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Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice

文献类型： 外文期刊

作者： Feng, Yilong 1 ; Luo, Zhenyu 1 ; Huang, Ranran 1 ; Yang, Xueming 2 ; Cheng, Xuejiao 1 ; Zhang, Wenli 1 ;

作者机构： 1.Nanjing Agr Univ, Collaborat Innovat Ctr Modern Crop Prod Prov & Mi, State Key Lab Crop Genet & Germplasm Enhancement, 1 Weigang, Nanjing 210095, Peoples R China

2.Jiangsu Acad Agr Sci, Nanjing 210014, Peoples R China

关键词： BG4-DNA-IP-seq; K+-; Na+-specific IP-G4; epigenetic features; functional relevance

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：6.208； 五年影响因子：6.628 ）

ISSN：

年卷期： 2022 年 23 卷 15 期

页码：

收录情况： SCI

摘要： 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.

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