Genomic and Functional Analyses of Conserved Noncoding R

基因组功能分析科的主要目标是通过比较分析确定脊椎动物基因组中顺式和反式作用的功能元件。该方法利用多物种全基因组序列比对来识别保守的非编码区，检查这些元件中序列突变的模式，并测试与通过物种形成事件获得的序列的变化相对应的表达水平的变化。正在考虑的功能元件包括任何组成转录因子结合位点集合的元件，如增强子、沉默因子、启动子和microRNA调节区，异常保守的元件，如超保守元件，或包含未表征的结构特征的元件，如复制起点。 除了功能元素的实验验证外，我们还进行计算分析来表征基因组中的功能元素。例如，启动子的进化分析正被用于研究人/黑猩猩/狗/鼠/鸡的多物种序列比对中TATA基序和CpG岛的选择。通过利用我们对转录起始点有信心的数据集，我们能够更好地记录TATA盒的出现并评估它们的进化历史。相关的计算方法正被用于研究调节microRNA表达的机制。利用EST数据库，我们在人类基因组中确定了以前没有表征的双向启动子，并显示出与乳腺癌和卵巢癌相关基因的统计学意义上的相关性。我们现在正在测试肿瘤样本，以检查肿瘤中与这些启动子相关的表观遗传学变化。一个项目正在探索将功能数据存档的方法，该项目旨在开发一个存储来自ENCODE联盟的微阵列数据的计算数据库。这些重要数据包含通过芯片分析确定的转录因子结合位点的信息。这些数据被用作前述基因组调节区预测的阳性对照，并用于识别作为未来实验分析目标的区域。

The major aims of the Genomic Functional Analysis Section are to identify cis-and trans-acting functional elements in vertebrate genomes using comparative analyses. The approach utilizes multi-species, whole-genome sequence alignments to identify conserved noncoding regions, examine patterns of sequence mutation within those elements, and test for changes in expression levels that correspond to changes in the sequences acquired through speciation events. Functional elements under consideration include any elements that comprise collections of transcription factor binding sites such as enhancers, silencers, promoters, and microRNA regulatory regions, elements that are exceptionally conserved, such as ultra-conserved elements, or those that contain uncharacterized structural features such as origins of replication. In addition to experimental verification of functional elements, we perform computational analyses to characterize functional elements in the genome. For instance, evolutionary analyses of promoters are being used to study selection on TATA motifs and CpG islands in multispecies sequence alignments of human/chimp/dog/mouse/chicken. By utilizing datasets in which we have confidence in the transcription start site, we are better able to document the occurrence of TATA boxes and assess evolutionary histories of them. Related computational approaches are being used to study mechanisms of regulated microRNA expression. Utilizing the database of ESTs, we identified bidirectional promoters in the human genome that were not previously characterized and showed a statistically significant association with genes implicated in breast and ovarian cancers. We are now testing tumor samples to check for epigenetic changes associated with these promoters in tumors. Methods to archive functional data are being explored in a project to develop a computational database housing microarray data from the ENCODE consortium. These important data contain information on transcription factor binding sites identified through ChIP-chip assays. The data are used as positive controls for the aforementioned predictions of genomic regulatory regions and for the identification of regions that are targets for future experimental analyses.