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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting
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Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting

机译：通过系统发育足迹识别酵母核糖体DNA中非基因非编码功能元件

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摘要

Sequences involved in the regulation of genetic and genomic processes are primarily located in noncoding regions. Identifying such cis-acting sequences from sequence data is difficult because their patterns are not readily apparent, and, to date, identification has concentrated on regions associated with gene-coding functions. Here, we used phylogenetic footprinting to look for gene-independent noncoding elements in the ribosomal RNA gene repeats from several Saccharomyces species. Similarity plots of ribosomal intergenic spacer alignments from six closely related Saccharomyces species allowed the identification of previously characterized functional elements, such as the origin-of-replication and replication-fork barrier sites, demonstrating that this method is a powerful predictor of noncoding functional elements. Seventeen previously uncharacterized elements, showing high levels of conservation, were also discovered. The conservation of these elements suggests that they are functional, and we demonstrate the functionality of two classes of these elements, a putative bidirectional noncoding promoter and a series of conserved peaks with matches to the origin-of-replication core consensus. Our results paint a comprehensive picture of the functionality of the Saccharomyces ribosomal intergenic region and demonstrate that functional elements not involved in gene-coding function can be identified by using comparative genomics based on sequence conservation.
机译：涉及遗传和基因组过程调控的序列主要位于非编码区。从序列数据中鉴定出这种顺式作用序列是困难的，因为它们的模式尚不明显，并且迄今为止，鉴定已集中在与基因编码功能有关的区域上。在这里，我们使用系统发育足迹，从几个酿酒酵母物种的核糖体RNA基因重复序列中寻找基因非依赖性非编码元件。来自六个密切相关的酿酒酵母物种的核糖体基因间间隔区比对的相似图可以鉴定先前表征的功能元件，例如复制起点和复制叉屏障位点，表明该方法是非编码功能元件的有力预测者。还发现了十七个以前未表征的元素，显示出高水平的保守性。这些元素的保守性表明它们是有功能的，并且我们展示了这两类元素的功能，一个推定的双向非编码启动子和一系列与复制起点核心一致性相匹配的保守峰。我们的结果描绘了酿酒酵母核糖体基因间区域的功能的全面情况，并证明可以通过使用基于序列保守性的比较基因组学来鉴定不参与基因编码功能的功能元件。

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