The evolutionary origin of DNA accessibility of a new cis-regulatory activity

动物形态的进化在很大程度上是由发育基因表达的变化驱动的，这些变化形成了新的表达模式。这些变化通常受调控变化的控制，例如获得新的顺式调控元件（克雷斯）或修饰控制基因转录的现有克雷斯。这些DNA序列在一定距离上调节特定基因转录的位置、时间和水平，适应控制其活性的转录因子（TF）的结合。然而，为了具有活性，克雷斯还需要是可接近的，即不被核小体覆盖，这与大多数基因组序列不同。因此，一个新的CRE的出现需要2个步骤，TF结合位点的收购，并获得其sequence.This建议的可访问性检查这2个步骤之间的关系在一个新的CRE的进化出现。我们专注于一个定义的进化过渡，在一些果蝇物种的翅膀尖端的暗色素点的增益，这涉及到一个新的色素沉着基因黄色，斑点CRE的出现。使用来自这组苍蝇的不同物种，代表祖先的无斑点状态，或衍生的斑点状态，我们将研究包含该元素的区域的活动和可访问性。特别是，我们将解开起源的DNA可访问性的信息赋予的空间活动的CRE。在第一个项目中，我们将描述使用ATAC-seq果蝇蛹翅膀上的斑点CRE可访问性的进化和发育起源。我们将进一步映射调节这种可访问性的决定因素，并测试可能的直接控制的染色质因子trithorax，我们确定在以前的遗传screen.In第二个独立的项目，我们将确定现场CRE的功能边界，问他们如何与该地区的可访问性。虽然DNA可及性结合染色质标记通常被用作增强子边界的代表，但没有关于两者之间实际关系的定量数据。我们将使用定制的定量成像系统来精确地绘制机翼中的空间CRE活动。这一映射将揭示在自然选择下的DNA的确切片段，从而代表完整的斑点CRE进化unit. All，这一建议将阐明CRE活性和可及性之间的关系，重要的是这种可及性的进化起源，在出现一种新的调节活动的关键步骤。

The evolution of animal forms is driven to a large extent by changes in the expression of developmental genes into new expression patterns. These changes are often governed by regulatory changes, such as the gain of new cis-regulatory elements (CREs) or the modification of existing CREs controlling the transcription of a gene. These DNA sequences, modulating at a distance the places, times and levels at which particular genes are transcribed, accomodate the binding of transcription factors (TFs) controlling their activity. To be active, however, CREs also need to be accessible, i.e. no covered by nucleosomes, unlike the majority of the genome sequence. The emergence of a new CRE therefore takes 2 steps, the acquisition of TF binding sites, and the gain of accessibility to its sequence.This proposal examines the relationship between these 2 steps during the evolutionary emergence of a new CRE. We focus on a defined evolutionary transition, the gain of a spot of dark pigment at the tip of the wings in some Drosophila species, that involves the emergence of a new CRE of the pigmentation gene yellow, the spot CRE. Using different species from this group of flies that represent either the ancestral unspotted state, or the derived spotted state, we will examine the activity and accessibility of the region containing this element. In particular, we will disentangle the origin of DNA accessibility from the information imparting the spatial activity of the CRE.In a first project, we will describe the evolutionary and developmental origin of the spot CRE accessibility using ATAC-seq on Drosophila pupal wings. We will further map the determinants regulating this accessibility, and test the possible direct control by the chromatin factor trithorax, that we identified in a previous genetic screen.In a second, independent project, we will determine the functional boundaries of the spot CRE to ask how they relate to the accessibility of the region. Although DNA accessibility combined to chromatin marks is often used as a proxy for enhancer boundaries, there is no quantitative data on the actual relationship between both. We will use a custom quantitative imaging system to precisely map spatial CRE activity in the wings. This mapping will reveal the exact segment of DNA under natural selection and thereby representing the full spot CRE evolutionary unit.Altogether, this proposal will shed light on the relationship between CRE activity and accessibility, and importantly on the evolutionary origin of this accessibility, a key step in the emergence of a new regulatory activity.