Genomic and Functional Analyses of Regulatory Regions in Vertebrate Sequences

双向启动子在基因组中大量存在。它们被定义为一个共享的调控区，福尔斯位于两个方向相反的基因之间的基因间空间，两个基因之间的距离不超过1,000 bp。这些基因以头对头的方式排列，并相互转录。每对基因的转录起始位点（TSS）的紧密排列被认为是基因组中的非随机事件，这一事实证明了大于预期数量的启动子具有这种结构。产生双向基因对的一种可能的情况是染色体重组，使两个TSS的末端非常接近。这种结合可能是不可逆的，因为基因间启动子区域的断裂会中断两个基因的正常调节，深刻影响正常的基因组功能，如DNA修复。我们已经绘制了许多脊椎动物基因组中的双向启动子。在这样做的过程中，我们正在创建脊椎动物谱系中共享的双向启动子序列的第一个高置信度调控图谱，并确定包括灵长类动物在内的单一脊椎动物谱系所特有的转录本。 除了表征启动子区域之外，我们还对鉴定新类型的元件如基因表达的负调节子感兴趣（NRE; Petrykowska等人，Genome Research 2008）。与大量关于正作用元件如增强子和启动子的文献相反，顺式作用NRE尚未被广泛研究。尽管它们在文献中很少见，但这些元素在基因组中可能很丰富。NRE的实例包括沉默子和增强子阻断（EB）元件，沉默子在其调控下降低基因的表达，增强子阻断（EB）元件在置于两者之间时阻止增强子对启动子的作用，但在其他情况下不阻止。通过开发一种实验测试NRE的策略，我们已经在人类基因组中发现了这些功能的新例子。 外显子剪接增强子（ESEs）是影响基因表达的第三类调控元件。我们比较了所有以前的ESE预测方法，以表明有些方法比其他方法更精确。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性，以评估它们是否会影响mRNA剪接（http：//research.nhgri.nih.gov/skippy）。 所有这些研究项目都研究顺式作用元件，并集中在识别转录因子结合位点或剪接调节子上，这些位点或剪接调节子与反式作用蛋白结合，代表基因调控的基本组成部分。上述每个项目都公布了监管主题。在我们的工作过程中，新的基序被牵连作为沉默剂和新的生物学见解被揭示为替代启动子的调节。已经建立了一个合作的努力，以确定涉及这些图案的调控网络，特别是在涉及癌症的生物学途径。此外，我们正在构建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中的基因表达。

Bidirectional promoters are abundant in the genome. They are defined as a shared regulatory region that falls in the intergenic space between two oppositely oriented genes that 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) each 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 union is likely to be irreversible because breakage of the intergenic promoter region would interrupt the normal regulation of two genes, profoundly affecting normal genomic function, such as DNA repair. We have mapped bidirectional promoters in numerous vertebrate genomes. In doing so, we are creating the first high-confidence regulatory map of bidirectional promoter sequences shared in vertebrate lineages as well as identifying transcripts that are unique to single vertebrate lineages, including primates. In addition to characterizing promoter regions, we are interested in identifying novel types of elements such as negative regulators of gene expression (NREs; Petrykowska et al, Genome Research 2008). 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 scarceness 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 test NREs, we have identified novel examples of these functions in the human genome. Exonic splicing enhancers (ESEs) are a third category of regulatory elements affecting gene expression. We have compared all former predictive methods for ESEs to show that some are more precise than others. We have produced an online toolkit to test polymorphisms that occur in coding sequences to assess whether they may affect mRNA splicing (http://research.nhgri.nih.gov/skippy). 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 and represent 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 tumors versus normal cells.