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

在黑腹果蝇（Drosophila melanogaster）雄性个体中，X染色体单体型通过全染色体范围的转录激活实现剂量补偿。我们发现，胚胎发生过程中的完全剂量补偿耗时远超预期。尽管具有激活功能的剂量补偿复合体（Dosage Compensation Complex, DCC）会较早结合染色体并催化组蛋白H4的乙酰化修饰，但仍有大量基因未完成剂量补偿。基因体区域的乙酰化水平在原肠胚形成后仍会持续升高数小时，这与剂量补偿的逐步推进过程同步。组成型表达基因的剂量补偿启动时间早于发育调控基因。值得注意的是，剂量补偿启动越晚的基因，其与DCC结合位点的距离越长。这种时空关联规律表明，DCC对靶基因的调控作用需要活性染色体区室的成熟过程作为基础。

整体实验设计：
1. 基于Covaris超声破碎的染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）：针对两个胚胎发育阶段，分别检测H4K16ac、H3K36me3以及Input对照，设置2次生物学重复。
2. 微球菌核酸酶（Micrococcal Nuclease, MNase）辅助染色质免疫共沉淀测序：针对两个胚胎发育阶段，分别检测MSL2、MOF、H4K16ac以及Input对照，设置3次生物学重复。