The cytological and molecular role of DOMAINS REARRANGED METHYLTRANSFERASE3 in RNA-dependent DNA methylation of Arabidopsis thaliana

Costa‐Nunes, Pedro; Kim, Ji Young; Hong, Evelyn; Pontes, Olga

doi:10.1186/1756-0500-7-721

Cited by 14 publications

(19 citation statements)

References 49 publications

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“…In addition to the aforementioned major players that regulate Pol V recruitment, several other RdDM components have also been shown to play more modest roles in association with Pol V function, including SU(VAR)3-9-RELATED PROTEIN 2 (SUVR2) [89,90], DOMAINS REARRANGED METHYLTRANSFERASE 3 (DRM3) [91–93], CHROMATIN REMODELING 27 (CHR27) and CHR28 (a.k.a. SNF2-RING-HELICASE LIKE 1 (FRG1) and FRG2) [89,94].…”

Section: Association Of Pol IV and Pol V With Chromatinmentioning

confidence: 99%

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

Zhou

Law

2015

Current Opinion in Plant Biology

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Noncoding RNAs regulate gene expression at both the transcriptional and post-transcriptional levels, and play critical roles in development, imprinting and the maintenance of genome integrity in eukaryotic organisms [1–3]. Therefore, it is important to understand how the production of such RNAs are controlled. In addition to the three canonical DNA dependent RNA polymerases (Pol) Pol I, II and III, two non-redundant plant-specific RNA polymerases, Pol IV and Pol V, have been identified and shown to generate noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway. Thus, somewhat paradoxically, transcription is required for gene silencing. This paradox extends beyond plants, as silencing pathways in yeast, fungi, flies, worms, and mammals also require transcriptional machinery [4,5]. As plants have evolved specialized RNA polymerases to carry out gene silencing in a manner that is separate from the essential roles of Pol II, their characterization offers unique insight into how RNA polymerases facilitate gene silencing. In this review, we focus on the mechanisms of Pol IV and Pol V function, including their compositions, their transcripts, and their modes of recruitment to chromatin.

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Section: Association Of Pol IV and Pol V With Chromatinmentioning

confidence: 99%

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

Zhou

Law

2015

Current Opinion in Plant Biology

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“…Although there are hundreds to thousands of rDNA units per genome, not all rRNA genes undergo transcription. The excess of rDNA units bears epigenetic modifications that are characteristic of heterochromatin and that stay transcriptionally silent (Bockor et al, 2014;Costa-Nunes et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum

et al. 2020

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Summary Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse‐transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S‐genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D‐genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.

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“…DRM2 is responsible for de novo methylation at all sites [ 55 , 56 ] and CMT2 has a clear-cut preference for asymmetric CHH sites [ 57 ]. DRM3 is likely to target- or chromatin context-dependent, and most likely functions exclusively with DRM2 in RNA-directed DNA methylation [ 58 ]. CMT3 is plant-specific DNA methyltransferase maintenance methylation of symmetric CHG sites and participates in CHH site methylation [ 55 , 59 , 60 ].…”

Section: Discussionmentioning

confidence: 99%

Plant DNA methylation is sensitive to parent seed N content and influences the growth of rice

Fan

Liu²,

Qian

et al. 2021

BMC Plant Biol

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Background Nitrogen (N) is an important nutrient for plant growth, development, and agricultural production. Nitrogen stress could induce epigenetic changes in plants. In our research, overexpression of the OsNAR2.1 line was used as a testing target in rice plants with high nitrogen-use efficiency to study the changes of rice methylation and growth in respond of the endogenous and external nitrogen stress. Results Our results showed that external N deficiency could decrease seed N content and plant growth of the overexpression line. During the filial growth, we found that the low parent seed nitrogen (LPSN) in the overexpression line could lead to a decrease in the filial seed nitrogen content, total plant nitrogen content, yield, and OsNAR2.1 expression (28, 35, 23, and 55%, respectively) compared with high parent seed nitrogen (HPSN) in high nitrogen external supply. However, such decreases were not observed in wild type. Furthermore, methylation sequencing results showed that LPSN caused massive gene methylation changes, which enriched in over 20 GO pathways in the filial overexpression line, and the expression of OsNAR2.1 in LPSN filial overexpression plants was significantly reduced compared to HPSN filial plants in high external N, which was not shown in wild type. Conclusions We suggest that the parent seed nitrogen content decreased induced DNA methylation changes at the epigenetic level and significantly decreased the expression of OsNAR2.1, resulting in a heritable phenotype of N deficiency over two generations of the overexpression line.

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The cytological and molecular role of DOMAINS REARRANGED METHYLTRANSFERASE3 in RNA-dependent DNA methylation of Arabidopsis thaliana

Cited by 14 publications

References 49 publications

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum

Plant DNA methylation is sensitive to parent seed N content and influences the growth of rice

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