectoderm, or mesoderm. Embryos are oriented with anterior to the left and dorsal up. B and G) ChIP-seq peaks for CBP in wild-type (wt) and gd7 mutant embryos (raw data without cut-off), as well as Dorsal ChIP-chip peaks in wild-type are shown for the twi and sna loci. Occupancy is plotted as log2-fold enrichment over input. C–E and H–J) ChIP-qPCR of CBP, Dorsal, H3K9ac, H3K18ac, H3K27ac, and H4ac, as well as H3K27me3 and H3K9me3 at the Dorsal target genes twi and sna in wild-type (wt) and mutant embryos. Occupancy is plotted as enrichment relative the average of two negative control loci (intergenic regions), and the histone acetylations normalized against histone H3 occupancy. ChIP was performed on 2–7 independent biological replicates for each genotype. Error bars indicate standard deviation, see Results for T-tests. At the twi locus, changes in CBP occupancy closely follow changes in Dorsal occupancy and gene expression, whereas at the sna locus, CBP occupancy is independent of Dorsal and gene expression. doi:10.1371/journal.pgen.1002769.g005 PLoS Genetics | www.plosgenetics.org 8 June 2012 | Volume 8 | Issue 6 | e1002769