Neural Cell-Fate Determinants Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.
PLoS One. 2013 Apr 22;8(4):e60137. doi: 10.1371/journal.pone.0060137. Print 2013.
Analysis of cis-regulatory enhancers has revealed that they consist of clustered blocks of highly conserved sequences. Although most characterized enhancers reside near their target genes, a growing number of studies have shown that enhancers located over 50 kb from their minimal promoter(s) are required for appropriate gene expression and many of these 'long-range' enhancers are found in genomic regions that are devoid of identified exons. To gain insight into the complexity of Drosophila cis-regulatory sequences within exon-poor regions, we have undertaken an evolutionary analysis of 39 of these regions located throughout the genome. This survey revealed that within these genomic expanses, clusters of conserved sequence blocks (CSBs) are positioned once every 1.1 kb, on average, and that a typical cluster contains multiple (5 to 30 or more) CSBs that have been maintained for at least 190 My of evolutionary divergence. As an initial step toward assessing the cis-regulatory activity of conserved clusters within gene-free genomic expanses, we have tested the in-vivo enhancer activity of 19 consecutive CSB clusters located in the middle of a 115 kb gene-poor region on the 3(rd) chromosome. Our studies revealed that each cluster functions independently as a specific spatial/temporal enhancer. In total, the enhancers possess a diversity of regulatory functions, including dynamically activating expression in defined patterns within subsets of cells in discrete regions of the embryo, larvae and/or adult. We also observed that many of the enhancers are multifunctional-that is, they activate expression during multiple developmental stages. By extending these results to the rest of the Drosophila genome, which contains over 70,000 non-coding CSB clusters, we suggest that most function as enhancers.
顺式调控增强子的分析表明，它们由高度保守序列的聚类块组成。虽然大多数已鉴定的增强子位于其靶基因附近，但越来越多的研究表明，位于其最小启动子（多个）50kb 以上的增强子对于适当的基因表达是必需的，并且许多这些“长距离”增强子位于缺乏鉴定外显子的基因组区域中。为了深入了解果蝇外显子贫乏区域内顺式调控序列的复杂性，我们对遍布基因组的 39 个此类区域进行了进化分析。这项调查显示，在这些基因组扩展区域内，保守序列块（CSB）的聚类平均每 1.1kb 定位一次，并且一个典型的聚类包含多个（5 到 30 个或更多）CSB，这些 CSB 至少在 190 个进化分歧的 My 中得到了维持。作为评估基因缺失基因组扩展区中保守簇的顺式调控活性的初始步骤，我们测试了位于第 3 号染色体上 115kb 基因贫乏区中部的 19 个连续 CSB 簇的体内增强子活性。我们的研究表明，每个聚类都可以独立作为特定的空间/时间增强子发挥作用。总的来说，这些增强子具有多种调控功能，包括在胚胎、幼虫和/或成虫的离散区域内的细胞亚群中以特定模式动态激活表达。我们还观察到，许多增强子具有多功能性，即它们在多个发育阶段激活表达。通过将这些结果扩展到果蝇基因组的其余部分（包含超过 70,000 个非编码 CSB 聚类），我们认为大多数作为增强子发挥作用。
