Knowles David W
Cold Spring Harb Protoc. 2012 Feb 1;2012(2):150-61. doi: 10.1101/pdb.top067843.
To properly understand the transcriptional network of animals, we must have full quantitative comprehension of the spatial and temporal expression patterns of transcription factors and their targets. Visual inspection of embryos stained to reveal the patterns of genes shows levels of expression that change from cell to cell in a complex manner. With our current wealth of knowledge regarding the basic biology of animal genomes and the components of their transcriptional regulatory networks, combined with current technologies in optical microscopy, computing, and image and vision analysis, we should be able to capture quantitative, three-dimensional (3D) information about the transcriptional network (all factors and targets) for an entire animal at cellular resolution. It should also be possible to assemble these data into a single computationally analyzable database--an atlas--that could be the basis for uncovering new biology governing regulatory gene networks. This article describes progress toward realizing these goals, with the focus on Drosophila melanogaster. It describes a suite of high-throughput methods that have been used to create the first quantitative 3D description of gene expression and morphology at cellular resolution in a whole animal, and it presents some of the new biology that has been revealed by this quantitative atlas.
为了恰当地理解动物的转录网络，我们必须对转录因子及其靶标的时空表达模式有全面的定量理解。对染色以揭示基因模式的胚胎进行肉眼观察，会发现基因表达水平在细胞间以复杂的方式变化。鉴于我们目前对动物基因组基础生物学及其转录调控网络组成部分的丰富知识，再结合光学显微镜、计算以及图像和视觉分析等当前技术，我们应该能够以细胞分辨率获取关于整个动物转录网络（所有因子和靶标）的定量三维（3D）信息。还应该能够将这些数据整合到一个单一的可进行计算分析的数据库——图谱中，该图谱可作为揭示调控基因网络新生物学的基础。本文描述了在实现这些目标方面所取得的进展，重点是黑腹果蝇。它描述了一套高通量方法，这些方法已被用于在全动物中以细胞分辨率创建基因表达和形态的首个定量3D描述，并展示了该定量图谱所揭示的一些新生物学现象。
