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

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.