Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement on the X chromosome [ChIP-seq]

In D. melanogaster males, X chromosome monosomy is compensated by chromosome-wide transcription activation. We found that complete dosage compensation during embryogenesis takes surprisingly long. Although the activating Dosage Compensation Complex (DCC) associates with the chromosome and acetylates histone H4 early, many genes are not compensated. Acetylation levels on gene bodies continue to increase for several hours after gastrulation in parallel with progressive compensation. Constitutive genes are compensated earlier than developmental genes. Remarkably, later compensation correlates with longer distances to DCC binding sites. This time-space relationship suggests that DCC action on target genes requires maturation of the active chromosome compartment. Covaris sheared ChIP-seq: H4K16ac, H3K36me3 and Input in 2 embryonic stages and in 2 biological replicates. MNase ChIP-seq: MSL2, MOF, H4K16ac, Input in 2 embryonic stages and in 3 biological replicates.