Large-scale DNA sequencing for comparative systems biology

用于比较系统生物学的大规模 DNA 测序

• 批准号: 17020009
• 负责人: KOHARA Yuji
• 金额: $ 481.02万
• 依托单位: National Institute of Genetics
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research on Priority Areas
• 财政年份: 2005
• 资助国家: 日本
• 起止时间: 2005 至 2009
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-17020009/
• 关键词: 胚発生; 母性遺伝子; mRNA局在化; UTR(非翻訳領域); トランスクリプトーム; in situハイブリダイゼーション; 転写調節領域; 多光子共焦点顕微鏡; 線虫C.elegans; 遺伝子発現; mRNA局在; RNAi; モチーフ探索; EST解析; 全ゲノムショットガン; whole mount in situハイブリダイゼーション; 計算機モデル; whole genome shotgun sequencing

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.

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。

项目成果

nfi-1 affects behavior and life-span in C.elegans but is not essential for DNA replication or survival.

nfi-1 影响线虫的行为和寿命，但对于 DNA 复制或生存并不是必需的。

• 发表时间: 2005
• 期刊: BMC Developmental Biology 5
• 作者: H. Kagoshima;H. Sawa;S. Mitani;T.R. Burglin;K. Shigesada;Y. Kohara;Hiroshi KAGOSHIMA;Elena Lazakovitch
• 通讯作者: Elena Lazakovitch

Systematic analyses of AFD-specific enhancers in C.elegans

线虫 AFD 特异性增强子的系统分析

• 发表时间: 2009
• 作者: X. Wang;Y. Zhao;K. Wong;P. Ehlers;Y. Kohara;S.J. Jones;M.A. Mara;R.A. Holt;D.G. Moerman;D. Hansen;Hiroshi Kagoshima
• 通讯作者: Hiroshi Kagoshima

Semi-automatic system for the creation of cell shape models in C.elegans embryogenesis

用于创建线虫胚胎发生细胞形状模型的半自动系统

• 发表时间: 2009
• 作者: Takei N;Miyashita A;Tsukie T;Arai H;Asada T;Imagawa M;Shoji M;Higuchi S;Urakami K;Kimura H;Kakita A;Takahashi H;Tsuji S;Kanazawa I;Ihara Y;Odani S;Kuwano R;the Japanese Genetic Study Consortium for Alzheimer Disease;Akihiro Mori;Hideaki Hiraki
• 通讯作者: Hideaki Hiraki

Combination of cis-regulatory modules for temporal regulation of gene expression in C.elegans : Towards promoter design

用于线虫基因表达时间调控的顺式调控模块组合：走向启动子设计

• 发表时间: 2009
• 作者: Fukuda Y;Nakahara Y;Date H;Takahashi Y;Goto J;Miyashita A;Kuwano R;Adachi H;Nakamura E;Tsuji S.;Akihiro Mori
• 通讯作者: Akihiro Mori

Genome and transcriptome analysis by the next-generation sequencer

通过下一代测序仪进行基因组和转录组分析

• 发表时间: 2009
• 作者: Fukuda Y;Nakahara Y;Date H;Takahashi Y;Goto J;Miyashita A;Kuwano R;Adachi H;Nakamura E;Tsuji S.;Akihiro Mori;Hara K.;Hiroshi Kagoshima;Fukuda Y.;Tadasu Shin-i
• 通讯作者: Tadasu Shin-i