3D Chromatin Structures Foreshadow the Drosophila Fate Map

3D structure of chromatin is thought to be critical for the regulation of gene expression during development. Here we employ the Micro-C assay to achieve 100 bp resolution for the genome organization of Drosophila melanogaster throughout the first half of embryogenesis. The resulting contact maps enable the identification of fine-scaled structures such as individual loops and boundaries delineating TADs. We observe that 3D structures form prior to zygotic genome activation in precellular embryos, and many of these organizational features persist during successive mitotic cycles. 3D structures are classified through the use of 149 ChIP-seq datasets. We present evidence for specialized elements associated with housekeeping genes that are enriched for BEAF-32 but not CTCF. We also characterize a distinct class of elements associated with developmental gene regulation that are enriched with GAF and Zld binding. This binding is maintained during mitotic cycles and exhibits evolutionary conservation of both sequence and 3D structures. In sum, this work provides a comprehensive genome-wide characterization at unprecedented resolution of the role of 3D chromatin organization in gene regulation during development. We propose that the 3D organization of the pre-cellular embryo facilitates deployment of the developmental control genes defining the Drosophila fate map. Overall design: Micro-C in Drosophila embryos at stages nc1-8, nc12 (mitotic), nc14, and s10-12 with two biological replicates and two technical replicates.

染色质三维结构被认为在发育过程中对基因表达调控发挥关键作用。本研究采用Micro-C实验（Micro-C assay），在黑腹果蝇（Drosophila melanogaster）胚胎发生前半阶段实现了分辨率达100 bp的基因组构象分析。所得的染色质相互作用图谱可用于鉴定精细尺度的结构，例如界定拓扑关联结构域（Topologically Associating Domains, TADs）的单个环结构与边界区域。我们观察到，三维染色质结构在合子基因组激活（zygotic genome activation）之前就已在前细胞胚胎中形成，且多数此类构象特征在后续的有丝分裂周期中得以保留。本研究通过149套染色质免疫共沉淀测序（ChIP-seq）数据集对三维染色质结构进行分类。我们发现了一类与持家基因相关的特殊调控元件，该类元件富集BEAF-32结合位点但不含CTCF结合位点。此外，我们还鉴定出另一类与发育基因调控相关的独特元件，该类元件富集GAF与Zld结合位点。此类结合模式在有丝分裂周期中得以维持，且其序列与三维结构均表现出进化保守性。综上，本研究以前所未有的分辨率完成了全基因组范围的染色质三维构象分析，阐明了其在发育过程中对基因调控的作用机制。我们提出，前细胞胚胎的三维染色质构象有助于调控决定黑腹果蝇命运图谱的发育控制基因的表达部署。实验整体设计：对黑腹果蝇胚胎的nc1-8、有丝分裂期nc12、nc14以及s10-12阶段样本开展Micro-C实验，每组设置2次生物学重复与2次技术重复。