The data show the RdDM pathway is a major regulatory contributor to generative development and heat stress responses in barley and demonstrates that rdr2 mutant shows reduced heat stress memory capacity rendering the mutant plants more vulnerable to high temperature.
Abstract
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.
A dual mechanism in which DNA methylation and CsRDR1a-related small RNAs coordinately regulate cucumber organ development is unveiled, highlighting the importance of epigenetic regulation in cucumber.
Xiaotao Ding, Yueying Mao, Yongxue Zhang et al.· Journal of Advanced Research· 0 citations
SunTag-NOVA robustly installed DNA methylation and repressed transcription at the endogenous FWA, FT and TMM genes with minimal genome-wide off-target consequences, and establishes SunTag-NOVA as a specific epigenome-editing platform for plants.
Yan He, Ming Wang, T. J. Buckley et al.· bioRxiv· 0 citations
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
Small RNA-mediated gene silencing contributes to plant immunity. The secondary small interfering RNA (siRNA) pathway promotes defense by silencing target genes in invading fungal and oomycete pathogens. Many secondary siRNAs are derived from transcripts potentially encoding pentatricopeptide repeat (PPR) proteins. Here, we report that siRNA production is an ancient function of a conserved clade of
PPR
genes that undergo extensive within-species diversification. In
Arabidopsis thaliana
, siRNA-source
PPR
s are physically clustered on Chromosome 1. These sequences are diversified through gene duplication followed by sequence diversification and accumulation of high-impact variations including pseudogenization, leading to the accumulation of a diverse siRNA pool. These features are consistent with the engagement of
PPR
-siRNAs in a co-evolutionary arms race with the pathogens. This study defines siRNA-producing
PPR
s as a class of defense genes and highlights the potential of
PPR
-siRNA-based engineering as a strategy to enhance disease resistance.
Li Feng, Yingnan Hou, AmirAli Toghani et al.· Nature Communications· 1 citation
Plant genomic and epigenomic integrity are perpetually threatened by exogenous and endogenous DNA damage. However, the interplay between DNA damage, DNA methylation (5mC), and transposable element (TE) activity remains poorly understood. Here, we demonstrate that defective single-strand break (SSB) repair acts as a potent trigger for genome-wide TE derepression and extensive de novo DNA methylation in Arabidopsis. Mutations in ZDP/APE2, which encode conserved DNA 3'-end repair enzymes, impair the repair of 3'-blocked SSBs arising from base excision repair, ultimately leading to widespread TE activation. Concurrently, inefficient SSB repair activates the ATR-SOG1-mediated DNA damage response, which enhances the RNA-directed DNA methylation (RdDM) pathway to counteract TE activation by depositing 5mC. Paradoxically, the resulting methylation is excised by the DNA demethylase ROS1-a process that itself generates 3'-blocked SSBs requiring resolution by ZDP/APE2. In zdp ape2 mutants, ROS1-mediated 5mC excision produces additional SSBs, which in turn reactivate RdDM. This establishes a self-sustaining SSB-5mC cycle that perpetuates DNA damage and drives massive TE activation in the mutant. Our findings reveal a critical mechanistic link between SSB repair, DNA methylation dynamics, and TE derepression, positioning defective SSB repair as a major inducer of epigenomic instability.
Wenjie Liang, Haokai Cao, Chen Zou et al.· Proceedings of the National...· 0 citations