RNA Polymerase V Functions in Arabidopsis Interphase Heterochromatin Organization Independently of the 24-nt siRNA-Directed DNA Methylation Pathway

Pontes, Olga; Costa‐Nunes, Pedro; Vithayathil, Paul J.; Pikaard, Craig S.

doi:10.1093/mp/ssp006

Cited by 69 publications

(56 citation statements)

References 61 publications

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“…We currently do not know how the SUMOylation affects the Pol V functions of protein activity, stability, localization, partner interaction, which in turn mediate the TGS of aberrant genes. Previous reports have demonstrated that Pol V affects heterochromatin organization, which is independent of Pol IV (Douet et al, 2009;Pontes et al, 2009). Our study provides another case that Pol V functions in the regulation of gene expression, which does not rely on Pol IV.…”

Section: Discussionsupporting

confidence: 61%

“…Pol IV collaborating with RDR2 and DCL3 is responsible for 24-nucleotide small-interfering RNA (siRNA) biogenesis, whereas with the help of chromatin-remodeling DDR complex (DRD1, DMS3, and RDM1), Pol V functions to generate scaffold RNAs for guiding sequence-specific DNA methylation by siRNAs (Onodera et al, 2005;Pontier et al, 2005;Wierzbicki et al, 2008;Zhou and Law, 2015). Loss of Pol V or DRD1 disrupts heterochromatin organization during interphase; on the contrary, loss of Pol IV, RDR2, or DCL3 does not (Pontes et al, 2009). Approximately 60% of Pol V-occupied regions overlap with the regions of 24-nucleotide siRNA complementarity and cytosine methylation; however, about one-quarter of Pol V peaks occur at loci (mostly genes) lacking significant cytosine methylation or siRNA signatures (Wierzbicki et al, 2012), indicating that Pol V may not function only in the RdDM pathway in Arabidopsis.…”

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confidence: 99%

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Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway

et al. 2016

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The expression of genes with aberrant structure is prevented at both the transcriptional and posttranscriptional regulation levels. Aberrant gene silencing at the posttranscriptional level is well studied; however, it is not well understood how aberrant genes are silenced at the transcriptional level. In this study, through genetic screening a transgenic report line that harbors an aberrant gene (35S-LUC, lacking 39-untranslated region [39-UTR]) and lacks luciferase (LUC) activity, we identify that the small ubiquitinlike modifier (SUMO) protease OTS1 gene is required for maintaining the silence of the reporter 35S-LUC and an endogenous mutator-like element MULE-F19G14 at the transcriptional level, which requires DNA-dependent RNA polymerase (Pol) V and DDR complex, but not Pol IV. The increased transcripts in ots1 mutants are terminated by the 39-UTRs of downstream genes. In addition to ots1 mutations, mutations in several known or putative SUMO proteases and two SUMO E3 ligases, SIZ1 and MMS21, have similar effects on this silencing regulation. Taken together, our results reveal that the enzymes involved in the SUMOylation process restrain aberrant gene transcription by using a downstream gene 39-UTR, and this regulation requires a functional Pol V-dependent pathway in Arabidopsis (Arabidopsis thaliana).

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Section: Discussionsupporting

confidence: 61%

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confidence: 99%

Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway

et al. 2016

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“…Thus, one possibility is that if we could examine siRNAs and transcription when paramutation is established, we might see a correlation between siRNAs or a larger RNA and establishment of silencing. There is precedence for a role of larger RNAs in silencing in Arabidopsis in that the heterochromatic silencing of certain 5S ribosomal DNA tandem repeats requires Pol V and most likely longer RNAs but not other RdDM components (42)(43)(44).…”

Section: Discussionmentioning

confidence: 99%

RNA-mediated trans -communication can establish paramutation at the b1 locus in maize

Arteaga-Vázquez

Сидоренко

Rabanal

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Paramutation is the epigenetic transfer of information between alleles that leads to the heritable change of expression of one allele. Paramutation at the b1 locus in maize requires seven noncoding tandem repeat (b1TR) sequences located ∼100 kb upstream of the transcription start site of b1, and mutations in several genes required for paramutation implicate an RNA-mediated mechanism. The mediator of paramutation (mop1) gene, which encodes a protein closely related to RNA-dependent RNA polymerases, is absolutely required for paramutation. Herein, we investigate the potential function of mop1 and the siRNAs that are produced from the b1TR sequences. Production of siRNAs from the b1TR sequences depends on a functional mop1 gene, but transcription of the repeats is not dependent on mop1. Further nuclear transcription assays suggest that the b1TR sequences are likely transcribed predominantly by RNA polymerase II. To address whether production of b1TR-siRNAs correlated with paramutation, we examined siRNA production in alleles that cannot undergo paramutation. Alleles that cannot participate in paramutation also produce b1TR-siRNAs, suggesting that b1TR-siRNAs are not sufficient for paramutation in the tissues analyzed. However, when b1TR-siRNAs are produced from a transgene expressing a hairpin RNA, b1 paramutation can be recapitulated. We hypothesize that either the b1TR-siRNAs or the dsRNA template mediates the trans-communication between the alleles that establishes paramutation. In addition, we uncovered a role for mop1 in the biogenesis of a subset of microRNAs (miRNAs) and show that it functions at the level of production of the primary miRNA transcripts.interchromosomal | transfer | epigenetic | information | trans-generational

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“…In addition, Pol V also mediates RdDM-independent silencing at pericentromeric repeats (Douet et al 2009;Pontes et al 2009). It was unknown how broadly Pol V is needed across the whole genome.…”

Section: Genome-wide Examination Of the Rddm Modelmentioning

confidence: 99%

Seeing the forest for the trees: a wide perspective on RNA-directed DNA methylation: Figure 1.

Zhang

Zhu

2012

Genes Dev.

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In this issue of Genes & Development, Wierzbicki and colleagues (pp. 1825-1836) examine the current model of RNA-directed DNA methylation (RdDM) by determining genome-wide distributions of RNA polymerase V (Pol V) occupancy, siRNAs, and DNA methylation. Their data support the key role of base-pairing between Pol V transcripts and siRNAs in targeting de novo DNA methylation. Importantly, the study also reveals unexpected complexity and provides a global view of the RdDM pathway.DNA methylation at the fifth position of cytosine regulates many critical biological processes, such as gene imprinting, silencing of transposable elements, and X-chromosome inactivation. In Arabidopsis, the DNA methyltransferase DRM2 (domains rearranged methyltransferase 2) catalyzes de novo methylation in all cytosine contexts, including CG, CHG, and CHH (H represents either A, T, or G) (Cao and Jacobsen 2002). The targeting of DRM2 for DNA methylation can be achieved by the RNA-directed DNA methylation (RdDM) pathway that consists of three phases: biogenesis of 24-nucleotide (nt) siRNAs, production of scaffold RNAs, and recruitment of DRM2 assisted by complementary pairing between 24-nt siRNAs and nascent scaffold RNAs. RNA polymerases in the RdDM pathwayIn the RdDM pathway, transcription of the noncoding RNAs involves three DNA-dependent RNA polymerases: Pol II, Pol IV, and Pol V. Arabidopsis Pol IV and Pol V are plant-specific RNA polymerases, each of which contains 12 subunits ). While six of these 12 subunits are identical among Pol IV, Pol V, and Pol II, the remaining subunits of Pol IV and/or Pol V are different but have apparently evolved from their paralogs in Pol II ). NRPD1 and NRPE1 are the unique and largest subunits of Pol IV and Pol V, respectively. Mutation in NRPD1 or NRPD/E2, which is the second largest subunit shared by Pol IV and Pol V, resulted in >90% reduction of 24-nt siRNA accumulation (Zhang et al. 2007;Mosher et al. 2008), thereby demonstrating a predominant role of Pol IV in generating 24-nt siRNAs. Although Pol IV transcripts remain to be identified, Pol IV has been thought to initiate siRNA production by generating an aberrant ssRNA, which is subsequently copied by RDR2 (RNA-dependent RNA polymerase 2) to produce dsRNAs that are cleaved by DCL3 (dicer-like 3) and then loaded onto AGO4 (argonaute 4) or its closely related argonaute proteins Haag and Pikaard 2011;Zhang and Zhu 2011). These argonaute-bound 24-nt siRNAs can then serve as sequencespecific guides for methylation by pairing with complementary DNA or nascent scaffold RNA. AGO4 can be cross-linked to scaffold RNAs, supporting the model of siRNA-scaffold RNA pairing ).Production of scaffold RNA is independent of siRNA biogenesis, as shown in Arabidopsis mutants defective in NRPD1, RDR2, or DCL3 (Wierzbicki et al. 2008). Wierzbicki et al. (2008) previously demonstrated that Pol V is necessary for scaffold RNA production. In addition to generating scaffold RNAs, Pol V can reinforce siRNA production at some RdDM target loci (Zhang et al. 2007;Mosher et a...

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RNA Polymerase V Functions in Arabidopsis Interphase Heterochromatin Organization Independently of the 24-nt siRNA-Directed DNA Methylation Pathway

Cited by 69 publications

References 61 publications

Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway

Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway

RNA-mediated trans -communication can establish paramutation at the b1 locus in maize

Seeing the forest for the trees: a wide perspective on RNA-directed DNA methylation: Figure 1.

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