ChromDB: Integrating Information About Plant Chromatin Proteins and Complexes

真核细胞以各种高度有序的结构包装核DNA，统称为“染色质”。染色质的主要功能是维持一种限制性的基态，在这种状态下，DNA不能被转录机制访问，但可以被特定的转录激活物和抑制物访问，这些转录激活物和抑制物招募能够局部重塑染色质的多蛋白复合体，从而允许转录发生。ChromDB(植物染色质数据库)最初是一个特定于项目的数据库，用于显示先前植物基因组研究计划拨款的结果，该计划研究了拟南芥和玉米染色质蛋白质的功能基因组学。利用已知的酵母、苍蝇、人和线虫染色质基因的蛋白质结构域查询拟南芥基因组序列和玉米EST集合，以组装一组可能的植物染色质蛋白。来自大米和单细胞藻类衣藻的染色质蛋白被添加到数据库中，以提供对数据库更多的系统发育观点。该奖项支持ChromDB从面向项目的数据库到支持整个植物生物学社区的社区数据库的广泛扩展。染色质蛋白质的补充将增加到包括所有可获得基因组或cdna序列的植物物种，以便提供预测的蛋白质结构域、转录本剪接产物、分子系统发育关系和选择的分子特征的全面、比较的总结。ChromDB将整合和展示有关基因功能的所有可用社区数据，如突变表型、生化活动和性质、转录本和蛋白质表达模式、基因和蛋白质之间的物理和遗传相互作用，以及染色质蛋白质在细胞核内的定位。ChromDB将为研究人员提供一个公共注释论坛，以提交和呈现这些信息，并由编辑顾问委员会审查提交的内容。一项教育推广计划将为高中教师提供生物信息学和功能基因组学领域的经验。这项推广活动有三个目标：(1)与教师合作，制作一套基于网络的综合教学模块，通过以脱氧核糖核酸、基因和染色体为中心的讨论，向学生介绍染色质的生物学重要性，并向学生介绍科学方法和实验分析；(2)向教师提供生物信息学某些方面的工作经验；以及(3)为在供应和设备有限的情况下在课堂上进行实验制定方案。所有项目产生的结果和材料将在数据库网站http://www.chromdb.org/.上查阅

Eukaryotic cells package nuclear DNA in a variety of highly ordered structures, collectively termed "chromatin". The primary function of chromatin is to maintain a restrictive ground state wherein the DNA is inaccessible to the transcriptional machinery but is accessible to specific transcriptional activators and repressors that recruit multi-protein complexes capable of remodeling chromatin locally to allow transcription to occur. ChromDB (Plant Chromatin Database) was established originally as a project-specific database to display the results of a previous Plant Genome Research Program grant that examined the functional genomics of chromatin proteins in Arabidopsis and maize. The Arabidopsis genomic sequence and, once available, the maize EST collection were queried using protein domains from known yeast, fly, human, and nematode chromatin genes to assemble a collection of putative plant chromatin proteins. Chromatin proteins from rice and the single-celled alga Chlamydomonas reinhardtii were added to the database to provide more phylogenetic perspective to the database. This award supports the broad expansion of ChromDB from a project-oriented database to a community database supporting the entire plant biology community. The complement of chromatin proteins will be increased to include all plant species for which either genomic or cDNA sequences are available in order to provide a comprehensive, comparative summary of predicted protein domains, transcript splicing products, molecular phylogenetic relationships and molecular signatures of selection. ChromDB will integrate and display all available community data regarding gene function such as mutant phenotypes, biochemical activities and properties, transcript and protein expression patterns, physical and genetic interactions between genes and proteins, and localization of chromatin proteins within the nucleus. ChromDB will provide a public annotation forum for researchers to submit and present this information with the submissions reviewed by an editorial advisory board. An educational outreach program will provide experience for high school teachers in the area of bioinformatics and functional genomics. There are three objectives associated with this outreach: (1) to produce, in partnership with teachers, a set of web-based, integrated teaching modules to introduce students to the biological importance of chromatin by way of discussions centered on DNA, genes, and chromosomes, as well introduce students to the scientific method and experimental analysis; (2) to provide teachers with working experience in select aspects of bioinformatics; and (3) to develop a protocol for experiments to be conducted in classroom locations under circumstances of limited supplies and equipment.All project-generated results and materials will be available at the database site, http://www.chromdb.org/.