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Jiankang Zhu - One of the best experts on this subject based on the ideXlab platform.
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pathway conversion enables a double lock mechanism to maintain DNA Methylation and genome stability
Proceedings of the National Academy of Sciences of the United States of America, 2021Co-Authors: Cheng Zhao, Qingzhu Zhang, Rosa Lozanoduran, Dong Wang, Gaurav Zinta, Jiankang ZhuAbstract:The CMT2 and RNA-Directed DNA Methylation (RdDM) pathways have been proposed to separately maintain CHH Methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeler DDM1 causes hundreds of genomic regions to switch from CMT2 dependency to RdDM dependency in DNA Methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that dysfunction in both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the DDM1 and RdDM pathways together are critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a pathway conversion-based backup mechanism to guarantee the maintenance of DNA Methylation and genome integrity.
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a virus encoded protein suppresses Methylation of the viral genome through its interaction with ago4 in the cajal body
eLife, 2020Co-Authors: Liping Wang, Guiping Zhang, Jiankang Zhu, Yi Ding, Rosa LozanoduranAbstract:In plants, establishment of de novo DNA Methylation is regulated by the RNA-Directed DNA Methylation (RdDM) pathway. RdDM machinery is known to concentrate in the Cajal body, but the biological significance of this localization has remained elusive. Here, we show that the antiviral Methylation of the Tomato yellow leaf curl virus (TYLCV) genome requires the Cajal body in Nicotiana benthamiana cells. Methylation of the viral genome is countered by a virus-encoded protein, V2, which interacts with the central RdDM component AGO4, interfering with its binding to the viral DNA; Cajal body localization of the V2-AGO4 interaction is necessary for the viral protein to exert this function. Taken together, our results draw a long sought-after functional connection between RdDM, the Cajal body, and antiviral DNA Methylation, paving the way for a deeper understanding of DNA Methylation and antiviral defences in plants.
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the ccr4 not complex component not1 regulates rna directed DNA Methylation and transcriptional silencing by facilitating pol iv dependent sirna production
Plant Journal, 2020Co-Authors: Haoran Zhou, Jiankang Zhu, Huanwei Huang, Tao Cai, Rongnan Lin, She ChenAbstract:Small interfering RNAs (siRNAs) are responsible for establishing and maintaining DNA Methylation through the RNA-Directed DNA Methylation (RdDM) pathway in plants. Although siRNA biogenesis is well known, it is relatively unclear about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana, we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for transcriptional silencing at RdDM target genomic loci. We demonstrated that NOT1 is required for Pol IV-dependent siRNA accumulation and DNA Methylation at a subset of RdDM target genomic loci. Furthermore, we revealed that NOT1 is a constituent of a multi-subunit CCR4-NOT deadenylase complex by immunoprecipitation combined with mass spectrometry and demonstrated that the CCR4-NOT components can function as a whole to mediate chromatin silencing. Therefore, our work establishes that the CCR4-NOT complex regulates the biogenesis of Pol IV-dependent siRNAs, and hence facilitates DNA Methylation and transcriptional silencing in Arabidopsis.
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a virus encoded protein suppresses Methylation of the viral genome through its interaction with ago4 in the cajal body
bioRxiv, 2019Co-Authors: Liping Wang, Guiping Zhang, Jiankang Zhu, Yi Ding, Rosa LozanoduranAbstract:ABSTRACT DNA Methylation is a eukaryotic anti-viral defence mechanism. In plants, establishment of de novo DNA Methylation is regulated by the RNA-Directed DNA Methylation pathway, which requires AGO4 function. The genome of the plant DNA viruses geminiviruses replicates in the nuclei of infected cells through not yet fully understood mechanisms and is subjected to Methylation, a modification that negatively impacts infectivity. In Tomato yellow leaf curl virus, the virus-encoded V2 protein suppresses Methylation of the viral DNA. Here, we identify AGO4 as a physical interactor of V2. AGO4 mediates Methylation of the viral genome, which is countered by V2. Accordingly, virulence of a V2 mutant virus is partially restored by AGO4 silencing, hinting at the inhibition of AGO4 as a crucial virulence function of V2. Virus-produced V2 does not affect accumulation of viral small interfering RNA nor prevents their loading into AGO4, but impairs binding of this protein to the viral DNA. Importantly, the association between V2 and AGO4 occurs in the Cajal body, uncovering this subnuclear compartment as a crucial site in the viral cycle.
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the DNA demethylase ros1 targets genomic regions with distinct chromatin modifications
Nature plants, 2016Co-Authors: Kai Tang, Heng Zhang, Jiankang Zhu, Zhaobo LangAbstract:The Arabidopsis ROS1/DEMETER family of 5-methylcytosine (5mC) DNA glycosylases are the first genetically characterized DNA demethylases in eukaryotes. However, the features of ROS1-targeted genomic loci are not well understood. In this study, we characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. We found that ROS1 preferentially targets transposable elements (TEs) and intergenic regions. Compared with most TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting that ROS1 may prevent DNA Methylation spreading from TEs to nearby genes. ROS1-targeted TEs are specifically enriched for H3K18Ac and H3K27me3, and depleted of H3K27me and H3K9me2. Importantly, we identified thousands of previously unknown RNA-Directed DNA Methylation (RdDM) targets following depletion of ROS1, suggesting that ROS1 strongly antagonizes RdDM at these loci. In addition, we show that ROS1 also antagonizes RdDM-independent DNA Methylation at some loci. Our results provide important insights into the genome-wide targets of ROS1 and the crosstalk between DNA Methylation and ROS1-mediated active DNA deMethylation.
Steven E Jacobsen - One of the best experts on this subject based on the ideXlab platform.
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DNA methylome of the 20 gigabase norway spruce genome
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Israel Ausin, Elise L Jacobsen, Javier Gallegobartolome, Jixian Zhai, Nathaniel R. Street, Chaowei Yu, Suhua Feng, Ulrika Egertsdotter, Lin Wang, Steven E JacobsenAbstract:DNA Methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA Methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA Methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution Methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA Methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH Methylation was found at a relatively low level; however, at least one copy of most of the RNA-Directed DNA Methylation pathway genes was found in Norway spruce, and CHH Methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG Methylation but higher level of CHH Methylation, suggesting that like in other species, these culture cells show abnormal Methylation patterns.
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polymerase iv occupancy at rna directed DNA Methylation sites requires shh1
Nature, 2013Co-Authors: Jiamu Du, Suhua Feng, Christopher J Hale, Krzysztof Krajewski, Ana Marie S Palanca, Dinshaw J Patel, Brian D Strahl, Steven E JacobsenAbstract:In Arabidopsis, RNA-Directed DNA Methylation is a poorly understood gene silencing pathway in which small interfering RNAs generated by RNA polymerase IV (Pol-IV) target a DNA methyltransferase to its sites of action; here structural and genomic analyses demonstrate that SHH binds chromatin via repressive histone modifications and recruits Pol-IV to enable siRNA production. In Arabidopsis, RNA-Directed DNA Methylation (RdDM) is a poorly understood gene-silencing pathway in which small interfering RNAs (siRNAs) generated by an RNA polymerase, Pol-IV, target a DNA methyltransferase to its sites of action. Here, Steven Jacobsen and colleagues report that the homeodomain protein SHH1 binds chromatin via repressive histone modifications and recruits Pol-IV to promote siRNA production. SHH1 has a novel chromatin-binding module that functions as a dual lysine reader for both K4 and K9 of the histone H3 tail. This work identifies an early targeting step that may be a critical control point in epigenetic modification through DNA Methylation. DNA Methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA Methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-Directed DNA Methylation (RdDM)1. This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors1,2. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1)3,4, a Pol-IV-interacting protein3. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA Methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between Methylation systems in plants and mammals1,5, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.
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ddr complex facilitates global association of rna polymerase v to promoters and evolutionarily young transposons
Nature Structural & Molecular Biology, 2012Co-Authors: Xuehua Zhong, Suhua Feng, Lianna M Johnson, Christopher J Hale, Julie A Law, Steven E JacobsenAbstract:The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-Directed DNA Methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found that Pol V is enriched at promoters and evolutionarily recent transposons. This localization pattern is highly correlated with Pol V-dependent DNA Methylation and small RNA accumulation. We also show that genome-wide chromatin association of Pol V is dependent on all members of a putative chromatin-remodeling complex termed DDR. Our study presents the first genome-wide view of Pol V occupancy and sheds light on the mechanistic basis of Pol V localization. Furthermore, these findings suggest a role for Pol V and RNA-Directed DNA Methylation in genome surveillance and in responding to genome evolution.
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the splicing factor sr45 affects the rna directed DNA Methylation pathway in arabidopsis
Epigenetics, 2012Co-Authors: Israel Ausin, Maxim V C Greenberg, Steven E JacobsenAbstract:Cytosine DNA Methylation is an epigenetic mark frequently associated with silencing of genes and transposons. In Arabidopsis, the establishment of cytosine DNA Methylation is performed by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2). DRM2 is guided to target sequences by small interfering RNAs (siRNAs) in a pathway termed RNA-Directed DNA Methylation (RdDM). We performed a screen for mutants that affect the establishment of DNA Methylation by investigating genes that contain predicted RNA-interacting domains. After transforming FWA into 429 T-DNA insertion lines, we assayed for mutants that exhibited a late-flowering phenotype due to hypomethylated, thus ectopically expressed, copies of FWA. A T-DNA insertion line within the coding region of the spliceosome gene SR45 (sr45-1) flowered late after FWA transformation. Additionally, sr45-1 mutants display defects in the maintenance of DNA Methylation. DNA Methylation establishment and maintenance defects present in sr45-1 mutants are enhanced in dcl3-1 mutant background, suggesting a synergistic cooperation between SR45 and DICER-LIKE3 (DCL3) in the RdDM pathway.
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shh1 a homeodomain protein required for DNA Methylation as well as rdr2 rdm4 and chromatin remodeling factors associate with rna polymerase iv
PLOS Genetics, 2011Co-Authors: Ajay A Vashisht, James A Wohlschlegel, Steven E JacobsenAbstract:DNA Methylation is an evolutionarily conserved epigenetic modification that is critical for gene silencing and the maintenance of genome integrity. In Arabidopsis thaliana, the de novo DNA methyltransferase, DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), is targeted to specific genomic loci by 24 nt small interfering RNAs (siRNAs) through a pathway termed RNA–directed DNA Methylation (RdDM). Biogenesis of the targeting siRNAs is thought to be initiated by the activity of the plant-specific RNA polymerase IV (Pol-IV). However, the mechanism through which Pol-IV is targeted to specific genomic loci and whether factors other than the core Pol-IV machinery are required for Pol-IV activity remain unknown. Through the affinity purification of NUCLEAR RNA POLYMERASE D1 (NRPD1), the largest subunit of the Pol-IV polymerase, we found that several previously identified RdDM components co-purify with Pol-IV, namely RNA–DEPENDENT RNA POLYMERASE 2 (RDR2), CLASSY1 (CLSY1), and RNA–DIRECTED DNA Methylation 4 (RDM4), suggesting that the upstream siRNA generating portion of the RdDM pathway may be more physically coupled than previously envisioned. A homeodomain protein, SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), was also found to co-purify with NRPD1; and we demonstrate that SHH1 is required for de novo and maintenance DNA Methylation, as well as for the accumulation of siRNAs at specific loci, confirming it is a bonafide component of the RdDM pathway.
Marjori Matzke - One of the best experts on this subject based on the ideXlab platform.
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rna directed DNA Methylation the evolution of a complex epigenetic pathway in flowering plants
Annual Review of Plant Biology, 2015Co-Authors: Marjori Matzke, Tatsuo Kanno, Antonius J M MatzkeAbstract: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.
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rna directed DNA Methylation an epigenetic pathway of increasing complexity
Nature Reviews Genetics, 2014Co-Authors: Marjori Matzke, Richard A MosherAbstract:RNA-Directed DNA Methylation (RdDM) is a major mechanism of transcriptional gene silencing in plants that is mediated through small interfering RNAs (siRNAs) and plant-specific RNA polymerases. This Review summarizes our latest understanding of RdDM, including its genomic targets, molecular mechanisms (such as emerging non-canonical pathways) and diverse biological roles.
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ago6 functions in rna mediated transcriptional gene silencing in shoot and root meristems in arabidopsis thaliana
PLOS ONE, 2011Co-Authors: Changho Eun, Antonius J M Matzke, Zdravko J Lorkovic, Ulf Naumann, Quan Long, Ericka R Havecker, Stacey A Simon, Blake C Meyers, Marjori MatzkeAbstract:RNA-Directed DNA Methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger Methylation and transcriptional gene silencing of homologous promoter sequences. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and transcriptional gene silencing in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points.
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genetic evidence that DNA methyltransferase drm2 has a direct catalytic role in rna directed DNA Methylation in arabidopsis thaliana
Genetics, 2011Co-Authors: Ulf Naumann, Tatsuo Kanno, Marjori Matzke, Lucia Daxinger, Zdravko J Lorkovic, Quan Long, Antonius J M MatzkeAbstract:RNA-Directed DNA Methylation (RdDM) is a small RNA-mediated epigenetic modification in plants. We report here the identification of DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) in a forward screen for mutants defective in RdDM in Arabidopsis thaliana. The finding of a mutation in the presumptive active site argues in favor of direct catalytic activity for DRM2.
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a structural maintenance of chromosomes hinge domain containing protein is required for rna directed DNA Methylation
Nature Genetics, 2008Co-Authors: Tatsuo Kanno, David P Kreil, Marjori Matzke, Bruno Huettel, Lucia Daxinger, Etienne Bucher, Gudrun Böhmdorfer, Wolfgang Gregor, Antonius J M MatzkeAbstract:RNA-Directed DNA Methylation (RdDM) is a process in which dicer-generated small RNAs guide de novo cytosine Methylation at the homologous DNA region1,2. To identify components of the RdDM machinery important for Arabidopsis thaliana development, we targeted an enhancer active in meristems for Methylation, which resulted in silencing of a downstream GFP reporter gene. This silencing system also features secondary siRNAs, which trigger Methylation that spreads beyond the targeted enhancer region. A screen for mutants defective in meristem silencing and enhancer Methylation retrieved six dms complementation groups, which included the known factors DRD1 (ref. 3; a SNF2-like chromatin-remodeling protein) and Pol IVb subunits4,5. Additionally, we identified a previously unknown gene DMS3 (At3g49250), encoding a protein similar to the hinge-domain region of structural maintenance of chromosomes (SMC) proteins. This finding implicates a putative chromosome architectural protein that can potentially link nucleic acids6 in facilitating an RNAi-mediated epigenetic modification involving secondary siRNAs and spreading of DNA Methylation.
Antonius J M Matzke - One of the best experts on this subject based on the ideXlab platform.
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rna directed DNA Methylation the evolution of a complex epigenetic pathway in flowering plants
Annual Review of Plant Biology, 2015Co-Authors: Marjori Matzke, Tatsuo Kanno, Antonius J M MatzkeAbstract: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.
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ago6 functions in rna mediated transcriptional gene silencing in shoot and root meristems in arabidopsis thaliana
PLOS ONE, 2011Co-Authors: Changho Eun, Antonius J M Matzke, Zdravko J Lorkovic, Ulf Naumann, Quan Long, Ericka R Havecker, Stacey A Simon, Blake C Meyers, Marjori MatzkeAbstract:RNA-Directed DNA Methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger Methylation and transcriptional gene silencing of homologous promoter sequences. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and transcriptional gene silencing in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points.
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genetic evidence that DNA methyltransferase drm2 has a direct catalytic role in rna directed DNA Methylation in arabidopsis thaliana
Genetics, 2011Co-Authors: Ulf Naumann, Tatsuo Kanno, Marjori Matzke, Lucia Daxinger, Zdravko J Lorkovic, Quan Long, Antonius J M MatzkeAbstract:RNA-Directed DNA Methylation (RdDM) is a small RNA-mediated epigenetic modification in plants. We report here the identification of DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) in a forward screen for mutants defective in RdDM in Arabidopsis thaliana. The finding of a mutation in the presumptive active site argues in favor of direct catalytic activity for DRM2.
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a structural maintenance of chromosomes hinge domain containing protein is required for rna directed DNA Methylation
Nature Genetics, 2008Co-Authors: Tatsuo Kanno, David P Kreil, Marjori Matzke, Bruno Huettel, Lucia Daxinger, Etienne Bucher, Gudrun Böhmdorfer, Wolfgang Gregor, Antonius J M MatzkeAbstract:RNA-Directed DNA Methylation (RdDM) is a process in which dicer-generated small RNAs guide de novo cytosine Methylation at the homologous DNA region1,2. To identify components of the RdDM machinery important for Arabidopsis thaliana development, we targeted an enhancer active in meristems for Methylation, which resulted in silencing of a downstream GFP reporter gene. This silencing system also features secondary siRNAs, which trigger Methylation that spreads beyond the targeted enhancer region. A screen for mutants defective in meristem silencing and enhancer Methylation retrieved six dms complementation groups, which included the known factors DRD1 (ref. 3; a SNF2-like chromatin-remodeling protein) and Pol IVb subunits4,5. Additionally, we identified a previously unknown gene DMS3 (At3g49250), encoding a protein similar to the hinge-domain region of structural maintenance of chromosomes (SMC) proteins. This finding implicates a putative chromosome architectural protein that can potentially link nucleic acids6 in facilitating an RNAi-mediated epigenetic modification involving secondary siRNAs and spreading of DNA Methylation.
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targets of rna directed DNA Methylation
Current Opinion in Plant Biology, 2007Co-Authors: Marjori Matzke, Tatsuo Kanno, Bruno Huettel, Lucia Daxinger, Antonius J M MatzkeAbstract:RNA-Directed DNA Methylation contributes substantially to epigenetic regulation of the plant genome. Methylation is guided to homologous DNA target sequences by 24 nt ‘heterochromatic’ small RNAs produced by nucleolar-localized components of the RNAi machinery and a plant-specific RNA polymerase, Pol IV. Plants contain unusually large and diverse populations of small RNAs, many of which originate from transposons and repeats. These sequences are frequent targets of Methylation, and they are able to bring plant genes in their vicinity under small RNA-mediated control. RNA-Directed DNA Methylation can be removed by enzymatic deMethylation, providing plants with a versatile system that facilitates epigenetic plasticity. In addition to subduing transposons, RNA-Directed DNA Methylation has roles in plant development and, perhaps, stress responses.
Kai Tang - One of the best experts on this subject based on the ideXlab platform.
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a histone h3k4me1 specific binding protein is required for sirna accumulation and DNA Methylation at a subset of loci targeted by rna directed DNA Methylation
Nature Communications, 2021Co-Authors: Qingfeng Niu, Kai Tang, Heng Zhang, Zhe Song, Lixian Chen, Lisi Wang, Ting Ban, Zhongxin Guo, Chanhong Kim, Cheng-guo DuanAbstract:In plants, RNA-Directed DNA Methylation (RdDM) is a well-known de novo DNA Methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized an RdDM factor, RDM15. Through DNA methylome and genome-wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA Methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monoMethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported monomethyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone H3K4me1-specific binding protein as an RdDM component, and structural analysis of RDM15 revealed a chemical feature-based lower methyllysine recognition mechanism.
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A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA Methylation at a subset of loci targeted by RNA-Directed DNA Methylation
'Springer Science and Business Media LLC', 2021Co-Authors: Qingfeng Niu, Kai Tang, Heng Zhang, Zhe Song, Lixian Chen, Lisi Wang, Ting Ban, Zhongxin Guo, Chanhong Kim, Cheng-guo DuanAbstract:In plants, RNA-Directed DNA Methylation (RdDM) is a de novo DNA Methylation pathway that is responsible for transcriptional silencing of repetitive elements. Here, the authors characterized a new RdDM factor, RDM15, and show that it is required for RdDM-dependent DNA Methylation and siRNA accumulation at a subset of RdDM target loci
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the DNA demethylase ros1 targets genomic regions with distinct chromatin modifications
Nature plants, 2016Co-Authors: Kai Tang, Heng Zhang, Jiankang Zhu, Zhaobo LangAbstract:The Arabidopsis ROS1/DEMETER family of 5-methylcytosine (5mC) DNA glycosylases are the first genetically characterized DNA demethylases in eukaryotes. However, the features of ROS1-targeted genomic loci are not well understood. In this study, we characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. We found that ROS1 preferentially targets transposable elements (TEs) and intergenic regions. Compared with most TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting that ROS1 may prevent DNA Methylation spreading from TEs to nearby genes. ROS1-targeted TEs are specifically enriched for H3K18Ac and H3K27me3, and depleted of H3K27me and H3K9me2. Importantly, we identified thousands of previously unknown RNA-Directed DNA Methylation (RdDM) targets following depletion of ROS1, suggesting that ROS1 strongly antagonizes RdDM at these loci. In addition, we show that ROS1 also antagonizes RdDM-independent DNA Methylation at some loci. Our results provide important insights into the genome-wide targets of ROS1 and the crosstalk between DNA Methylation and ROS1-mediated active DNA deMethylation.
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dicer independent rna directed DNA Methylation in arabidopsis
Cell Research, 2016Co-Authors: Donglei Yang, Huan Huang, Lan Yang, Guiping Zhang, Kai Tang, Jingwen Li, Heng ZhangAbstract:RNA-Directed DNA Methylation (RdDM) is an important de novo DNA Methylation pathway in plants. Small interfering RNAs (siRNAs) generated by Dicers from RNA polymerase IV (Pol IV) transcripts are thought to guide sequence-specific DNA Methylation. To gain insight into the mechanism of RdDM, we performed whole-genome bisulfite sequencing of a collection of Arabidopsis mutants, including plants deficient in Pol IV (nrpd1) or Dicer (dcl1/2/3/4) activity. Unexpectedly, of the RdDM target loci that required Pol IV and/or Pol V, only 16% were fully dependent on Dicer activity. DNA Methylation was partly or completely independent of Dicer activity at the remaining Pol IV- and/or Pol V-dependent loci, despite the loss of 24-nt siRNAs. Instead, DNA Methylation levels correlated with the accumulation of Pol IV-dependent 25-50 nt RNAs at most loci in Dicer mutant plants. Our results suggest that RdDM in plants is largely guided by a previously unappreciated class of Dicer-independent non-coding RNAs, and that siRNAs are required to maintain DNA Methylation at only a subset of loci.
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protocol a beginner s guide to the analysis of rna directed DNA Methylation in plants
Plant Methods, 2014Co-Authors: Huiming Zhang, Kai Tang, Cheng-guo Duan, Bangshing Wang, Zhaobo LangAbstract:Background DNA Methylation is a conserved epigenetic mark that controls genome stability, development and environmental responses in many eukaryotes. DNA Methylation can be guided by non-coding RNAs that include small interfering RNAs and scaffold RNAs. Although measurement of DNA Methylation and regulatory non-coding RNAs is desirable for many biologists who are interested in exploring epigenetic regulation in their areas, conventional methods have limitations and are technically challenging. For instance, traditional siRNA detection through RNA hybridization requires relatively large amount of small RNAs and involves radioactive isotopes. An alternative approach is RT-qPCR that employs stem loop primers during reverse transcription; however, it requires a prerequisite that the exact sequences of siRNAs should be known.
