Division of Developmental Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt Am Main, Frankfurt am Main, Germany.
Elife. 2023 Jul 11;12:e84969. doi: 10.7554/eLife.84969.
A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called 'enhancers.' Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such a view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the embryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expression patterns in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetle ) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. Here, we establish the AP patterning of the short-germ beetle as a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, we established an enhancer prediction system in based on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, we discovered several enhancers, and assessed the spatiotemporal activities of some of them in live embryos. We found our data consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expression patterns (that we call 'dynamic enhancers') and enhancers that stabilize gene expression patterns (that we call 'static enhancers'). However, more data is needed for a strong support for this or any other alternative models.
胚胎发生过程中，基因如何在适当的位置和时间开启或关闭是一个关键问题。这种决策是由称为“增强子”的非编码序列做出的。我们对增强子如何工作的模型很大程度上依赖于这样的假设，即基因作为稳定的域在胚胎组织中从头被激活。这种观点得到了胚胎前后（AP）轴早期模式形成的标志性研究的强化，事实上，基因表达域似乎或多或少稳定地出现。然而，对其他模型系统（包括脊椎动物的 AP 模式形成和短体昆虫，如甲虫）中的基因表达模式的仔细分析描绘了一个非常不同的、非常动态的基因调控观点，其中基因经常以波浪式的方式表达。到目前为止， enhancer 水平上的这种基因表达波是如何介导的还不清楚。在这里，我们将短体甲虫的 AP 模式形成确立为一个模型系统，以研究 enhancer 水平上的动态和时间模式形成。为此，我们在 中建立了一个增强子预测系统，该系统基于时间和组织特异性的 ATAC-seq 和基于 MS2 标记的增强子活体报告系统。使用这个实验框架，我们发现了几个 增强子，并评估了其中一些在活体胚胎中的时空活性。我们发现我们的数据与一个模型一致，即在胚胎模式形成过程中基因表达的时间由增强子之间的平衡行为介导，这些增强子诱导基因表达模式的快速变化（我们称之为“动态增强子”）和稳定基因表达模式的增强子（我们称之为“静态增强子”）。然而，需要更多的数据来支持这一模型或任何其他替代模型。
