Temporal Coordination of Gene Networks by Zelda in the Early <em>Drosophila</em> Embryo

In past years, much attention has focused on the gene networks that regulate early developmental processes, but less attention has been paid to how multiple networks and processes are temporally coordinated. Recently the discovery of the transcriptional activator Zelda (Zld), which binds to CAGGTAG and related sequences present in the enhancers of many early-activated genes in Drosophila, hinted at a mechanism for how batteries of genes could be simultaneously activated. Here we use genome-wide binding and expression assays to identify Zld target genes in the early embryo with the goal of unraveling the gene circuitry regulated by Zld. We found that Zld binds to genes involved in early developmental processes such as cellularization, sex determination, neurogenesis, and pattern formation. In the absence of Zld, many target genes failed to be activated, while others, particularly the patterning genes, exhibited delayed transcriptional activation, some of which also showed weak and/or sporadic expression. These effects disrupted the normal sequence of patterning-gene interactions and resulted in highly altered spatial expression patterns, demonstrating the significance of a timing mechanism in early development. In addition, we observed prevalent overlap between Zld-bound regions and genomic “hotspot” regions, which are bound by many developmental transcription factors, especially the patterning factors. This, along with the finding that the most over-represented motif in hotspots, CAGGTA, is the Zld binding site, implicates Zld in promoting hotspot formation. We propose that Zld promotes timely and robust transcriptional activation of early-gene networks so that developmental events are coordinated and cell fates are established properly in the cellular blastoderm embryo.过往研究中，学界对调控早期发育进程的基因调控网络已有广泛关注，但针对多套基因网络与发育进程如何实现时序协同调控的相关探索仍相对不足。近期，研究人员发现转录激活因子Zelda（Zld）可结合果蝇中众多早期激活基因增强子内的CAGGTAG及其相关序列，这为多组基因的同步激活机制提供了重要线索。本研究通过全基因组结合分析与表达检测，鉴定果蝇早期胚胎中的Zld靶基因，旨在解析Zld所调控的基因回路。研究发现，Zld可结合参与早期发育进程的各类基因，包括细胞化、性别决定、神经发生以及模式形成相关基因。在Zld缺失的条件下，大量靶基因无法正常激活；而其余靶基因（尤其是模式形成相关基因）则表现出转录激活延迟，其中部分基因还存在表达微弱或散发性表达的异常。这些异常破坏了模式形成基因间的正常互作时序，最终导致空间表达模式发生显著改变，证实了时序调控机制在早期发育中的关键作用。此外，我们观察到Zld结合区域与众多发育相关转录因子（尤其是模式形成因子）所结合的基因组"热点"区域存在广泛重叠。结合热点区域中最富集的基序CAGGTA正是Zld结合位点这一发现，表明Zld参与促进基因组热点区域的形成。我们提出，Zld可促进早期基因网络实现及时且稳健的转录激活，从而确保发育事件有序协同，并在细胞囊胚胚胎中正确建立细胞命运。