DNA methylation in plants Gallego-Bartolomé, Javier
New phytologist,
07/2020, Letnik:
227, Številka:
1
Journal Article
Recenzirano
Odprti dostop
DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been instrumental in the study of ...this mark in plants, although their genome-wide effect complicates the direct association between changes in methylation and a particular phenotype. A variety of tools that allow locus-specific manipulation of DNA methylation can be used to assess its direct role in specific processes, as well as to create novel epialleles. Recently, new tools that recruit the methylation machinery directly to target loci through programmable DNA-binding proteins have expanded the tool kit available to researchers. This review provides an overview of DNA methylation in plants and discusses the tools that have recently been developed for its manipulation.
The C‐REPEAT‐BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. How the CBF genes themselves are activated after cold acclimation remains poorly understood. In this ...study, we characterized cold tolerance of null mutant of RNA‐DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol V and Pol II, and is required for RNA‐directed DNA methylation (RdDM) in Arabidopsis. The results showed that dysfunction of RDM4 reduced cold tolerance, as evidenced by decreased survival and increased electrolyte leakage. Mutation of RDM4 resulted in extensive transcriptomic reprogramming. CBFs and CBF regulon genes were down‐regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 constitutively increased the expression of CBFs and regulon genes and decreased cold‐induced membrane injury. A great proportion of genes affected by rdm4 overlapped with those affected by CBFs. Chromatin immunoprecipitation results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF2 and CBF3. We present evidence of a considerable role for RDM4 in regulating gene expression at low temperature, including the CBF pathway in Arabidopsis.
Transposable elements (TEs) generate mutations and chromosomal instability when active. To repress TE activity, eukaryotic cells evolved mechanisms to both degrade TE mRNAs into small interfering ...RNAs (siRNAs) and modify TE chromatin to epigenetically inhibit transcription. Since the populations of small RNAs that participate in TE post‐transcriptional regulation differ from those that establish RNA‐directed DNA methylation (RdDM), the mechanism through which transcriptionally active TEs transition from post‐transcriptional RNAi regulation to chromatin level control has remained unclear. We have identified the molecular mechanism of a plant pathway that functions to direct DNA methylation to transcriptionally active TEs. We demonstrated that 21–22 nucleotide (nt) siRNA degradation products from the RNAi of TE mRNAs are directly incorporated into the ARGONAUTE 6 (AGO6) protein and direct AGO6 to TE chromatin to guide its function in RdDM. We find that this pathway functions in reproductive precursor cells to primarily target long centromeric high‐copy transcriptionally active TEs for RdDM prior to gametogenesis. This study provides a direct mechanism that bridges the gap between the post‐transcriptional regulation of TEs and the establishment of TE epigenetic silencing.
Synopsis
Transcriptional activation of transposable elements (TEs) in plants leads to initial mRNA destruction through RNAi. AGO6 incorporates the resulting siRNAs and induces DNA methylation at TE target loci, thus establishing de novo epigenetic silencing.
RNA‐directed DNA methylation targets transcriptionally active transposable elements
AGO6 incorporates 21–22nt siRNAs produced by RNAi from transposable element mRNAs
Transposon‐derived siRNAs target AGO6 to chromatin and direct de novo DNA methylation
AGO6 plays a dual role by maintaining epigenetic silencing and initiating establishment of repressive chromatin states
This mechanism bridges the worlds of post‐transcriptional and transcriptional gene silencing by linking mRNA degradation via RNAi to the establishment of DNA methylation
Transcriptional activation of transposable elements (TEs) in plants leads to initial mRNA destruction through RNAi. AGO6 incorporates the resulting siRNAs and induces DNA methylation at TE target loci, thus establishing de novo epigenetic silencing.
RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to ...target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA–DNA methylation interactions and the limits of current knowledge. Finally, we discuss potential applications of mobile sRNAs in modifying plant traits.
SUMMARY
Chromatin in eukaryotes folds into a complex three‐dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in ...biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low‐Pi treatment led to greater chromatin volume. Furthermore, low‐Pi stress increased the insulation score and the number of TAD‐like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD‐like boundaries, whereas RdDM peak levels at conserved TAD‐like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome‐wide RdDM sites near TAD‐like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low‐Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low‐Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP‐seq results revealed that ZmDDM1A could bind to Pi‐ and root development‐related genes. Strong associations were found between interacting genes in significantly different chromatin‐interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low‐Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.
Significance Statement
This study is a pioneering study in the field of plant nutrient utilization. For the first time, this study discovered that the plant's low‐Pi response was closely linked to the RdDM pathway and chromatin spatial structure, and the low‐Pi response was validated by a mutant of chromatin remodeling gene ZmDDM1a (RdDM pathway gene). In addition, the results of ChIP‐seq and multi‐point GWAS for 2 years revealed the interaction of a large number of candidate genes related to Pi and roots with ZmDDM1A. We believe that the results presented in this article will have a great influence in this field and will be concerned and cited by many researchers.
Long Noncoding RNAs in Plants Wierzbicki, Andrzej T; Blevins, Todd; Swiezewski, Szymon
Annual review of plant biology,
06/2021, Letnik:
72, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs ...(lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex ...transcriptional machineries comprising two plant-specific, RNA polymerase II (Pol II)-related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins. We present current views on the mechanism of RdDM with a focus on evolutionary innovations that occurred during the transition from a Pol II transcriptional pathway, which produces mRNA precursors and numerous noncoding RNAs, to the Pol IV and Pol V pathways, which are specialized for RdDM and gene silencing. We describe recently recognized deviations from the canonical RdDM pathway, discuss unresolved issues, and speculate on the biological significance of RdDM for flowering plants, which have a highly developed Pol V pathway.
SUMMARY
DNA methylation is an important epigenetic mark. In plants, de novo DNA methylation occurs mainly through the RNA‐directed DNA methylation (RdDM) pathway. Researchers have previously inferred ...that a flowering regulator, MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)/FVE, is involved in non‐CG methylation at several RdDM targets, suggesting a role of FVE in RdDM. However, whether and how FVE affects RdDM genome‐wide is not known. Here, we report that FVE is required for DNA methylation at thousands of RdDM target regions. In addition, dysfunction of FVE significantly reduces 24‐nucleotide siRNA accumulation that is dependent on factors downstream in the RdDM pathway. By using chromatin immunoprecipitation and sequencing (ChIP‐seq), we show that FVE directly binds to FVE‐dependent 24‐nucleotide siRNA cluster regions. Our results also indicate that FVE may function in RdDM by physically interacting with RDM15, a downstream factor in the RdDM pathway. Our study has therefore revealed that FVE, by associating with RDM15, directly regulates DNA methylation and siRNA accumulation at a subset of RdDM targets.
Significance Statement
The RNA‐directed DNA methylation (RdDM) pathway is one of the most important DNA methylation pathways in plants. In this manuscript, we show that FVE is required for DNA methylation and for 24‐nucleotide siRNA accumulation at a subset of RdDM targets. Moreover, FVE physically interacts with RDM15 and shares DNA methylation targets with RDM15 in the genome. Our results support the notion that FVE functions in RdDM, particularly in RNA polymerase V‐mediated downstream step.
SUMMARY
Plants respond to adverse environmental cues by adjusting a wide variety of processes through highly regulated mechanisms to maintain plant homeostasis for survival. As a result of the ...sessile nature of plants, their response, adjustment and adaptation to the changing environment is intimately coordinated with their developmental programs through the crosstalk of regulatory networks. Germination is a critical process in the plant life cycle, and thus plants have evolved various strategies to control the timing of germination according to their local environment. The mechanisms involved in these adjustment responses are largely unknown, however. Here, we report that mutations in core elements of canonical RNA‐directed DNA methylation (RdDM) affect the germination and post‐germination growth of Arabidopsis seeds grown under salinity stress. Transcriptomic and whole‐genome bisulfite sequencing (WGBS) analyses support the involvement of this pathway in the control of germination timing and post‐germination growth under salinity stress by preventing the transcriptional activation of genes implicated in these processes. Subsequent transcriptional effects on genes that function in relation to these developmental events support this conclusion.
Significance Statement
Germination is a key process in the plant life cycle, such that plants have evolved various strategies to control the timing of germination according to their local environment. We show that canonical RNA‐directed DNA methylation (RdDM), one of the transcriptional regulation mechanisms in plants, participates in the control of germination timing and post‐germination growth under salinity stress in Arabidopsis thaliana by preventing the transcriptional activation of genes implicated in these processes.
Mobile small RNAs regulate genome-wide DNA methylation Lewsey, Mathew G.; Hardcastle, Thomas J.; Melnyk, Charles W. ...
Proceedings of the National Academy of Sciences - PNAS,
02/2016, Letnik:
113, Številka:
6
Journal Article
Recenzirano
Odprti dostop
RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses. Key ...components of the mechanism are small RNAs (sRNAs) of 21–24 nt that guide the silencing machinery to their nucleic acid targets in a nucleotide sequence-specific manner. Transcriptional gene silencing is associated with 24-nt sRNAs and RNA-directed DNA methylation (RdDM) at cytosine residues in three DNA sequence contexts (CG, CHG, and CHH). We previously demonstrated that 24-nt sRNAs are mobile from shoot to root in Arabidopsis thaliana and confirmed that they mediate DNA methylation at three sites in recipient cells. In this study, we extend this finding by demonstrating that RdDM of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot and that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. Mobile sRNA-dependent non-CG methylation is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) RdDM pathway but is independent of the CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. Specific superfamilies of TEs, including those typically found in gene-rich euchromatic regions, lose DNA methylation in a mutant lacking 22- to 24-nt sRNAs (dicer-like 2, 3, 4 triple mutant). Transcriptome analyses identified a small number of genes whose expression in roots is associated with mobile sRNAs and connected to DNA methylation directly or indirectly. Finally, we demonstrate that sRNAs from shoots of one accession move across a graft union and target DNA methylation de novo at normally unmethylated sites in the genomes of root cells from a different accession.
PDF
