State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China.
Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
Int J Mol Sci. 2022 Jul 29;23(15):8404. doi: 10.3390/ijms23158404.
DNA G-quadruplexes (G4s) are non-canonical four-stranded DNA structures involved in various biological processes in eukaryotes. Molecularly crowded solutions and monovalent cations have been reported to stabilize in vitro and in vivo G4 formation. However, how K and Na affect G4 formation genome-wide is still unclear in plants. Here, we conducted BG4-DNA-IP-seq, DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing, under K and Na + PEG conditions in vitro. We found that K-specific IP-G4s had a longer peak size, more GC and PQS content, and distinct AT and GC skews compared to Na-specific IP-G4s. Moreover, K- and Na-specific IP-G4s exhibited differential subgenomic enrichment and distinct putative functional motifs for the binding of certain trans-factors. More importantly, we found that K-specific IP-G4s were more associated with active marks, such as active histone marks, and low DNA methylation levels, as compared to Na-specific IP-G4s; thus, K-specific IP-G4s in combination with active chromatin features facilitate the expression of overlapping genes. In addition, K- and Na-specific IP-G4 overlapping genes exhibited differential GO (gene ontology) terms, suggesting they may have distinct biological relevance in rice. Thus, our study, for the first time, explores the effects of K and Na on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.
DNA 四链体（G4s）是涉及真核生物中各种生物学过程的非经典四链 DNA 结构。已报道分子拥挤溶液和单价阳离子可稳定体外和体内 G4 形成。然而，K 和 Na 如何影响植物基因组范围内的 G4 形成仍不清楚。在这里，我们在体外进行了 K 和 Na + PEG 条件下的 BG4-DNA-IP-seq（用抗 BG4 抗体进行 DNA 免疫沉淀结合测序）。我们发现，与 Na 特异性 IP-G4s 相比，K 特异性 IP-G4s 具有更长的峰大小、更多的 GC 和 PQS 含量以及独特的 AT 和 GC 倾斜。此外，K 和 Na 特异性 IP-G4s 表现出不同的亚基因组富集和不同的假定功能基序，用于某些转录因子的结合。更重要的是，我们发现与 Na 特异性 IP-G4s 相比，K 特异性 IP-G4s 与活性标记（如活性组蛋白标记）和低 DNA 甲基化水平的关联更密切；因此，K 特异性 IP-G4s 与活跃染色质特征相结合，促进重叠基因的表达。此外，K 和 Na 特异性 IP-G4 重叠基因表现出不同的 GO（基因本体论）术语，表明它们在水稻中可能具有不同的生物学相关性。因此，我们的研究首次探索了 K 和 Na 对体外全局 G4 形成的影响，从而为水稻中功能 G4 研究提供了有价值的资源。它将为未来水稻的生物技术工程提供某些 G4 基因座。
