The Pattern and Evolution of Looped Gene Bendability
The Pattern and Evolution of Looped Gene Bendability
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环状基因弯曲性的模式和演化
DOI：
10.1093/molbev/mst188
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发表时间：
2014-02-01
影响因子：
10.7
通讯作者：
Dai, Xianhua
中科院分区：
文献类型：
--
作者：
Dai, Zhiming;Xiong, Yuanyan;Dai, Xianhua
基因环，定义为RNA聚合酶II转录基因的启动子和终止子区域之间的物理相互作用，广泛存在于酵母和哺乳动物细胞中。基因成环在转录过程中起着重要的作用。基因环的形成依赖于位于基因50和30端的调节蛋白，如TFIIB。然而，其他因素是否有助于基因循环仍有待阐明。在这里，我们研究了内在的DNA和染色质结构的基因循环的贡献。我们发现酿酒酵母环状基因在开放阅读框（ORF）的中部和3/4区域具有较高的DNA弯曲性。这种可弯曲性模式在酵母物种之间是保守的，而可弯曲性峰的位置在物种之间变化很大。人类细胞中的环状基因也显示出高DNA弯曲性。环状ORF中间区域周围的核小体定位是不稳定的。我们还提出的证据表明，这种不稳定的核小体定位参与基因循环。这些结果表明，DNA的可弯曲性和不稳定的核小体定位可能有助于形成基因环的机制。
Gene looping, defined as the physical interaction between the promoter and terminator regions of a RNA polymerase II-transcribed gene, is widespread in yeast and mammalian cells. Gene looping has been shown to play important roles in transcription. Gene-loop formation is dependent on regulatory proteins localized at the 50 and 30 ends of genes, such as TFIIB. However, whether other factors contribute to gene looping remains to be elucidated. Here, we investigated the contribution of intrinsic DNA and chromatin structures to gene looping. We found that Saccharomyces cerevisiae looped genes show high DNA bendability aroundmiddle and 3/4 regions in open reading frames (ORFs). This bendability pattern is conserved between yeast species, whereas the position of bendability peak varies substantially among species. Looped genes in human cells also show high DNA bendability. Nucleosome positioning around looped ORF middle regions is unstable. We also present evidence indicating that this unstable nucleosome positioning is involved in gene looping. These results suggest a mechanism by which DNA bendability and unstable nucleosome positioning could assist in the formation of gene loops.