Mutation of a major CG methylase alters genome-wide lncRNA expression in rice

Li, Juzuo; Li, Ning; Zhu, Ling; Zhang, Zhibin; Li, Xiaochong; Wang, Jinbin; Xun, Hongwei; Zhao, Jing; Wang, Xiaofei; Wang, Tianya; Wang, Hongyan; B, Liu; Yu, Li; Gong, Lei

doi:10.1093/g3journal/jkab049

Cited by 6 publications

(8 citation statements)

References 65 publications

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“…For the second constraint (phase separation), the established protein-chromatin interactions mediated by the bridge protein factors and non-coding RNAs are known to be involved into the formation of animal TADs as well (Michieletto and Gilbert, 2019). Given the positive association between CHH methylation and lncRNA (long non-coding RNAs) expression as recently recognized in rice (Li et al, 2021), methylation-regulated lncRNA could recruit specific bridge protein factors to achieve establishing the plant TADs/ TAD-like structures. In other words, DNA methylation may be indirectly involved in formation of TAD-like structures through its regulation of local lncRNA expression.…”

Section: Discussionmentioning

confidence: 99%

“…Identifiable TAD‐like structures in rice allow us to explore the potential roles of specific epigenetic modifications in formation of TAD‐like structures, given the existence of loss‐of‐function mutations in specific DNA methyltransferases. Rice DNA methyltransferase mutants, such as osmet1‐2 , oscmt3a , and osdrm2 , exhibit genome‐wide variation in CG, CHG, and CHH DNA methylation and are available for further analyses (Moritoh et al, 2012; Cheng et al, 2015; Li et al, 2021). The moderate genome size (~370 M) and low‐complexity genomic composition of rice enable the generation of a high‐resolution Hi‐C interaction map (Zhang et al, 2019b; Jia et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Chromatin architectural alterations due to null mutation of a major CG methylase in rice

Wang

Dong

et al. 2022

JIPB

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Associations between 3D chromatin architectures and epigenetic modifications have been characterized in animals. However, any impact of DNA methylation on chromatin architecture in plants is understudied, which is confined to Arabidopsis thaliana. Because plant species differ in genome size, composition, and overall chromatin packing, it is unclear to what extent findings from A. thaliana hold in other species. Moreover, the incomplete chromatin architectural profiles and the low‐resolution high‐throughput chromosome conformation capture (Hi‐C) data from A. thaliana have hampered characterizing its subtle chromatin structures and their associations with DNA methylation. We constructed a high‐resolution Hi‐C interaction map for the null OsMET1‐2 (the major CG methyltransferase in rice) mutant (osmet1‐2) and isogenic wild‐type rice (WT). Chromatin structural changes occurred in osmet1‐2, including intra‐/inter‐chromosomal interactions, compartment transition, and topologically associated domains (TAD) variations. Our findings provide novel insights into the potential function of DNA methylation in TAD formation in rice and confirmed DNA methylation plays similar essential roles in chromatin packing in A. thaliana and rice.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Chromatin architectural alterations due to null mutation of a major CG methylase in rice

Wang

Dong

et al. 2022

JIPB

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“…Both genetic and epigenetic changes were found to be associated with tissue cultureinduced somaclonal variation [13,47,48]. Misregulation of microRNAs and small RNA pathways can make a significant contribution to the phenomenon [31,49]. The miRNA pathway was unusually susceptible to tissue culture caused by potential alterations in both the microRNA and their target genes [44].…”

Section: Discussionmentioning

confidence: 99%

Modification of Gene Expression, DNA Methylation and Small RNAs Expression in Rice Plants under In Vitro Culture

Wang

Zhang

et al. 2022

Agronomy

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Tissue culture is an important experimental technique widely used for plant transformation and can induce somaclonal variation that is shown to be associated with genetic and epigenetic changes. However, the molecular basis of somaclonal variation and plant cell response to tissue culture has yet to be fully understood. In this study, we investigated gene expression, DNA methylation, and small RNA changes in regenerated lines (RL) compared with the wild-type progenitor plants (WT) of rice cv. Hitomebore. Using microarray, we identified many genes that were differentially expressed in the shoot-tip tissue and showed that TEs were generally activated in RL. Methylation Sensitive Amplification Polymorphism (MSAP) analysis of 5′CCGG sites combined with bisulfite sequencing detected a generally reduced DNA methylation in the RL lines. Small RNA sequencing analysis detected widespread changes in small RNA accumulation between RL and WT. In particular, repeat and TE-associated 24-nt size class of small RNAs, the inducer of RNA-directed DNA methylation, was in general down-regulated in RL, consistent with reduced CHG and CHH methylation at some of the differentially methylated TE loci. A large number of differentially expressed miRNAs were identified in RL and WT lines, including known and novel miRNAs. The expression of some of these miRNAs exhibited inverse correlation with the predicted target genes, suggesting a regulatory function. The RL plants looked similar to WT plants under normal conditions but showed significant phenotypic alterations under abiotic stress conditions. The widespread changes in DNA methylation, small RNA accumulation and gene expression in regenerated plants supports the role of epigenetic changes in tissue culture-induced somaclonal variation.

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“…Researchers had highlighted that in a null mutant of OsMET1–2 −/− , a DNA methyltransferase 1 in rice, the TEs family En/Spm experienced transcriptional de-repression because of the genome-wide erasure of CG methylation. This phenomenon led to the production of plenty of specific lncRNAs [ 92 ]. Additionally, there was an accumulation of RdDM-mediated CHH hypermethylation in the 5′-upstream genomic regions of lncRNAs.…”

Section: Coordinated Regulation Among Ncrnasmentioning

confidence: 99%

LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response

Zhang,

Lin,

Zhu

et al. 2023

Horticulture Research

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With the advent of advanced sequencing technologies, non-coding RNAs (ncRNAs) are increasingly pivotal and play highly regulated roles in the modulation of diverse aspects of plant growth and stress response. This includes a spectrum of ncRNA classes, ranging from small RNAs to long non-coding RNAs (lncRNAs). Notably, among these, lncRNAs emerge as significant and intricate components within the broader ncRNA regulatory networks. Here, we categorize ncRNAs based on their length and structure into small RNAs, medium-sized ncRNAs, lncRNAs, and circle RNAs. Furthermore, the review delves into the detailed biosynthesis and origin of these ncRNAs. Subsequently, we emphasize the diverse regulatory mechanisms employed by lncRNAs that are located at various gene regions of coding genes, embodying promoters, 5'UTRs, introns, exons, and 3'UTR regions. Furthermore, we elucidate these regulatory modes through one or two concrete examples. Besides, lncRNAs have emerged as novel central components that participate in phase separation processes. Moreover, we illustrate the coordinated regulatory mechanisms among lncRNAs, miRNAs, and siRNAs with a particular emphasis on the central role of lncRNAs in serving as sponges, precursors, spliceosome, stabilization, scaffolds, or interaction factors to bridge interactions with other ncRNAs. The review also sheds light on the intriguing possibility that some ncRNAs may encode functional micropeptides. Therefore, the review underscores the emergent roles of ncRNAs as potent regulatory factors that significantly enrich the regulatory network governing plant growth, development, and responses to environmental stimuli. There are yet-to-be-discovered roles of ncRNAs waiting for us to explore.

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Mutation of a major CG methylase alters genome-wide lncRNA expression in rice

Cited by 6 publications

References 65 publications

Chromatin architectural alterations due to null mutation of a major CG methylase in rice

Chromatin architectural alterations due to null mutation of a major CG methylase in rice

Modification of Gene Expression, DNA Methylation and Small RNAs Expression in Rice Plants under In Vitro Culture

LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response

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