Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand.
School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
Biochimie. 2020 Oct;177:190-197. doi: 10.1016/j.biochi.2020.07.022. Epub 2020 Aug 14.
Next generation DNA sequencing and analysis of amplicons spanning the pharmacogene CYP2D6 suggested that the Nextera transposase used for fragmenting and providing sequencing priming sites displayed a targeting bias. This manifested as dramatically lower sequencing coverage at sites in the amplicon that appeared likely to form G-quadruplex structures. Since secondary DNA structures such as G-quadruplexes are abundant in the human genome, and are known to interact with many other proteins, we further investigated these sites of low coverage. Our investigation revealed that G-quadruplex structures are formed in vitro within the CYP2D6 pharmacogene at these sites, and G-quadruplexes can interact with the hyperactive Tn5 transposase (EZ-Tn5) with high affinity. These findings indicate that secondary DNA structures such as G-quadruplexes may represent preferential transposon integration sites and provide additional evidence for the role of G-quadruplex structures in transposition or viral integration processes.
下一代 DNA 测序和对跨越药物代谢酶 CYP2D6 的扩增子的分析表明，用于片段化和提供测序引物结合位点的 Nextera 转座酶表现出靶向偏好。这表现为在扩增子中似乎形成 G-四链体结构的位点的测序覆盖率显著降低。由于 G-四链体等二级 DNA 结构在人类基因组中大量存在，并已知与许多其他蛋白质相互作用，因此我们进一步研究了这些低覆盖率的位点。我们的研究表明，在这些位点，CYP2D6 药物代谢酶中的 G-四链体结构在体外形成，并且 G-四链体可以与高活性 Tn5 转座酶（EZ-Tn5）高亲和力相互作用。这些发现表明，二级 DNA 结构如 G-四链体可能代表优先转座子整合位点，并为 G-四链体结构在转座或病毒整合过程中的作用提供了额外的证据。
