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.

我们对线虫秀丽隐杆线虫进行了彻底的 cDNA 分析。通过V-capping方法获得了约150,000个全长cDNA克隆的EST，产生了4,909个新的cDNA物种。通过整体原位杂交，总共分析了 11,309 个 cDNA 物种的表达模式。通过下一代DNA测序仪对cDNA文库的mRNA进行分析，以获得完整的转录组信息。这些数据被集成到 NEXTDB 中，并与 C.elegans 中央数据库 WormBase 链接。在基因表达调控网络的研究中，我们确定了1）早期肠谱系中特定阶段的顺式调控序列及其反式因子，2）热感觉神经元AFD和它的调节基因。对于mRNA定位机制的研究，我们确定了1）其3'-UTR中用于pos-1 mRNA定位的顺式元件及其反式因子，以及2）用于mex-3 mRNA定位的顺式元件。我们开发了一种半自动系统，用于创建线虫胚胎发生中的细胞形状模型。我们利用桑格法和新一代测序仪，采用混合法对一种线虫D. cronatus进行了全基因组测序。

项目成果

The landscape of C. elegans 3'UTRs.

• DOI: 10.1126/science.1191244
• 发表时间: 2010-07-23
• 期刊: Science (New York, N.Y.)
• 作者: Mangone M;Manoharan AP;Thierry-Mieg D;Thierry-Mieg J;Han T;Mackowiak SD;Mis E;Zegar C;Gutwein MR;Khivansara V;Attie O;Chen K;Salehi-Ashtiani K;Vidal M;Harkins TT;Bouffard P;Suzuki Y;Sugano S;Kohara Y;Rajewsky N;Piano F;Gunsalus KC;Kim JK
• 通讯作者: Kim JK

WHOLE TRANSCRIPTOME ANALYSIS OF THE NEMATODEC. ELEGANS

线虫的全转录组分析。

• 发表时间: 2008
• 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;Hara K.;Hideaki Hiraki;Tadasu Shin-i
• 通讯作者: Tadasu Shin-i

Latrophilin signalling links anterior-posterior tissue polarity and oriented cell divisions in the C.elegans embryo

Latrophilin 信号传导连接线虫胚胎中的前后组织极性和定向细胞分裂

• 发表时间: 2009
• 期刊: Developmental Cell 17(4)
• 作者: Kawano T;Zheng H;Merz DC;Kohara Y;Tamai KK;Nishiwaki K;Culotti JG.;J.D. McGhee; T. Fukushige; M.W. Krause; S.E. Minnema; B. Goszczynski; J. Gaudet; Y. Kohara; O. Bossinger; Y. Zhao; J. Khattra; M. Hirst; S.J. Jones; M.A. Marra; P. Ruzanov; A. Warner; R. Zapf; D.G. Moerman; J.M. Kalb;Tobias Langenhan
• 通讯作者: Tobias Langenhan

Studies on localization mechanisms of the maternal pos-1 mRNA in Caenorhabditis elegans embryos.

秀丽隐杆线虫胚胎中母体 pos-1 mRNA 定位机制的研究。

• 发表时间: 2007
• 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;Hara K.;Hideaki Hiraki;Tadasu Shin-i;森明弘;住吉英輔;鹿児島浩;野口 浩毅
• 通讯作者: 野口 浩毅

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