Whole genome experimental maps of DNA G-quadruplexes in multiple species
Whole genome experimental maps of DNA G-quadruplexes in multiple species
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DOI：
10.1093/nar/gkz179
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发表时间：
2019-05-07
影响因子：
14.9
通讯作者：
Balasubramanian, Shankar
中科院分区：
文献类型：
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作者：
Marsico, Giovanni;Chambers, Vicki S.;Balasubramanian, Shankar
DNA G-四联体(G4S)的基因组图谱可以帮助阐明这些二级结构在各种生物中所起的作用。在这里，我们使用一种改进的G-四链测序方法(G4-SEQ)来生成12个物种的全基因组G4图谱，这些物种包括广泛研究的模式生物和临床相关的病原体。我们确定了在生理K+条件下形成的G4结构，以及由G4靶向小分子吡哆醇他汀(PDS)稳定的G4S。我们讨论了实验观察到的G-四联体(OQS)的各种结构特征，强调了它们在不同物种中的流行率和丰富度的差异。我们的研究描述了OQS在不同物种中的序列组成和基因组位置的多样性，并揭示了在所研究的物种中，OQS在基因启动子中的丰富是哺乳动物所特有的，如小鼠和人类。多物种地图已作为资源公开提供给研究界。这些地图可以作为在这些模式生物中进行生物实验的蓝图，G4结构可能会在其中发挥作用。
Genomic maps of DNA G-quadruplexes (G4s) can help elucidate the roles that these secondary structures play in various organisms. Herein, we employ an improved version of a G-quadruplex sequencing method (G4-seq) to generate whole genome G4 maps for 12 species that include widely studied model organisms and also pathogens of clinical relevance. We identify G4 structures that form under physiological K+ conditions and also G4s that are stabilized by the G4-targeting small molecule pyridostatin (PDS). We discuss the various structural features of the experimentally observed G-quadruplexes (OQs), highlighting differences in their prevalence and enrichment across species. Our study describes diversity in sequence composition and genomic location for the OQs in the different species and reveals that the enrichment of OQs in gene promoters is particular to mammals such as mouse and human, among the species studied. The multi-species maps have been made publicly available as a resource to the research community. The maps can serve as blueprints for biological experiments in those model organisms, where G4 structures may play a role.