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基态，其中DNA无法进入转录机制，但特定的转录激活因子和抑制因子可以进入，这些转录激活因子和抑制因子招募能够局部重塑染色质的多蛋白复合物以允许转录发生。ChromDB（植物染色质数据库）最初是作为一个项目特定数据库建立的，用于显示先前植物基因组研究计划资助的结果，该计划研究了拟南芥和玉米染色质蛋白的功能基因组学。利用已知酵母、蝇、人和线虫染色质基因的蛋白质结构域对拟南芥基因组序列和玉米EST收集进行查询，以组装推定的植物染色质蛋白集合。将水稻和莱茵衣藻（Chlamydomonas reinhardtii）的染色质蛋白添加到数据库中，为数据库提供更多的系统发育视角。该奖项支持ChromDB从面向项目的数据库扩展到支持整个植物生物学社区的社区数据库。染色质蛋白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，以便对预测的蛋白质结构域、转录物剪接产物、分子系统发育关系和选择的分子特征提供全面、比较的总结。ChromDB将整合和显示所有关于基因功能的可用社区数据，如突变表型，生化活性和特性，转录和蛋白质表达模式，基因和蛋白质之间的物理和遗传相互作用，以及染色质蛋白在细胞核内的定位。ChromDB将提供一个公共注释论坛，供研究人员提交和展示这些信息，并由编辑顾问委员会审查。一项教育拓展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。与此相关的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DNA、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)为教师提供生物信息学选择方面的工作经验；(3)制定在物资和设备有限的情况下在教室进行实验的方案。所有项目产生的结果和材料将在数据库网站http://www.chromdb.org/上提供。

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/.