scholarly journals The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

2021 ◽  
Vol 118 (30) ◽  
pp. e2100709118
Author(s):  
Kezhi Zheng ◽  
Lili Wang ◽  
Longjun Zeng ◽  
Dachao Xu ◽  
Zhongxin Guo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Histone Modifications ◽  
Noncoding Rna ◽  
De Novo ◽  
Noncoding Rnas ◽  
Reproductive Development ◽  
Small Interfering Rnas ◽  
Pol V ◽  
Specific Manner

RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of RNA polymerase V (Pol V), a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long noncoding RNAs. Pol V influences the accumulation of 24-nucleotide small interfering RNAs (24-nt siRNAs) in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V–independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V–dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V–dependent loci but not on Pol V–independent loci. Our results reveal the function of rice Pol V for long noncoding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.

scholarly journals Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba

2021 ◽  
Author(s):  
Sergio Alan Cervantes-Pérez ◽  
Lenin Yong-Villalobos ◽  
Nathalia M.V. Florez-Zapata ◽  
Araceli Oropeza-Aburto ◽  
Felix Rico-Reséndiz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genome Size ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Initial Step ◽  
Global Dna Methylation ◽  
Small Interfering Rnas ◽  
Utricularia Gibba ◽  
The Impact ◽  
Female Gametogenesis

Abstract The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in compact plant genomes. Because the small genome size of the carnivorous plant Utricularia gibba we investigate the noncoding RNA landscape and global DNA methylation in a compact genome. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of noncoding RNAs and reduced global DNA methylation levels, as determined by a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, reduced DNA methylation correlates with lack of a functional RdDM pathway, as U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs lost key domains required for complete function. Our findings unveil that lack of a functional DCL3 in U. gibba correlates with a decreased proportion of 24-nt small-interfering RNAs, low genome methylation levels, and developmental abnormalities during female gametogenesis that are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of apomixis in compact genomes.

scholarly journals Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sergio Alan Cervantes-Pérez ◽  
Lenin Yong-Villalobos ◽  
Nathalia M. V. Florez-Zapata ◽  
Araceli Oropeza-Aburto ◽  
Félix Rico-Reséndiz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Initial Step ◽  
Carnivorous Plant ◽  
Small Interfering Rnas ◽  
Developmental Abnormalities ◽  
Utricularia Gibba ◽  
The Impact ◽  
Female Gametogenesis

AbstractThe most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.

scholarly journals DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

2015 ◽  
Vol 112 (3) ◽  
pp. 911-916 ◽  
Author(s):  
Xuehua Zhong ◽  
Christopher J. Hale ◽  
Minh Nguyen ◽  
Israel Ausin ◽  
Martin Groth ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Noncoding Rna ◽  
Dna Methyltransferase ◽  
Transcript Abundance ◽  
Transcriptional Elongation ◽  
Rna Transcripts ◽  
Pol V ◽  
Genome Defense ◽  
Eukaryotic Organisms

DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase DOMAINS REARRANGED METHYLASE 2 (DRM2) controls RNA-directed DNA methylation in a pathway that also involves the plant-specific RNA Polymerase V (Pol V). Additionally, the Arabidopsis genome encodes an evolutionarily conserved but catalytically inactive DNA methyltransferase, DRM3. Here, we show that DRM3 has moderate effects on global DNA methylation and small RNA abundance and that DRM3 physically interacts with Pol V. In Arabidopsis drm3 mutants, we observe a lower level of Pol V-dependent noncoding RNA transcripts even though Pol V chromatin occupancy is increased at many sites in the genome. These findings suggest that DRM3 acts to promote Pol V transcriptional elongation or assist in the stabilization of Pol V transcripts. This work sheds further light on the mechanism by which long noncoding RNAs facilitate RNA-directed DNA methylation.

scholarly journals An siRNA-guided Argonaute protein directs RNA Polymerase V to initiate DNA methylation

2021 ◽  
Author(s):  
Meredith J Sigman ◽  
Kaushik Panda ◽  
Rachel Kirchner ◽  
Lauren L McLain ◽  
Hayden Payne ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Argonaute Protein ◽  
Unanswered Question ◽  
Small Interfering Rnas ◽  
Pol V ◽  
Target Locus ◽  
Target Sites ◽  
Foreign Dna ◽  
Epigenetic Repression

In mammals and plants, cytosine DNA methylation is essential for the epigenetic repression of transposable elements and foreign DNA. In plants, DNA methylation is guided by small interfering RNAs (siRNAs) in a self-reinforcing cycle termed RNA-directed DNA methylation (RdDM). RdDM requires the specialized RNA Polymerase V (Pol V), and the key unanswered question is how Pol V is first recruited to new target sites without preexisting DNA methylation. We find that Pol V follows and is dependent upon the recruitment of an AGO4-clade ARGONAUTE protein, and any siRNA can guide the ARGONAUTE protein to the new target locus independent of preexisting DNA methylation. These findings reject long-standing models of RdDM initiation and instead demonstrate that siRNA-guided ARGONAUTE targeting is necessary, sufficient and first to target Pol V recruitment and trigger the cycle of RdDM at a transcribed target locus, thereby establishing epigenetic silencing.

scholarly journals An siRNA-guided ARGONAUTE protein directs RNA polymerase V to initiate DNA methylation

Nature Plants ◽  
2021 ◽  
Author(s):  
Meredith J. Sigman ◽  
Kaushik Panda ◽  
Rachel Kirchner ◽  
Lauren L. McLain ◽  
Hayden Payne ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Argonaute Protein ◽  
Unanswered Question ◽  
Small Interfering Rnas ◽  
Pol V ◽  
Target Locus ◽  
Target Sites ◽  
Foreign Dna ◽  
Epigenetic Repression

AbstractIn mammals and plants, cytosine DNA methylation is essential for the epigenetic repression of transposable elements and foreign DNA. In plants, DNA methylation is guided by small interfering RNAs (siRNAs) in a self-reinforcing cycle termed RNA-directed DNA methylation (RdDM). RdDM requires the specialized RNA polymerase V (Pol V), and the key unanswered question is how Pol V is first recruited to new target sites without pre-existing DNA methylation. We find that Pol V follows and is dependent on the recruitment of an AGO4-clade ARGONAUTE protein, and any siRNA can guide the ARGONAUTE protein to the new target locus independent of pre-existing DNA methylation. These findings reject long-standing models of RdDM initiation and instead demonstrate that siRNA-guided ARGONAUTE targeting is necessary, sufficient and first to target Pol V recruitment and trigger the cycle of RdDM at a transcribed target locus, thereby establishing epigenetic silencing.

scholarly journals Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus

Science ◽  
2011 ◽  
Vol 332 (6031) ◽  
pp. 848-852 ◽  
Author(s):  
T. Watanabe ◽  
S.-i. Tomizawa ◽  
K. Mitsuya ◽  
Y. Totoki ◽  
Y. Yamamoto ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Noncoding Rna ◽  
De Novo

scholarly journals Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Todd Blevins ◽  
Ram Podicheti ◽  
Vibhor Mishra ◽  
Michelle Marasco ◽  
Jing Wang ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Cytosine Methylation ◽  
De Novo ◽  
Transferase Activity ◽  
Small Interfering Rnas ◽  
Pol Iv ◽  
Nuclear Rna ◽  
Rna Polymerase Iv ◽  
Nuclear Rna Polymerase

In Arabidopsis thaliana, abundant 24 nucleotide small interfering RNAs (24 nt siRNA) guide the cytosine methylation and silencing of transposons and a subset of genes. 24 nt siRNA biogenesis requires nuclear RNA polymerase IV (Pol IV), RNA-dependent RNA polymerase 2 (RDR2) and DICER-like 3 (DCL3). However, siRNA precursors are mostly undefined. We identified Pol IV and RDR2-dependent RNAs (P4R2 RNAs) that accumulate in dcl3 mutants and are diced into 24 nt RNAs by DCL3 in vitro. P4R2 RNAs are mostly 26-45 nt and initiate with a purine adjacent to a pyrimidine, characteristics shared by Pol IV transcripts generated in vitro. RDR2 terminal transferase activity, also demonstrated in vitro, may account for occasional non-templated nucleotides at P4R2 RNA 3’ termini. The 24 nt siRNAs primarily correspond to the 5’ or 3’ ends of P4R2 RNAs, suggesting a model whereby siRNAs are generated from either end of P4R2 duplexes by single dicing events.

scholarly journals DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling

PLoS Genetics ◽  
2011 ◽  
Vol 7 (8) ◽  
pp. e1002243 ◽  
Author(s):  
Wei Li ◽  
Hui Liu ◽  
Zhi Juan Cheng ◽  
Ying Hua Su ◽  
Hua Nan Han ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Histone Modifications ◽  
Shoot Regeneration ◽  
De Novo ◽  
Auxin Signaling

Dynamics in the expression of epigenetic modifiers and histone modifications in perinatal rat germ cells during de novo DNA methylation†

2020 ◽  
Author(s):  
Arlette Rwigemera ◽  
Rhizlane El omri-Charai ◽  
Laetitia L Lecante ◽  
Geraldine Delbes
Keyword(s):  
Dna Methylation ◽  
Germ Cell ◽  
Histone Modifications ◽  
Germ Cells ◽  
Posttranslational Modifications ◽  
Fluorescent Protein ◽  
De Novo ◽  
Expression Patterns ◽  
Dna Methyltransferases ◽  
Epigenetic Modifiers

Abstract Epigenetic reprogramming during perinatal germ cell development is essential for genomic imprinting and cell differentiation; however, the actors of this key event and their dynamics are poorly understood in rats. Our study aimed to characterize the expression patterns of epigenetic modifiers and the changes in histone modifications in rat gonocytes at the time of de novo DNA methylation. Using transgenic rats expressing Green Fluorescent Protein (GFP) specifically in germ cells, we purified male gonocytes by fluorescent activated cell sorting at various stages of perinatal development and established the transcriptomic profile of 165 epigenetic regulators. Using immunofluorescence on gonad sections, we tracked six histone modifications in rat male and female perinatal germ cells over time, including methylation of histone H3 on lysines 27, 9, and 4; ubiquitination of histone H2A on lysine119; and acetylation of histone H2B on lysine 20. The results revealed the dynamics in the expression of ten-eleven translocation enzymes and DNA methyltransferases in male gonocytes at the time of de novo DNA methylation. Moreover, our transcriptomic data indicate a decrease in histone ubiquitination and methylation coinciding with the beginning of de novo DNA methylation. Decreases in H2AK119Ub and H3K27me3 were further confirmed by immunofluorescence in the male germ cells but were not consistent for all H3 methylation sites examined. Together, our data highlighted transient chromatin remodeling involving histone modifications during de novo DNA methylation. Further studies addressing how these dynamic changes in histone posttranslational modifications could guide de novo DNA methylation will help explain the complex establishment of the male germ cell epigenome.

scholarly journals Metagenomic Noncoding RNA Profiling and Biomarker Discovery

2020 ◽  
Author(s):  
Ben Liu ◽  
Sirisha Thippabhotla ◽  
Jun Zhang ◽  
Cuncong Zhong
Keyword(s):  
Gut Microbiome ◽  
Noncoding Rna ◽  
Biomarker Discovery ◽  
Gene Expression Regulation ◽  
De Novo ◽  
Structural Information ◽  
Noncoding Rnas ◽  
Homology Search ◽  
Metagenomic Sequencing ◽  
Homology Detection

AbstractNoncoding RNA plays important regulatory and functional roles in microorganisms, such as gene expression regulation, signaling, protein synthesis, and RNA processing. Given its essential role in microbial physiology, it is natural to question whether we can use noncoding RNAs as biomarkers to distinguish among environments under different biological conditions, such as those between healthy versus disease status. The current metagenomic sequencing technology primarily generates short reads, which contain incomplete structural information that may complicate noncoding RNA homology detection. On the other hand, de novo assembly of the metagenomics sequencing data remains fragmentary and has a risk of missing low-abundant noncoding RNAs. To tackle these challenges, we have developed DRAGoM (Detection of RNA using Assembly Graph from Metagenomics data), a novel noncoding RNA homology search algorithm. DRAGoM operates on a metagenome assembly graph, rather than on unassembled reads or assembled contigs. Our benchmark experiments show DRAGoM’s improved performance and robustness over the traditional approaches. We have further demonstrated DRAGoM’s real-world applications in disease characterization via analyzing a real case-control gut microbiome dataset for Type-2 diabetes (T2D). DRAGoM revealed potential ncRNA biomarkers that can clearly separate the T2D gut microbiome from those of healthy controls. DRAGoM is freely available from https://github.com/benliu5085/DRAGoM.

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