A three-dimensional atlas of gene expression during chick development with cross comparisons to the mouse

当人们想到地图集时，他们想到的是一幅世界地图，显示海洋，国家边界，时间线，标有城市，河流等名称。这里提出的地图集将显示发育中的鸡胚解剖结构上的基因表达模式，标有结构，基因等名称。正如世界地图集帮助我们了解我们生活在哪里，胚胎发育的图谱将帮助我们理解我们是如何形成的。我们都是从一个受精细胞增殖成大量的细胞，这经历了复杂的形状变化，同时生长形成组成我们身体的不同器官和组织。通过对发育过程中不同时期的鸡胚进行成像，我们将绘制出它们形成时的解剖结构的详细地图。最早的阶段相对简单，因为它们是平坦的，但较老的胚胎变得越来越复杂，我们将使用一种名为“光学投影断层扫描”的3D成像技术对它们进行成像。如果没有一个系统的方法来命名它的特征，一个地图集就不是很有用，所以我们将创建一个标准的单词集，这将使得使用基于计算机科学的工具来查询地图集成为可能。但是发育中的胚胎的明显结构隐藏了更深层次的解剖学，即称为“组织者”的特殊细胞群。这些组织者指导周围的细胞，以便在正确的时间在正确的地点制造正确的结构。组织者并不总是那么容易识别的;例如，负责形成肢体手指图案的“极化区域”看起来就像它周围的组织一样。大约有六个组织者已经被发现，其中许多是通过鸡胚胎的移植实验发现的，我们现在知道，它们最好的区别是在细胞中活跃（“表达”）的特定基因。在我们的项目中，我们计划检查哪些基因在四个明确的组织者中表达，并在整个发育过程中产生整个胚胎中精确表达模式的3D图谱。将绘制约1000个基因的基因表达模式。这是一个显着数量的基因与开始填充鸡图谱将公开提供给每个人在互联网上。为了确定什么基因在早期鸡胚的这四个不同区域（下胚层，Hensen结，神经管底板和肢体极化区域）中表达，我们将解剖这些组织，并使用“微阵列”来筛选它们表达的所有基因，并识别共享的基因组。在同一个地方表达的基因（“共表达组”）很可能参与同一个生物过程，因此我们希望发现一组基因，这些基因共同作用来定义一个“组织者”。但是为什么要关注小鸡而不是更接近人类的动物呢？令人惊讶的是，组织者和其他信号中心在不同的物种中以相似的方式发挥作用，从鱼类到人类，因此在小鸡身上的发现与人类的发育有关，而且小鸡比小鼠胚胎更容易获得和解剖，因此这两种模型非常互补。然而，小鸡图谱将基于为小鼠开发的相同系统，从而允许进行比较。鸡和小鼠中保守的表达模式将为基因在功能上相关提供强有力的证据，而细微的差异可以解释为什么鸡和小鼠看起来不一样。我们将建立一个数据库来组织和管理这个关于基因表达模式、解剖结构、基因等的庞大数据集，并开发新的计算机工具来查询和分析数据，以发现基因在发育中的新关系和新功能。这项研究将导致对基本生物过程的更深入了解，这反过来又有助于了解先天性异常，癌症和组织修复等健康问题。

When people think of an atlas, they think of a world map, showing oceans, country borders, timelines, labelled with names of cities, rivers, etc. The atlas proposed here will show patterns of gene expression layered onto anatomical structures of the developing chick embryo, labelled with the names of structures, genes, etc. Just as a world atlas helps us to understand where we live, an atlas of the developing embryo will help us to comprehend how we form. We all develop from a single fertilized cell which multiplies into a mass of cells, this undergoes complex changes in shape, while growing to form the different organs and tissues that make up our bodies. By imaging chick embryos at different times during development, we will make a detailed map of anatomical structures as they form. The earliest stages are relatively simple as they are flat, but older embryos become increasingly more complicated and we will use a 3D imaging technique called 'Optical Projection Tomography' to image them. An atlas is not very useful without a systematic way to name its features so we will create a standard set of words, which will make it possible to query the atlas using tools based on computer science. But the overt structure of developing embryos hides a further level of anatomy, special groups of cells called 'organizers'. These organizers instruct cells around them so that the correct structures are made in the right place at the right time. Organizers are not always easy to identify; the 'polarizing region' responsible for patterning the digits of the limb for example looks just like the tissue all around it. About half a dozen organizers have been discovered, many through transplantation experiments in chick embryos, and we now know that they are best distinguished by specific genes that are active ('expressed) in their cells. In our project we plan to examine exactly which genes are expressed in four well defined organizers and produce a 3D map of their precise expression patterns in the whole embryo throughout development. Gene expression patterns of ~1000 genes will be mapped. This is a significant number of genes with which to begin to populate the chicken Atlas to be made publicly available to everyone over the internet. To determine what genes are expressed in these four different regions of early chick embryos (the hypoblast, Hensen's node, floor plate of the neural tube and limb polarizing region) we will dissect out these tissues and use 'microarrays' to screen for all the genes they express and identify shared sets of genes. Genes expressed in the same place ('synexpression groups') are likely to be involved in the same biological process, so we hope to uncover sets of genes which work together to define an 'organizer'. But why focus on chicks rather than animals closer to humans? Amazingly, organizers and other signalling centres act in similar ways in different species as diverse as fish and man. Thus discoveries in the chick are relevant to human development and chicks are much easier to obtain and dissect than mouse embryos, so these two models are very complementary. The chick atlas however will be based on the same system developed for the mouse thus allowing comparisons. Conserved patterns of expression in chick and mouse will provide strong evidence for genes being functionally related while subtle differences can cast light on why a chick and mouse do not look the same. We will create a database to organize and manage this huge collection of data on gene expression patterns, anatomical structures, genes, etc. and develop new computer tools to query and analyse the data to discover new relationships and new functions for genes in development. This research will lead to a deeper understanding of the basic biological processes which will in turn help understanding of health issues such as congenital abnormalities, cancers and tissue repair.