Large-scale DNA sequencing for comparative systems biology

我们对线虫进行了粗略的cDNA分析。用V封顶法获得了约150,000个全长cDNA克隆的EST，共产生了4,909个新物种。通过整体原位杂交，共分析了11,309个物种的表达模式。利用新一代DNA测序仪对文库的mRNAs进行分析，以获得完整的转录组信息。这些数据被整合到NEXTDB中，该数据库与线虫中央数据库WormBase相连。在基因表达调控网络的研究方面，我们确定了1)早期肠道谱系中的阶段特异性顺式调控序列及其反式因子，以及2)温度感觉神经元AFD及其调控基因中表达的调控序列。在信使核糖核酸定位机制的研究中，我们确定了1)在其3‘-非编码区中的顺式元件用于pos-1及其反式因子的信使定位，2)顺式元件用于Mex-3信使核糖核酸的定位。我们开发了一个半自动系统，用于创建线虫胚胎发生中的细胞形状模型。我们利用Sanger方法和新一代测序仪的杂交方法对一种线虫的全基因组进行了测序。

We performed cDNA analysis of the nematode C.elegans thouroughly. ESTs of about 150,000 full-length cDNA clones that had been made by the V-capping method were obtained to produce 4,909 new cDNA species. Altogether 11,309 cDNA species have been analysed for their expression patterns by the whole mount in situ hybridization. The mRNAs for the cDNA libraries were analysed by the next generation DNA sequencer to obtain the whole transriptome information. These data were integrated in NEXTDB, which were linked with the C.elegans central database WormBase. As to the studies for gene expression regulation network, we identified 1) the stage-specific cis-regulatory sequences and their trans-factors in the early intestine lineage, and 2) the regulatory sequence for the expression in the thermo-sensory neuron AFD and its ragulatory genes. As to the studies for mRNA localization mechanisms, we identified 1) cis-element in its 3`-UTR for pos-1 mRNA localization and its trans-factor, and 2) cis-element for mex-3 mRNA localization. We developed a semi-automatic system for the creation of cell shape models in C. elegans embryogenesis. We carried out whole genome sequencing of a nematode D. cronatus by the hybrid method using the Sanger method and the new generation sequencer.