State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China.
Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France.
Plant Physiol. 2022 Mar 4;188(3):1632-1648. doi: 10.1093/plphys/kiab566.
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
DNA 四链体（G4）是一种非经典的四链核酸结构，参与哺乳动物的许多生物学过程。然而，目前关于植物 DNA G4 的知识有限；DNA G4 是否以及如何影响植物中的基因表达仍在很大程度上未知。在这里，我们应用了一种称为 BG4-DNA-IP-seq 的方案，随后对水稻（Oryza sativa L.）中的 DNA G4 进行了全面表征；接下来，我们将 dG4s（可实验检测到的 G4s）与现有的组学数据进行了整合，发现 dG4s 在转座元件（TE）和非 TE 基因之间表现出不同的 DNA 甲基化。dG4 区域显示出与基因组特征的基因依赖性富集；最后，我们表明这些位点位于启动子时与含有 DNA G4 的基因的表达呈正相关，而位于基因体中时则呈负相关，表明 DNA G4 在调节基因转录中具有定位依赖性的促进/抑制作用。本研究揭示了 DNA G4 与表观基因组特征之间的相互关系，并表明 DNA G4 参与调节水稻中的基因转录。我们的研究为水稻中一些关键 DNA G4 的功能表征或生物工程提供了有价值的资源。
