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，他们想到的是一张世界地图，上面显示着海洋、国家边界、时间轴，并标有城市、河流的名称等。这里提出的图谱将显示发育中的鸡胚胎的基因表达模式，并以结构、基因等的名称标记。就像世界地图集帮助我们了解我们生活的地方一样，胚胎发育的地图集将帮助我们了解我们是如何形成的。我们都是从一个单一的受精卵细胞繁殖成大量细胞，这些细胞在形状上经历了复杂的变化，同时成长为构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小鸡胚胎进行成像，我们将绘制出它们形成时的详细解剖结构图。最初的阶段相对简单，因为它们是平坦的，但年龄较大的胚胎变得越来越复杂，我们将使用一种称为“光学投影断层扫描”的3D成像技术对它们进行成像。如果没有一种系统的方式来命名它的特征，地图集就不是很有用，所以我们将创建一套标准的词，这将使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显性结构隐藏着更深层次的解剖结构，一组特殊的细胞被称为“组织者”。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方形成正确的结构。组织者并不总是那么容易识别；例如，负责塑造肢体手指图案的“极化区”看起来就像它周围的组织一样。已经发现了大约6个组织者，其中许多是通过鸡胚胎的移植实验发现的，我们现在知道，通过细胞中活跃（“表达”）的特定基因，可以最好地区分它们。在我们的项目中，我们计划准确地检查哪些基因在四个明确的组织者中表达，并绘制出它们在整个胚胎发育过程中精确表达模式的3D地图。将绘制约1000个基因的基因表达模式。这是一笔数目可观的基因数目，我们可以利用这些基因来建立鸡的基因图谱，并通过互联网向所有人公开。为了确定在早期鸡胚胎的这四个不同区域（下胚层、Hensen’s结、神经管底板和肢体极化区）中表达的基因，我们将解剖这些组织，并使用“微阵列”筛选它们表达的所有基因，并识别共享的基因集。在同一位置表达的基因（“共表达组”）很可能参与相同的生物过程，因此我们希望发现一起工作的基因集来定义一个“组织者”。但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，包括鱼类和人类。因此，在小鸡身上的发现与人类发育有关，而且小鸡比小鼠胚胎更容易获得和解剖，因此这两种模型是非常互补的。然而，小鸡地图集将基于为老鼠开发的相同系统，从而允许进行比较。小鸡和老鼠的保守表达模式将为基因功能相关提供强有力的证据，而细微的差异可以解释为什么小鸡和老鼠看起来不一样。我们将建立一个数据库来组织和管理基因表达模式、解剖结构、基因等方面的庞大数据集，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层次的理解，这将反过来有助于理解健康问题，如先天性异常，癌症和组织修复。

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 (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.