Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of “open” chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear whether open chromatin is a product of activity - transcription at promoters and patterning transcription factor binding at enhancers - or whether it is established by independent mechanisms. Recent work has implicated the ubiquitously expressed maternal factor Zelda in this process. To assess the relative contribution of activity in the establishment of open chromatin , we have probed chromatin accessibility across the anterior-posterior axis of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is remarkably similar between the two halves. Promoters and enhancers that are active in exclusively one half of the embryo have open chromatin in the other half, demonstrating that chromatin accessibility is not a direct result of activity. However there is a small skew at enhancers that drive transcription exclusively in either the anterior or posterior half of the embryo, with greater accessibility in the region of activity. Taken together these data support a model in which regions of chromatin accessibility are defined and established by ubiquitous factors, and fine tuned subsequently by activity. Overall design: We perfomed ATAC-seq on 20 anterior and 20 posterior stage 5 Drosophila melanogaster (OregonR) embryos that were frozen and sliced in half with a razor blade.

当果蝇胚胎从母源RNA的使用转向合子转录时，在参与模式化胚胎转录的启动子与增强子区域，会形成核小体密度较低、带有特定组蛋白修饰的“开放”染色质结构域。然而目前仍不清楚，开放染色质究竟是转录活性（启动子处的转录与增强子处的模式化转录因子结合）的产物，还是通过独立机制建立的。近期研究表明，普遍表达的母源因子Zelda参与了这一过程。为了评估转录活性在开放染色质建立过程中的相对贡献，我们通过对人工解剖的细胞化囊胚期黑腹果蝇（Drosophila melanogaster）胚胎的前、后两半实施基于转座子的染色质开放性检测（ATAC-seq），探究了早期果蝇胚胎沿前后轴分布的染色质开放性特征。我们发现，全基因组范围内的染色质开放性在前后两半胚胎中极为相似。仅在胚胎单侧具有活性的启动子与增强子，在另一侧却呈现开放染色质状态，这表明染色质开放性并非转录活性的直接结果。但对于仅在胚胎前半或后半区域驱动转录的增强子而言，存在轻微的偏向性：其在具有转录活性的区域中开放性更高。综合以上数据，我们支持如下模型：染色质开放性区域由普遍表达的因子定义并建立，随后再通过转录活性进行精细调控。实验设计：我们对20枚前半段与20枚后半段的第5期黑腹果蝇（Drosophila melanogaster，品系OregonR）胚胎进行了ATAC-seq测序，这些胚胎经冷冻后用刀片切成两半。