Virtual Center for Analysis of Rice Genome Transcription

随着国际上对水稻基因组测序工作的完成，确定水稻基因组中编码的每个转录单位(或基因)变得至关重要。计算机辅助的基因组注释表明，水稻基因组中可能有大约6万个基因。然而，据估计，所有可用的实验数据的组合只为大约一半的预测基因提供了表达验证。此外，由于水稻基因编码区GC含量较高，现有的基因预测程序可能会遗漏很大一部分活性基因。因此，迫切需要对所有预测基因进行实验验证，并发现当前预测程序遗漏的水稻基因。本项目将试图发现刚刚完成测序的水稻的所有可能的转录单位。将使用无掩模阵列合成器(MAS)技术生产的高密度基因组平铺寡核苷酸阵列，这允许在随后的每个阵列载玻片生产中重复寡核苷酸设计。工作流程将首先对水稻10号染色体进行优化，然后应用于所有剩余的染色体。从正常生长的大米和经过各种诱导处理的代表性RNA样本中提取的混合探针将被包括在内，以最大限度地发现转录单位。这些数据将被整合到当前和正在进行的基因组注释中，以测试预测的基因模型并定义新转录单位的结构。一旦结果受到质量控制，原始数据将被存入符合MIAME标准的GEO数据库。所有原始数据，包括原始杂交数据以及基因模型，一旦经过质量控制和核实，将通过一个项目网站(www.ants genomics.yale.edu)向公众提供。该网站将在第一个供资年度结束时(2005年8月30日)上线，最后一组数据将在2007年8月30日前提供。所有从这项工作中创建的新的或改进的水稻基因模型都将发布在我们的项目网站上，也将每隔两个月转发给基因组研究所由NSF支持的水稻基因组注释小组，以便将它们纳入他们的公共水稻基因注释网站。整个数据集将在该项目结束前(2007年8月)向TIGR和公众开放。广泛影响：所有粳稻转录单位的实验鉴定将为未来的水稻功能基因组学和蛋白质组学研究提供必要的基础，并为其他谷物提供有用的比较数据。在我们拟议的研究过程中，一些博士后研究人员和学生(包括研究生和本科生)将接受植物基因组学和信息学方面的培训。该项目将与耶鲁大学皮博迪博物馆合作，向普通公众和学童传授水稻种植在世界各地文化中的作用，以及水稻基因组进步对社会的潜在好处。

As the international effort to sequence the rice genome is completed, it becomes essential to define each and every transcriptional unit (or gene) encoded in the rice genome. Computer assisted genome annotation suggests that there may be about 60,000 genes in the rice genome. However, it is estimated that the combination of all experimental data available provides expression validation for only approximately half of the predicted genes. Further, due to the high GC content in rice gene coding regions, existing gene prediction program will likely miss a significant fraction of the active genes. Thus there is an urgent need for experimental verification of all predicted genes and discovery of rice genes that were missed by current prediction programs.This project will attempt to discover all possible transcription units of the just completely sequenced Japonica rice. A high-density genome tiling oligonucleotide array produced with the Maskless Array Synthesizer (MAS) technology will be used, which permits reiteration of the oligo design for each subsequent array slide production. The workflow will be optimized first with rice chromosome 10 and then applied to all remaining chromosomes. Pooled probes derived from representative RNA samples from both normal grown rice and those subjected to various inductive treatments will be included to maximize transcription unit discovery. The data will be integrated into the current and ongoing genome annotation to test predicted gene models and to define structures of the novel transcription units. The raw data will be deposited in the MIAME compliant GEO database as soon as the results are subject to quality control. All the original data, including raw hybridization data as well as gene models, will be made available to the public through a project web site (www.plantgenomics.yale.edu) once they are quality controlled and verified. This web site will be online at the end of this first funding year (August 30, 2005) and the last data set will be made available by August 30, 2007. All the new or improved rice gene models created from this work be posted on our project web site and will also be forwarded to the NSF-supported rice genome annotation group at The Institute for Genome Research at bimonthly intervals for their incorporation into their public rice gene annotation web site. The full data set will be made available to TIGR and the public by the end of this project (August, 2007).Broader Impacts:The experimental identification of all Japonica rice transcription units will provide an essential foundation for rice functional genomics and proteomics research in the future and provide useful comparative data for other cereals. In the process of our proposed studies, a number of postdoctoral researchers and students (both graduate and undergraduate) will obtain training in plant genomics and informatics. The project will work with the Peabody Museum at Yale University to teach the general public and school children about the role of rice cultivation in cultures around the world, and on the potential benefits of rice genomic advances for society.