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首页> 外文期刊>BMC Genomics >Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster
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Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

机译：通过对果蝇的单个和其他启动子进行全基因组分析，揭示了基因组的复杂组织结构。

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Background The promoter is a critical necessary transcriptional cis-regulatory element. In addition to its role as an assembly site for the basal transcriptional apparatus, the promoter plays a key part in mediating temporal and spatial aspects of gene expression through differential binding of transcription factors and selective interaction with distal enhancers. Although many genes have multiple promoters, little attention has been focused on how these relate to one another; nor has much study been directed at relationships between promoters of adjacent genes. Results We have undertaken a systematic investigation of Drosophila promoters. We divided promoters into three groups: unique promoters, first alternative promoters (the most 5' of a gene's multiple promoters), and downstream alternative promoters (the remaining alternative promoters 3' to the first). We observed distinct nucleotide distribution and sequence motif preferences among these three classes. We also investigated the promoters of neighboring genes and found that a greater than expected number of adjacent genes have similar sequence motif profiles, which may allow the genes to be regulated in a coordinated fashion. Consistent with this, there is a positive correlation between similar promoter motifs and related gene expression profiles for these genes. Conclusions Our results suggest that different regulatory mechanisms may apply to each of the three promoter classes, and provide a mechanism for "gene expression neighborhoods," local clusters of co-expressed genes. As a whole, our data reveal an unexpected complexity of genomic organization at the promoter level with respect to both alternative and neighboring promoters.
机译：背景启动子是关键的必需转录顺式调控元件。除了充当基础转录装置的装配位点外，启动子还通过转录因子的差异结合和与远端增强子的选择性相互作用，在介导基因表达的时空方面发挥关键作用。尽管许多基因具有多个启动子，但很少关注这些启动子之间的关系。相邻基因启动子之间的关系也没有很多研究。结果我们对果蝇启动子进行了系统的研究。我们将启动子分为三类：独特的启动子，第一个替代启动子（一个基因的多个启动子中最靠前的5'）和下游替代启动子（剩下的第一个替代启动子3'）。我们观察到这三类中独特的核苷酸分布和序列基序偏好。我们还研究了邻近基因的启动子，发现数目比预期多的邻近基因具有相似的序列基序谱，这可能允许以协调的方式调节基因。与此相一致，这些基因的相似启动子基序和相关基因表达谱之间存在正相关。结论我们的结果表明，不同的调控机制可能适用于三种启动子类别，并为“基因表达邻域”，共表达基因的局部簇提供了机制。总体而言，我们的数据揭示了相对于替代启动子和邻近启动子而言，在启动子水平上基因组组织的意外复杂性。

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