Methylation of the cytosine bases of DNA as a regulator of chromatin structure and gene expression in the stems of rice supports methylation of the cytosine bases of DNA as a regulator of chromatin structure and gene expression in the stems of rice.
Abstract
Elongating rice internodes present a developmental gradient from dividing meristem to mature cells, providing an elegant pseudo-time course for study of plant vegetative development. We tested the hypothesis that DNA methylation regulates gene expression during rice internode development by integrating RNA-seq and bisulfite DNA sequencing across eight internode segments. Previously described topologically associated chromatin domain borders aligned with transcription start sites of constitutive expressed genes. CpG and CHG differential methylation was enriched in young segments, consistent with maintenance methylation; whereas CHH methylation showed similar differential abundance in young and old segments. CHH and CHG methylation in upstream regions, CpG methylation within gene bodies, and any methylation in 5′ and 3′ untranslated regions were permissive of moderate to high gene expression. Very low expression was associated with CpG methylation upstream, CHG and CHH methylation within gene bodies, and CpG and CHG methylation downstream. A nonrandom subset of genes, including cell wall-related glycoside hydrolases, lignin and tricin biosynthesis enzymes, and WD40 proteins, showed methylation-expression correlations, with expression changes enriched in triple-marked elements. These results suggest that internode phenotypes of DNA methylation machinery mutants relate to alteration of specific target genes, opening approaches for grass culm improvement for lodging resistance and biomass production. Graphical Abstract Significance statement Stems of cereals and other grasses have an important function in supporting grain production and serving as a source of carbon for the bioeconomy. This study supports methylation of the cytosine bases of DNA as a regulator of chromatin structure and gene expression in the stems of rice. Different methylation contexts are implicated in specific roles in both positive and negative gene expression regulation that might be leveraged to improve stem properties.
It is found that heat-induced CHH methylation targets specific genomic loci in a developmental stage-specific manner, with a differentially methylated window located within 6 kb of AT5G44410, an F-box protein-encoding gene.
This study focused on addressing molecular mechanisms of maize response to HAT-NSD by multi-level approaches, and provided new insights into mechanisms for maize responses to HAT-NSD through WGDM.
Y. Pei, Ya-Xing Liu, Jia-Ming Song et al.· Plant, Cell and Environment· 1 citation
This study provides a comprehensive integrative analysis of DNA methylation and transcriptome reprogramming in ‘Shine Muscat’ grapevine under salt stress, revealing potential epigenetic mechanisms involved in transcriptional regulation and salt adaptation.
Ao Li, Ke Li, Fengxia Wang et al.· Agronomy· 0 citations
INTRODUCTION
Cucumber fruits, with a relatively high rate of fruit expansion, are harvested at an early developmental stage once moderately expanded. Although DNA methylation regulating fruit ripening has been well studied, its function in organ development of cucumber remains unknown.
OBJECTIVES
In this study, the regulation and underlying mechanism of DNA methylation in cucumber fruit development were investigated.
METHODS
Chemical treatment with DNA methylation inhibitor 5-aza, together with whole genome bisulfite sequencing (WGBS), flow cytometry, small RNA sequencing, and functional validation via virus-induced gene silencing (VIGS), were comprehensively employed.
RESULTS
Treating cucumber fruits with 5-aza at 0 or 4 days after anthesis (DAA) caused stage-dependent inhibition of fruit expansion, with stronger inhibition observed at 0 DAA. WGBS revealed that DNA methylation at CG and CHG contexts remained at high levels before 4 DAA, while mCG levels peaked at 20 DAA and mCHH levels increased throughout. Before 4 DAA, DNA methylation levels at CHG and CG contexts were higher in fruit than fruit neck, revealing spatiotemporal dynamics of DNA methylation during the development of cucumber fruit. These dynamics were functionally enriched in genes related to cell cycle transition, and this finding was further confirmed by impaired endoreduplication observed in 5-aza treated fruits when compared with control. In addition, CsRDR1a, an RNA-dependent RNA polymerase 1 homolog, displayed fruit stage-specific expression patterns, accompanied by significant accumulation of 19---23 nt small RNAs. Cross-tissue validation by silencing CsCMT3 or CsRDR1a showed reduced leaf size, inhibited endoreduplication, and increased expression of cell-cycle genes with decreased DNA methylation levels at their promoter regions, demonstrating that DNA methylation was essential for cell cycle transition during cucumber organ development.
CONCLUSION
Our results unveil a dual mechanism in which DNA methylation and CsRDR1a-related small RNAs coordinately regulate cucumber organ development, highlighting the importance of epigenetic regulation in cucumber.
Xiaotao Ding, Yueying Mao, Yongxue Zhang et al.· Journal of Advanced Research· 0 citations
It is suggested that Al stress triggers genotype- and sequence-context-specific epigenomic reprogramming in rice, and that tolerance is associated with a targeted methylation response rather than a diffuse one.
J. Gallo-Franco, Chrystian C. Sosa, F. Johannes et al.· Frontiers in Plant Science· 0 citations
Plant specific RNA-directed DNA methylation (RdDM) mediates the DNA methylation of specific DNA sequences directed by 24-nucleotide long (nt) small interfering (si)RNAs. In crop plants we have limited information about the biological roles of the RdDM pathway including barley (Hordeum vulgare L). Here, we show that knockout of barley NRPD/E2A gene by genome editing, bringing about the drastic inhibition of RdDM pathway, results in the early arrest of developing caryopses rendering the mutant plants sterile. The knockout of the downstream component RDR2 gene, responsible for generating double stranded precursor RNAs for the production of 24-nt siRNAs, was associated with the loss of the majority of these siRNAs and also typically induced the early arrest of caryopsis development. However, the rdr2 mutants were able to produce a limited number of seeds exhibiting smaller size, endosperm filling anomalies and inhibited germination, which phenomenon was predominantly inherited maternally. Genome-wide analyses of gene expression revealed drastic up-and down-regulations in rdr2 mutants compared to the wild type. We did not find direct correlation between the changes of gene expression and the localization of 24-nt siRNA producing clusters indicating the indirect action of RdDM in these regulatory events. We also demonstrate that rdr2 mutant shows reduced heat stress memory capacity rendering the mutant plants more vulnerable to high temperature. Altogether, our data show the RdDM pathway is a major regulatory contributor to generative development and heat stress responses in barley.
Auwalu Abdu, H. Szaker, András Kis et al.· bioRxiv· 0 citations