Genomic and Functional Analyses of Regulatory Regions in Vertebrate Sequences

脊椎动物序列调节区域的基因组和功能分析

• 批准号: 7968905
• 负责人: Laura L Elnitski
• 金额: $ 110.13万
• 依托单位: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7968905
• 关键词: Address; Affect; Architecture; Binding; Binding Sites; Biological; Categories; Characteristics; Code; Disease; Elements; Enhancers; Environment; Epigenetic Process; Event; Gene Expression; Gene Expression Regulation; Genes; Genetic Polymorphism; Genetic Recombination; Genome; Genomics; Goals; Grouping; Head; Human Genome; Indium; Literature; Malignant Neoplasms; Malignant neoplasm of ovary; Maps; Messenger RNA; Methods; Modeling; Modification; Normal Cell; Nucleic Acid Regulatory Sequences; Pathway interactions; Promoter Regions; Proteins; Publishing; RNA Splicing; Regulation; Regulator Genes; Regulatory Element; Research; Research Project Grants; Site; Testing; Transcription Initiation Site; Work; cell type; cis acting element; falls; functional genomics; insight; interest; novel; prevent; promoter; tool; transcription factor; tumor; vertebrate genome

A bidirectional promoter is defined as the shared regulatory region that falls in the intergenic space between two oppositely oriented genes, which are separated by no more than 1,000 bp. These genes are organized in a head-to-head arrangement and transcribed away from one another. The closely spaced arrangement of the transcription start sites (TSSs) for such a pair of genes is recognized as a nonrandom event in the genome, proven by the fact that a greater than expected number of promoters have this architecture. One plausible scenario for the creation of bidirectional gene pairs is chromosomal recombination bringing the ends of two TSSs in close proximity. This formation is likely to be irreversible because breakage of the union (within or near the bidirectional promoter) would interrupt the normal regulation of two genes profoundly affecting normal genomic function. We have mapped bidirectional promoters in numerous vertebrate genomes. In doing so, we are creating the first high-confidence regulatory map of promoter sequences in vertebrate lineages. In addition to characterizing promoter regions, we are interested in identifying novel types of elements such as negative regulators of gene expression (NREs). In contrast to the large body of literature on positively acting elements such as enhancers and promoters, cis-acting NREs have not been extensively studied. Despite their scarcity in the literature, these elements are likely to be abundant in the genome. Examples of NREs include silencers, which decrease expression of a gene under their regulation and enhancer-blocking (EB) elements, which prevent the action of an enhancer on a promoter when placed between the two, but not otherwise. By developing a strategy to experimentally identify NREs, we have identified novel elements with these functions in the human genome. Exonic splicing enhancers (ESEs) are a third category of regulatory elements affecting gene expression. We have compared all predictive methods for ESEs to show that some predict sites more successfully than others. WE have produced an online toolkit to test polymorphisms that occur in coding sequences to assess whether they may affect mRNA splicing. All of these research projects examine cis-acting elements and converge on the identification of transcription factor binding sites or splicing regulators, which are bound by trans-acting proteins, together representing the basic components of gene regulation. Regulatory motifs have been published for each of the projects above. During the course of our work, novel motifs were implicated as silencers and new biological insights were revealed for the regulation of alternative promoters. A collaborative effort has been established to define the regulatory networks involving these motifs, especially in biological pathways implicated in cancer. Moreover, we are building tools to assess epigenetic events that aberrantly affect gene expression in these same pathways in tumors versus normal cells.

双向启动子被定义为位于两个相反定向基因之间的共同调控区，这两个基因之间的距离不超过1,000个核苷酸。这些基因是以头对头的方式组织起来的，并相互转录。这对基因转录起始点(TSS)的紧密排列被认为是基因组中的一个非随机事件，事实证明，比预期数量更多的启动子具有这种结构。创造双向基因对的一个看似合理的方案是染色体重组，使两个SSs的末端非常接近。这种形成很可能是不可逆转的，因为联合的破坏(在双向启动子内部或附近)将中断两个基因的正常调节，从而深刻地影响正常的基因组功能。我们已经在许多脊椎动物基因组中定位了双向启动子。在这样做的过程中，我们正在创建第一个脊椎动物谱系中启动子序列的高置信度调控图。 除了确定启动子区域的特征外，我们还对识别新类型的元件感兴趣，例如基因表达的负调节因子(NRES)。与大量关于促进剂和启动子等积极作用元件的文献相反，顺式作用的NRES还没有得到广泛的研究。尽管它们在文献中很稀少，但这些元素在基因组中很可能是丰富的。NRES的例子包括消音器和增强子阻断(EB)元件，前者在其调控下降低基因的表达，后者当被放置在两者之间时阻止增强子对启动子的作用，但不是在其他情况下。通过开发一种实验性地识别NRES的策略，我们已经在人类基因组中识别出具有这些功能的新元件。 外显子剪接增强子(ESES)是影响基因表达的第三类调控元件。我们比较了ESES的所有预测方法，以表明一些方法预测站点比其他方法更成功。我们已经制作了一个在线工具包来测试编码序列中出现的多态，以评估它们是否可能影响mRNA剪接。 所有这些研究项目都在研究顺式作用元件，并集中在鉴定转录因子结合部位或剪接调节因子，它们由反式作用蛋白结合，共同代表基因调控的基本组成部分。已经为上述每个项目发布了监管主题。在我们的工作过程中，新的基序被认为是消音器，并为调节替代启动子提供了新的生物学见解。已经建立了一个合作努力来定义涉及这些基序的调控网络，特别是在与癌症有关的生物途径中。此外，我们正在建立工具来评估表观遗传事件，这些事件异常地影响肿瘤与正常细胞在这些相同途径中的基因表达。