A Link Between mRNA Turnover and RNA Interference in
            <i>Arabidopsis</i>

Gazzani, Silvia Eleonora; Lawrenson, Tom; Woodward, Claire; Headon, Denis J.; Sablowski, Robert

doi:10.1126/science.1101092

Cited by 297 publications

(282 citation statements)

References 27 publications

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“…This is also consistent with AGO4's capacity to slice RNA (15), and decapped RNA serving as a substrate for RDR6 to induce RNA silencing (37). In this scenario, the Pol IVa-RDR2-DCL3-AGO4 pathway precedes the RDR6/DCL4 production of 21-nt siRNAs, and provides the prediction that 24-nt but not 21-nt siRNAs, should be present in rdr6 scions grafted on S2 rootstocks.…”

Section: Nuclear Gene Silencing Directs Reception Of Mrna Silencing Isupporting

confidence: 56%

“…The presence of only P-specific siRNAs in S1-or S2-silenced scions (Fig. 1c) suggests that the initiation of silencing via the Pol IVa-RDR2-DCL3-AGO4 pathway could result in the production of a decapped RNA substrate (37)(38)(39) for the amplification of P-specific dsRNA. In an effort to identify decapped RNAs, we performed 5Ј-RACE on RNA extracted from S2-silenced scions (Fig.…”

Section: Nuclear Gene Silencing Directs Reception Of Mrna Silencing Imentioning

confidence: 99%

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Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

Brosnan

Mitter

Christie

et al. 2007

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

218

292

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In plants, silencing of mRNA can be transmitted from cell to cell and also over longer distances from roots to shoots. To investigate the long-distance mechanism, WT and mutant shoots were grafted onto roots silenced for an mRNA. We show that three genes involved in a chromatin silencing pathway, NRPD1a encoding RNA polymerase IVa, RNA-dependent RNA polymerase 2 (RDR2), and DICER-like 3 (DCL3), are required for reception of long-distance mRNA silencing in the shoot. A mutant representing a fourth gene in the pathway, argonaute4 (ago4), was also partially compromised in the reception of silencing. This pathway produces 24-nt siRNAs and resulted in decapped RNA, a known substrate for amplification of dsRNA by RDR6. Activation of silencing in grafted shoots depended on RDR6, but no 24-nt siRNAs were detected in mutant rdr6 shoots, indicating that RDR6 also plays a role in initial signal perception. After amplification of decapped transcripts, DCL4 and DCL2 act hierarchically as they do in antiviral resistance to produce 21-and 22-nt siRNAs, respectively, and these guide mRNA degradation. Several dcl genotypes were also tested for their capacity to transmit the mobile silencing signal from the rootstock. dcl1-8 and a dcl2 dcl3 dcl4 triple mutant are compromised in micro-RNA and siRNA biogenesis, respectively, but were unaffected in signal transmission.epigenetics ͉ long-distance signaling ͉ RNA interference

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Section: Nuclear Gene Silencing Directs Reception Of Mrna Silencing Isupporting

confidence: 56%

Section: Nuclear Gene Silencing Directs Reception Of Mrna Silencing Imentioning

confidence: 99%

Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

Brosnan

Mitter

Christie

et al. 2007

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

218

292

View full text Add to dashboard Cite

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“…In animals, some of these complexes are associated with components of the RNA silencing machinery (Leung et al, 2006), and there is evidence that Drosophila P-bodies are involved in miRNA-directed target decay through deadenylation and decapping, whereas translational repression is P-body independent (Eulalio et al, 2007). In plants, components of the RNA decapping machinery were found involved in RNA silencing (Gazzani et al, 2004;Gy et al, 2007), and the existence of P-bodies was recently demonstrated (Xu et al, 2006). Thus, it will be interesting to investigate which type of proteins, such as other members of the large AGO family, are linked to miRNAs and their mRNA targets in nonpolysomal fractions.…”

Section: Discussionmentioning

confidence: 99%

Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs

et al. 2009

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MicroRNAs (miRNAs) regulate gene expression posttranscriptionally through RNA silencing, a mechanism conserved in eukaryotes. Prevailing models entail most animal miRNAs affecting gene expression by blocking mRNA translation and most plant miRNAs, triggering mRNA cleavage. Here, using polysome fractionation in Arabidopsis thaliana, we found that a portion of mature miRNAs and ARGONAUTE1 (AGO1) is associated with polysomes, likely through their mRNA target. We observed enhanced accumulation of several distinct miRNA targets at both the mRNA and protein levels in an ago1 hypomorphic mutant. By contrast, translational repression, but not cleavage, persisted in transgenic plants expressing the slicing-inhibitor 2b protein from Cucumber mosaic virus. In agreement, we found that the polysome association of miR168 was lost in ago1 but maintained in 2b plants, indicating that translational repression is correlated with the presence of miRNAs and AGO1 in polysomes. This work provides direct biochemical evidence for a translational component in the plant miRNA pathway.

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“…In general, uncapped fragments derived from mRNAs in eukaryotic transcriptomes are generated by decapping or endonucleolytic cleavage, and these RNA fragments are then rapidly recognized and degraded by 59 to 39 (e.g., XRN4) (Gazzani et al, 2004) and 39 to 59 (e.g., exosome) (Chekanova et al, 2007) exonucleases. Thus, they represent the degrading fraction of the transcriptome.…”

Section: Resultsmentioning

confidence: 99%

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

et al. 2015

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Posttranscriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as tRNAs, growing evidence indicates that mRNAs and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our highthroughput annotation of modified ribonucleotides (HAMR) pipeline to identify and classify modifications that affect WatsonCrick base pairing at three different levels of the Arabidopsis thaliana transcriptome (polyadenylated, small, and degrading RNAs). We find this type of modifications primarily within uncapped, degrading mRNAs and lncRNAs, suggesting they are the cause or consequence of RNA turnover. Additionally, modifications within stable mRNAs tend to occur in alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis across multiple RNA classes yields insights into the functions of covalent RNA modifications in plant transcriptomes.

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A Link Between mRNA Turnover and RNA Interference in Arabidopsis

Cited by 297 publications

References 27 publications

Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

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