Establishment of the haemopoietic transcriptional programme: From systems approaches to molecular mechanisms

我们的基因控制我们的身体如何从一个受精卵细胞发育，我们身体中的所有细胞都包含相同的基因组。这种细胞迅速分裂并发育成各种不同的细胞类型，组成我们身体的各种器官。所有这些细胞都表达不同的基因程序，这意味着并非所有的基因在每种细胞类型中都始终活跃。这种细胞类型特异性基因激活模式由另一层控制（在基因层之上）控制，该控制告诉细胞哪些基因打开和关闭，从而决定哪种细胞类型的发展。这个额外的控制层被称为“表观遗传”层，由两个组成部分组成：（1）基因组范围的网络，基因通过该网络相互调节以产生适当的基因表达模式;（2）DNA包装装置。每个细胞含有一米的DNA，为了能够将其装入细胞核，它被所谓的染色质蛋白质紧密压缩，使得非活性基因高度紧凑，它们的DNA隐藏，而活性基因位于压缩减少的区域。为了激活一个不活跃的紧凑基因，蛋白质复合物，所谓的“转录因子”将染色质推到一边或对其进行修改，以便基因可以接近激活它们的因子。过去几年的研究集中在一个基因上，并导致了控制其活性的转录因子和染色质成分的发现。我们学会了提取单个基因演奏的曲调，但却听不到交响乐。我们对哺乳动物的所有基因是如何按照正确的顺序进行启动和关闭的理解仍然很肤浅。此外，我们所知道的大部分是基于对细胞系的研究，这些细胞系代表固定的细胞类型或癌细胞，以及来自更简单的生物体，如酵母。哺乳动物的情况要复杂得多，因为从受精卵构建生物体涉及到以精确的等级顺序将一种细胞类型转变为另一种细胞类型（所谓的“分化”），这需要所有基因的活动紧密协调。换句话说，建造一个有机体就像建造一座房子：我们必须将各个组件按照精确的顺序放在一起，而不是先从屋顶开始，然后再从地窖开始。该提案将使用小鼠的血细胞发育作为研究哺乳动物细胞分化动力学的模型。我们将研究给定细胞类型的所有基因，并使用基于胚胎干细胞的复杂体外系统，在那里我们可以生成和纯化不同的血细胞类型。然后，我们将确定哪些转录因子和染色质组分在不同的发育阶段调节哪些基因，并研究它们在哪个水平和何时表达。直到最近，这种全球性或“系统生物学”的研究是遥不可及的，因为缺乏技术。然而，通过最新的技术，我们可以在很短的时间内确定一种细胞类型的整个DNA序列。这项技术已经被修改，以研究所有基因的表观遗传变化，现在可以用来识别一种细胞类型的基因与另一种细胞类型的基因的区别。然而，这类实验的一个特点是，它们产生大量的数据，需要专业知识来理解它们。这是通过生物信息学家开发新的计算机程序和数学模型来实现的，数学模型运行模拟来预测基因的综合“集体”行为。为此，我们成立了一个由实验研究人员和计算生物学家组成的跨学科联盟，他们将合作了解数千个基因如何共同作用以产生特定的细胞类型。这些研究的最终目的是能够理解个体发育如何在DNA序列中编码，并预测DNA序列的变化如何影响发育过程。

Our genes control how our body develops from one fertilized egg cell and all cells in our body contain the same set of genes. This cell rapidly divides and develops into a large variety of distinct cell types that make up the various organs in our body. All these cells express different genetic programs, meaning that not all of our genes are always active in every cell type. This cell-type-specific gene activation pattern is governed by another layer of control (on top of the layer of the genes) that tells cells which genes to switch on and off, thereby deciding which cell type develops. This additional control layer is called the 'epigenetic' layer and consists of two components: (1) a genome-wide network through which genes regulate each other to generate the appropriate gene expression patterns; (2) the DNA packing apparatus. Each cell contains one meter of DNA, and to be able to fit it into the nucleus, it is densely compacted by so called chromatin proteins such that inactive genes are highly compact and their DNA hidden, whereas active genes are in areas of reduced compaction. To activate an inactive, compact gene, protein complexes, so called 'transcription factors' push chromatin aside or modify it, so that genes become accessible to the factors that activate them. Studies in the past years focused on one gene at a time and led to the discovery of the transcription factors and chromatin components that control their activity. We learned to extract the tune that individual genes play but failed to hear the symphony. Our understanding of how all the genes in mammals are orchestrated to switch on and off in the right order is still superficial. Moreover, much of what we know is based on studies from cell lines, which represent fixed cell types or are cancer cells, and from simpler organisms, such as yeast. The situation in mammals is much more complex because building an organism from a fertilized egg involves turning one cell type into another (so called 'differentiation') in a precise hierarchical order which requires tight coordination of the activity of all the genes. In other words, building an organism is like building a house: we have to put the individual components together in a precise order and not start with the roof before the cellar. This proposal will use blood cell development in the mouse as a model to investigate the dynamics of cell differentiation in mammals. We will study all genes of a given cell type and use a sophisticated in vitro system based on embryonic stem cells where we can generate and purify different blood cell types. We then will identify which transcription factors and chromatin components regulate which genes at the different developmental stages and study at which level and when they are expressed. Until recently such global or 'systems biology' studies were beyond reach since the technology was lacking. However, with the latest technology we can determine the entire DNA sequence of one cell type in a very short time. This technology has been modified to study epigenetic changes at all genes and can now be used to identify what distinguishes genes of one cell type from those of another. However, one feature of such experiments is that they produce enormous amounts of data and require specialist knowledge to make sense of them. This is achieved by bioinformaticians developing new computer programs and mathematical modelers running simulations to predict the integrated, 'collective' behavior of genes. To this end we have formed an interdisciplinary consortium consisting of experimental researchers and computational biologists who will collaborate to understand how thousands of genes work together to generate specific cell types. The ultimate aim of these studies is to be able to understand how individual development is encoded in the DNA-sequence and to predict how changes in the DNA sequence impact on developmental processes.