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

Abstract

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.

The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice

“…However, the differential impacts of PDS and PEG on G4 formation on a genome-wide scale are still largely unknown. To address this question, we performed a BG4-DNA-IP-seq as described previously [ 55 ] for the identification of in vitro G4s under K+PEG or PDS conditions. We obtained two well-correlated biological replicates for each condition (R = 0.90 and 0.87 for K+PEG/PDS, respectively) ( Figure S1 ; Table S1 ).…”

“…Compared to the fruitful progress of G4s in non-plant systems, G4 studies in plants are still at the early stage, even though the global prediction of PQFSs has already started in several plant species [ 8 , 25 , 49 , 50 , 51 , 52 , 53 , 54 ], including Arabidopsis , rice, maize, wheat and barley, and genome-wide experimental characterizations of G4s have been initiated in Arabidopsis [ 32 ] and rice [ 7 , 35 , 55 ]. G4 studies in plants indicate that plant G4s can be involved in various biological processes, including the regulation of gene expression and translation, TE activities, telomere functions, epigenetic modifications, and plant growth and development, as well as stress responses [ 6 , 7 , 8 , 25 , 27 , 53 , 56 , 57 , 58 , 59 ].…”

“…PEG and PDS chemicals have already been applied to promote G4 folding in vitro in rice [ 7 , 35 , 55 ] and Arabidopsis [ 32 ], respectively. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown.…”

Special Issue “Bioinformatics of Unusual DNA and RNA Structures”

“…The study by Feng, Luo et al explores the effects of potassium (K + ) and sodium (Na + ) ions on global G-quadruplex formation in rice (Oryza sativa) [53]. The authors utilized a high-throughput method called BG4-DNA-IP-seq (DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing).…”

“…One of the exciting findings is that K + -specific G-quadruplexes are more associated with active histone marks and low DNA methylation levels compared to Na + -specific G-quadruplexes. This important research will facilitate the functional characterization of G-quadruplexes in rice and allow the potential use of specific G-quadruplex locations for biotechnological advancements in the future [53].…”