Silencing signals in plants: a long journey for small RNAs
© BioMed Central Ltd. 2011
Published: 11 January 2011
Recent research shows that short RNA molecules act as mobile signals that direct mRNA cleavage and DNA methylation in recipient cells.
RNA silencing is a nucleotide-sequence-specific gene regulation mechanism that controls development, maintains heterochromatin and defends many eukaryotic organisms against viruses. It is a non-cell-autonomous process in flowering plants and in nematodes. In plants, RNA silencing generates a signal that spreads from the site of initiation to neighboring cells through channels called plasmodesmata that allow direct communication of molecules between adjacent plant cells. RNA silencing also spreads systemically over long distances through the phloem tissue, which translocates metabolites. Mobile silencing operates in a nucleotide-sequence-specific manner, which is consistent with the signal including an RNA component. However, until recently the identity of the mobile RNA species that silences gene expression was unknown. Recent research has conclusively shown that small non-coding RNA molecules (sRNA, which are 21 to 24 nucleotides (nt) in length) are components of mobile silencing. Here we review the genes and RNA molecules associated with mobile RNA silencing and discuss the implications and future directions of this recently discovered phenomenon.
RNA silencing in plants
sRNAs are generated from partially or perfectly double-stranded RNA (dsRNA) precursors by an RNase III-like nuclease called Dicer or Dicer-like (DCL). They are incorporated into another nuclease named Argonaute (AGO) and they use Watson-Crick base-pairing to guide the AGO complex to target nucleic acids. The targeting mechanism involves transcriptional regulation (DNA/histone methylation) or post-transcriptional regulation (mRNA cleavage/destabilization or translational inhibition) of the target sequence . In some eukaryotes, including plants, RNA-dependent RNA polymerases (RDRs) can convert the targeted mRNAs into dsRNAs. As this process generates further substrates for DCL processing, RDRs have a vital role in the amplification of silencing RNAs and the production of secondary sRNAs .
In eukaryotic lineages the gene families encoding the core components of RNA silencing (DCLs, AGOs and RDRs) have expanded so that there are diversified silencing pathways that control the expression of endogenous genes, repeated sequences, transgenes and viruses . The model plant Arabidopsis thaliana (thale cress) has four DCL proteins and ten AGO paralogs, which have distinct roles in a broad spectrum of endogenous RNA silencing pathways [4, 5].
In some instances there is a crosstalk between the different RNA silencing pathways. For example, 22-nt miRNAs can initiate the production of tasiRNAs [16, 17]. In addition, siRNAs derived from perfect dsRNA can trigger secondary 24-nt siRNA production via the POL IV-RDR2-DCL3 pathway (Figure 1) .
Spreading of RNA silencing
Almost a century ago, Wingard  described a phenomenon in virus-infected plants that can now be explained through movement of the silencing signal. He found that lower leaves of tobacco plants infected with the tobacco ringspot virus showed strong symptoms of infection but the upper leaves remained asymptomatic and became resistant to subsequent infection with the same virus . We now understand that this effect probably occurs because a mobile signal can move from the site of virus infection to distant tissues and can confer nucleotide-sequence-specific resistance.
Experiments in the 1990s showed that spatial spreading of RNA silencing occurs in plants expressing chitinase [20, 21], SAM synthase , nitrate reductase and nitrite reductase  transgenes. Systemic (long-distance) transmission of post-transcriptional gene silencing was revealed by a grafting experiment in which silencing of a nitrate reductase or nitrite reductase and/or a transgene encoding glucuronidase was transmitted from silenced rootstocks to non-silenced scions . A similar phenomenon occurred when localized silencing of a green fluorescent protein (GFP) transgene initiated systemic silencing of GFP in transgenic plants [25, 26].
Research in the past decade indicated that movement of silencing over short distances (such as over 10 to 15 cells) [15, 27, 28] is distinct from long-distance transmission between tissues and organs through the phloem [24, 25, 27], because these processes can be selectively inhibited by viral silencing suppressors [27, 28] and by cadmium . These findings suggest that the silencing signal might not be a single molecule and that the production, spread and perception of RNA silencing signal(s) may rely on multiple silencing pathways.
Identifying genes associated with mobile RNA silencing
The SUC-SUL genetic screen [15, 28, 31] also recovered several mutants in the miRNA pathway that showed reduced silencing spread due to the loss or reduced activity of AGO1, DCL1, HEN1 (an sRNA methyltransferase ) and HYL1 (a nuclear dsRNA binding protein ). Intriguingly, the spreading phenotype was sensitive to mutations in RDR2 and NRPD1 (which encodes the largest subunit of POL IV), indicating an unexpected link between the RNA silencing mechanisms associated with spreading and heterochromatin silencing .
Our parallel SUC-PDS mutant screen  also revealed roles for a similar panel of genes in miRNA, tasiRNA and POL-IV-dependent siRNA pathways. In addition, this genetic screen  identified an SNF2-domain-containing protein (CLSY1) implicated in DNA methylation in the POL IV pathway, a THO/TREX complex protein likely to be involved in mRNA export in the tasiRNA pathway and a JmjC-domain-containing histone H3 lysine 4 demethylase (JMJ14) [30, 34, 35]. These proteins were not identified in the SUC-SUL screen . More extensive screening will be needed to analyze the role of CLSY1, THO/TREX complex proteins and JMJ14 in the SUC-SUL system.
However, mutations of DCL3 and AGO4 have revealed an important difference between the SUC-SUL [15, 28, 31] and the SUC-PDS  system. Mutations of these genes in SUC-PDS have an enhanced silencing phenotype , whereas those in SUC-SUL have no effect . This difference can be explained if the SUC-PDS transgene differs from SUC-SUL such that it is subject to self-silencing that is dependent on DCL3 and AGO4. Mutation of these genes would relieve the self-silencing so that greater transcription of the transgene would generate a more abundant dsRNA and silencing signal. This difference in self-silencing between the two transgene systems might be associated with the molecular architecture of the inverted repeat T-DNA constructs (a recombinant transgene cassette used to create transgenic Arabidopsis lines via Agrobacterium-mediated gene transfer). Alternatively, the chromosomal context of the transgene DNA could influence the likelihood of self silencing .
The main conclusion from these genetic screens [15, 28, 30, 31] is that multiple silencing pathways are associated with the mobile silencing phenotypes. These pathways or modules (a set of interacting proteins in the same pathway) might act either in parallel, sequentially or in opposition. The self-silencing pathway in SUC-PDS, for example, acts oppositely to the other modules. The POL IV module (Figure 1d and 2b,c) is likely to act sequentially to other components of the silencing pathways and to be involved in an amplification step. However, the screens do not provide spatial information and the different modules could function in various subcellular compartments or in the cells that either produce or receive the silencing signal. Thus, the POL IV module containing CLSY1, RDR2 and NRPD1 might operate in the nucleus to generate a dsRNA substrate for DCL .
Brosnan et al.  and our group  overcame the lack of spatial information by using grafted plants in which the tissue generating the signal was genetically distinct and physically separated from the recipient tissue. These studies monitored the movement of the signal using a GFP transgene as a reporter of RNA silencing [37, 38]. The results of Brosnan et al.  are partially consistent with the genetic screens showing that the POL IV(NRPD1)-RDR2-DCL3-AGO4 chromatin silencing pathway is required for the reception of long-distance silencing in the scion but not for the transmission of the silencing signal from the rootstock. However, unlike the SUC-SUL and SUC-PDS systems [15, 28, 30, 31], the grafting experiments [37, 38] revealed a requirement for RDR6 in cells that receive the silencing signal, probably as part of an amplification system. The different results from the SUC promoter systems and the grafting approach might be associated with the distinct mechanisms in long- and short-distance silencing signaling referred to earlier. The grafting systems are inevitably dependent on long-distance movement of the silencing signal, whereas the SUC-SUL and SUC-PDS systems might be dependent on short-distance cell-to-cell movement.
The sequential action of the silencing pathway modules in these mobile silencing systems resembles the involvement of multiple Dicers in antiviral defense [8, 39]. A likely scenario is that the antiviral defense also involves the mobile silencing signal, as in Wingard's early experiments , and perhaps that the different Dicers are in silencing modules acting sequentially in different cell types.
RNA species associated with the mobile silencing signal
Mobile RNA silencing is likely to have an RNA component because its effects are nucleotide-sequence-specific. In principle this mobile RNA could be the single-stranded sRNAs (21 to 24 nt), the immediate 21- to 24-nt sRNA precursors that exist in a double-stranded form, the longer dsRNAs that are processed into double-stranded sRNA by DCL, or long single-stranded RNA, but until recently the data were ambiguous.
In the Brosnan et al. GFP system , the long-distance spread of silencing was unaffected by mutations in individual Dicer genes in the silencing source, consistent with long RNAs being the mobile signal. However, Dicer family members are functionally redundant  and, formally, this analysis did not rule out conclusively that sRNAs are the mobile species.
An alternative system that we have recently set up  was based on grafting of wild-type shoots and mutant roots of A. thaliana plants. However, it differed from Brosnan and colleagues' approach  in that it used high-throughput sequencing (a sensitive and direct method) to detect mobile sRNA molecules. Using silencing pathway mutants with defective DCL2, DCL3 and DCL4, the enzymes required for the biogenesis of 22-nt and 24-nt siRNAs, as donor and recipient tissue, we demonstrated that transgene-derived and endogenous 22- to 24-nt siRNAs had moved across the graft union from the wild-type shoot to the mutant root . Most of these mobile sRNAs were of the 24-nt size class that is associated with DNA methylation of targeted loci .
The identification of mobile 24-nt sRNA  is consistent with the analysis of viral suppressors on systemic silencing in Nicotiana benthamiana (a wild tobacco species)  and the presence of 24-nt sRNA in the phloem sap of oilseed rape  and pumpkin . However, this result contrasts with the findings of the Voinnet group , who used the SUC-SUL transgenic system and concluded that 21-nt siRNAs are mobile. Their approach  was based on phloem-cell-specific rescue of DCL4 function and cell-specific inhibition of siRNA movement using the viral silencing suppressor P19, which sequesters 21-bp siRNA duplexes but not their longer dsRNA precursors. They also showed that the mechanically delivered, fluorescently labeled 21-nt and 24-nt siRNAs move from cell to cell and over long distances [43, 44]. Furthermore, the spreading of target gene silencing was associated with the movement of 21-nt siRNAs .
To reconcile these various results, we propose that in addition to multiple size classes of sRNA, sRNA precursors may be mobile and may contribute to the accumulation of newly processed sRNAs in the recipient tissues. Supporting this idea, in grafting experiments using a GFP silenced scion and a root deficient in GFP, we observed an increased abundance of 21-nt GFP sRNAs in wild-type root compared with a triple dcl2,dcl3,dcl4 mutant root that is unable to produce 22- to 24-nt sRNAs and certain 21-nt sRNAs . This observation is consistent with a precursor GFP RNA moving to the root and being acted on by DCL4 in wild-type tissue.
What are the consequences of mobile silencing?
It is likely that the mobile forms of sRNA can direct the same diverse targeting mechanisms as do the non-mobile equivalents. Thus, the mobile 21-nt and 22-nt sRNAs are likely to regulate target gene expression post-transcriptionally via target mRNA cleavage . Consistent with that idea, the physical movement of 21-nt siRNA coincided with the spread of target mRNA (GFP) silencing . The mobile 22-nt sRNAs could induce mRNA cleavage or they could initiate the production of secondary siRNAs in an analogous manner to 22-nt miRNAs [16, 17].
Similarly, the 24-nt sRNAs can direct epigenetic modifications (DNA methylation) in the genome of the recipient cells , as do the non-mobile forms of this RNA [52–55]. However, there is evidence that the movement process is selective. Approximately 35% of sRNA loci produce mobile sRNA in our experimental system, and features of the genomic locus or the precursor molecule from which the sRNA is generated could perhaps determine whether the sRNA is mobile. Indeed, we found  a strong correlation between DNA methylation and the production of mobile sRNAs, consistent with an effect related to the epigenetic status of the locus. At the phosphoribosylanthranilate isomerase (PAI) locus (a natural inverted repeat) there was preferential movement of POL-IV-dependent over POL-IV-independent sRNAs. Features of the different sRNA precursors from loci producing mobile sRNAs or the cell type in which the sRNAs are generated could perhaps determine mobility . Expression of sRNAs in the phloem, for example, is more likely to result in movement than epidermal expression. Channeling of sRNAs into cellular compartments from which extracellular movement might take place could also influence mobility. It is tempting to speculate that the recently discovered 24-nt miRNAs that are processed from miRNA precursors by DCL3 and direct the methylation of complementary DNA sequences  might be mobile and might follow similar spreading characteristics to those associated with mobile 24-nt siRNAs.
The size exclusion limit of plasmodesmata is probably high enough for sRNAs to spread from cell to cell . However, the sensitivity of sRNA molecules to endogenous RNases might suggest that sRNAs move as part of a larger complex that protects them from degradation. We found a strong bias in mobility or stability of the sRNAs towards the coding strand of transgene sRNA and, to a lesser extent, of the mobile PAI sRNAs . There was the same strand bias in the source and recipient tissue. The simplest interpretation of these observations is that the sRNAs move in single-stranded form, potentially associated with AGO or other proteins. By contrast, 21-nt siRNAs were found to move independently of AGO1 in dsRNA form in the SUC-SUL system .
Two independent sets of grafting experiments revealed that mobile sRNAs follow photosynthetic source-sink relationships, that is, that movement is more efficient from the shoot to the root than reciprocally [40, 44]. It is striking that the transgene-derived mobile sRNAs were very rare - as low as 10 parts per million - in the recipient tissues, but that they nevertheless have easily detectable effects . To explain the potency of this effect in the GFP transgene systems, we propose that the mobile sRNA could initiate an amplification process involving RDRs and secondary RNA production in the recipient tissue . Consistent with this idea, wild-type roots containing GFP mRNA accumulated 100-fold more GFP-specific sRNAs than the non-transformed roots deficient in DCL2, DCL3 and DCL4 . Mobile sRNA might also initiate amplification via an epigenetic mark in the meristems (the initiating tissue for new organs in plants, consisting of undifferentiated cells) of recipient roots. Consistent with this idea, silencing of the GFP reporter gene appears first in the lateral roots, which emerge after silencing is initiated by grafting, rather than in the cells immediately adjacent to the graft junction .
Both 21-nt and 24-nt silencing RNAs have the potential to move from cell to cell and over long distances and they can direct mRNA cleavage and DNA methylation in recipient cells. The mobile 24-nt siRNAs associated with epigenetic modifications could have roles in genome defense and in the response to external stimuli as proposed previously for this size class of sRNAs associated with a transposon (Mu) [58, 59] and an inverted repeat (IR71) . For example, these RNAs could be involved in transmitting signals to meristematic tissue to reinforce the epigenetic silencing of transposons, direct- and inverted-repeat DNA sequences. They might also mediate defense against DNA and RNA viruses in a similar manner to that in which RNA signals mediate suppression and meristem exclusion of RNA viruses [38, 60]. In responses to external stimuli, the mobile RNAs could transmit signals to the meristem to initiate epigenetic changes associated with adaptation to these stimuli. Epigenetic marks directed by sRNAs could, for example, be associated with competency to flower or responses to stress, two processes that have been linked to silencing RNAs [61–63]. It is also possible that the RNA silencing signal moves into the developing seed or pollen [46, 64] to induce epigenetic changes that ultimately initiate transgenerational effects to better adapt progeny to future stress . Finally, mobile sRNAs might contribute to copying epigenetic marks from one allele to another.
The mobile sRNA loci identified so far could be used to develop new genetic screens to identify both the function of mobile sRNAs and the genetic factors involved in the mobility and induction of epigenetic changes. Combined with very sensitive high-throughput sequencing of RNA and DNA, this approach could help us to further understand the mobility and biological role of sRNAs and their precursor molecules.
We thank Andrew Bassett for critically reading the manuscript. DCB is a Royal Society Research Professor. CWM is supported by the Natural Sciences and Engineering Research Council of Canada and the Cambridge Commonwealth Trust.
- Ghildiyal M, Zamore PD: Small silencing RNAs: an expanding universe. Nat Rev Genet. 2009, 10: 94-108. 10.1038/nrg2504.PubMedPubMed CentralView ArticleGoogle Scholar
- Voinnet O: Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci. 2008, 13: 317-328. 10.1016/j.tplants.2008.05.004.PubMedView ArticleGoogle Scholar
- Baulcombe D: RNA silencing in plants. Nature. 2004, 431: 356-363. 10.1038/nature02874.PubMedView ArticleGoogle Scholar
- Margis R, Fusaro AF, Smith NA, Curtin SJ, Watson JM, Finnegan EJ, Waterhouse PM: The evolution and diversification of Dicers in plants. FEBS Lett. 2006, 580: 2442-2450. 10.1016/j.febslet.2006.03.072.PubMedView ArticleGoogle Scholar
- Hutvagner G, Simard MJ: Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol. 2008, 9: 22-32. 10.1038/nrm2321.PubMedView ArticleGoogle Scholar
- Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD: A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 2001, 293: 834-838. 10.1126/science.1062961.PubMedView ArticleGoogle Scholar
- Park W, Li J, Song R, Messing J, Chen X: CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol. 2002, 12: 1484-1495. 10.1016/S0960-9822(02)01017-5.PubMedView ArticleGoogle Scholar
- Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O: Hierarchical action and inhibition of plant dicer-like proteins in antiviral defense. Science. 2006, 313: 68-71. 10.1126/science.1128214.PubMedView ArticleGoogle Scholar
- Mlotshwa S, Pruss GJ, Peragine A, Endres MW, Li J, Chen X, Poethig RS, Bowman LH, Vance V: DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis. PLoS ONE. 2008, 3: e1755-10.1371/journal.pone.0001755.PubMedPubMed CentralView ArticleGoogle Scholar
- Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC: Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004, 2: E104-10.1371/journal.pbio.0020104.PubMedPubMed CentralView ArticleGoogle Scholar
- Pontes O, Li CF, Nunes PC, Haag JR, Ream T, Vitins A, Jacobsen SE, Pikaard CS: The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell. 2006, 126: 79-92. 10.1016/j.cell.2006.05.031.PubMedView ArticleGoogle Scholar
- Yoshikawa M, Peragine A, Park MY, Poethig RS: A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 2005, 19: 2164-2175. 10.1101/gad.1352605.PubMedPubMed CentralView ArticleGoogle Scholar
- Allen E, Xie Z, Gustafson AM, Carrington JC: microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell. 2005, 121: 207-221. 10.1016/j.cell.2005.04.004.PubMedView ArticleGoogle Scholar
- Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC: Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell. 2008, 133: 128-141. 10.1016/j.cell.2008.02.033.PubMedView ArticleGoogle Scholar
- Dunoyer P, Himber C, Voinnet O: DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet. 2005, 37: 1356-1360. 10.1038/ng1675.PubMedView ArticleGoogle Scholar
- Chen H-M, Chen L-T, Patel K, Li Y-H, Baulcombe DC, Wu S-H: 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci USA. 2010, 107: 15269-15274. 10.1073/pnas.1001738107.PubMedPubMed CentralView ArticleGoogle Scholar
- Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC: Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol. 2010, 17: 997-1003. 10.1038/nsmb.1866.PubMedPubMed CentralView ArticleGoogle Scholar
- Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJ, Matzke M: A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J. 2009, 28: 48-57. 10.1038/emboj.2008.260.PubMedPubMed CentralView ArticleGoogle Scholar
- Wingard SA: Hosts and symptoms of ring spot, a virus disease of plants. J Agric Res. 1928, 37: 127-153.Google Scholar
- Hart CM, Fischer B, Neuhaus JM, Meins F: Regulated inactivation of homologous gene expression in transgenic Nicotiana sylvestris plants containing a defense-related tobacco chitinase gene. Mol Gen Genet. 1992, 235: 179-188. 10.1007/BF00279359.PubMedView ArticleGoogle Scholar
- Kunz C, Hanspeter S, Stam M, Kooter JM, Meins FJ: Developmentally regulated silencing and reactivation of tobacco chitinase transgene expression. Plant J. 1996, 10: 437-450. 10.1046/j.1365-313X.1996.10030437.x.View ArticleGoogle Scholar
- Boerjan W, Bauw G, Van Montagu M, Inzé D: Distinct phenotypes generated by overexpression and supression of S-adenosyl-L-methionine synthetase reveal developmental patterns of gene silencing in tobacco. Plant Cell. 1994, 6: 1401-1414. 10.1105/tpc.6.10.1401.PubMedPubMed CentralView ArticleGoogle Scholar
- Palauqui JC, De Borne FD, Elmayan T, Crete P, Charles C, Vaucheret H: Frequencies, timing, and spatial patterns of co-suppression of nitrate reductase and nitrite reductase in transgenic tobacco plants. Plant Physiol. 1996, 112: 1447-1456.PubMedPubMed CentralGoogle Scholar
- Palauqui J-C, Elmayan T, Pollien J-M, Vaucheret H: Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO J. 1997, 16: 4738-4745. 10.1093/emboj/16.15.4738.PubMedPubMed CentralView ArticleGoogle Scholar
- Voinnet O, Baulcombe DC: Systemic signalling in gene silencing. Nature. 1997, 389: 553-10.1038/39215.PubMedView ArticleGoogle Scholar
- Voinnet O, Vain P, Angell S, Baulcombe DC: Systemic spread of sequence-specific transgene RNA degradation is initiated by localised introduction of ectopic promoterless DNA. Cell. 1998, 95: 177-187. 10.1016/S0092-8674(00)81749-3.PubMedView ArticleGoogle Scholar
- Hamilton AJ, Voinnet O, Chappell L, Baulcombe DC: Two classes of short interfering RNA in RNA silencing. EMBO J. 2002, 21: 4671-4679. 10.1093/emboj/cdf464.PubMedPubMed CentralView ArticleGoogle Scholar
- Himber C, Dunoyer P, Moissiard G, Ritzenthaler C, Voinnet O: Transitivity-dependent and -independent cell-to-cell movement of RNA silencing. EMBO J. 2003, 22: 4523-4533. 10.1093/emboj/cdg431.PubMedPubMed CentralView ArticleGoogle Scholar
- Ueki S, Citovsky V: Inhibition of systemic onset of post-transcriptional gene silencing by non-toxic concentrations of cadmium. Plant J. 2001, 28: 283-291. 10.1046/j.1365-313X.2001.01145.x.PubMedView ArticleGoogle Scholar
- Smith LM, Pontes O, Searle L, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC: An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell. 2007, 19: 1507-1521. 10.1105/tpc.107.051540.PubMedPubMed CentralView ArticleGoogle Scholar
- Dunoyer P, Himber C, Ruiz-Ferrer V, Alioua A, Voinnet O: Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nat Genet. 2007, 39: 848-856. 10.1038/ng2081.PubMedView ArticleGoogle Scholar
- Yang Z, Ebright YW, Yu B, Chen X: HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res. 2006, 34: 667-675. 10.1093/nar/gkj474.PubMedPubMed CentralView ArticleGoogle Scholar
- Han M-H, Goud S, Song L, Fedoroff N: The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci USA. 2004, 101: 1093-1098. 10.1073/pnas.0307969100.PubMedPubMed CentralView ArticleGoogle Scholar
- Yelina NE, Smith LM, Jones AME, Patel K, Kelly KA, Baulcombe DC: Putative Arabidopsis THO/TREX mRNA export complex is involved in transgene and endogenous siRNA biosynthesis. Proc Natl Acad Sci USA. 2010, 107: 13948-13953. 10.1073/pnas.0911341107.PubMedPubMed CentralView ArticleGoogle Scholar
- Searle IR, Pontes O, Melnyk CW, Smith LM, Baulcombe DC: JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev. 2010, 24: 986-991. 10.1101/gad.579910.PubMedPubMed CentralView ArticleGoogle Scholar
- Smith LM, Baulcombe DC: Dissection of silencing signal movement in Arabidopsis. Plant Signal Behav. 2007, 2: 501-502.PubMedPubMed CentralView ArticleGoogle Scholar
- Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM, Carroll BJ: Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc Natl Acad Sci USA. 2007, 104: 14741-14746. 10.1073/pnas.0706701104.PubMedPubMed CentralView ArticleGoogle Scholar
- Schwach F, Vaistij FE, Jones L, Baulcombe DC: An RNA-dependent RNA-polymerase prevents meristem invasion by Potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiol. 2005, 138: 1842-1852. 10.1104/pp.105.063537.PubMedPubMed CentralView ArticleGoogle Scholar
- Blevins T, Rajeswaran R, Shivaprasad PV, Beknazariants D, Si-Ammour A, Park HS, Vazquez F, Robertson D, Meins F, Hohn T, Pooggin MM: Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res. 2006, 34: 6233-6246. 10.1093/nar/gkl886.PubMedPubMed CentralView ArticleGoogle Scholar
- Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC: Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science. 2010, 328: 872-875. 10.1126/science.1187959.PubMedView ArticleGoogle Scholar
- Buhtz A, Springer F, Chappell L, Baulcombe DC, Kehr J: Identification and characterization of small RNAs from the phloem of Brassica napus. Plant J. 2008, 53: 739-749. 10.1111/j.1365-313X.2007.03368.x.PubMedView ArticleGoogle Scholar
- Yoo B-C, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, Lee YM, Lough TJ, Lucas WJ: A systemic small RNA signaling system in plants. Plant Cell. 2004, 16: 1979-2000. 10.1105/tpc.104.023614.PubMedPubMed CentralView ArticleGoogle Scholar
- Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC, Voinnet O: Small RNA duplexes function as mobile silencing signals between plant cells. Science. 2010, 328: 912-916. 10.1126/science.1185880.PubMedView ArticleGoogle Scholar
- Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, Alioua A, Himber C, Voinnet O: An endogenous, systemic RNAi pathway in plants. EMBO J. 2010, 29: 1699-1712. 10.1038/emboj.2010.65.PubMedPubMed CentralView ArticleGoogle Scholar
- Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D: Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell. 2006, 18: 1121-1133. 10.1105/tpc.105.039834.PubMedPubMed CentralView ArticleGoogle Scholar
- Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA: Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell. 2009, 136: 461-472. 10.1016/j.cell.2008.12.038.PubMedPubMed CentralView ArticleGoogle Scholar
- Pant BD, Buhtz A, Kehr J, Scheible WR: MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J. 2008, 53: 731-738. 10.1111/j.1365-313X.2007.03363.x.PubMedPubMed CentralView ArticleGoogle Scholar
- Carlsbecker A, Lee JY, Roberts CJ, Dettmer J, Lehesranta S, Zhou J, Lindgren O, Moreno-Risueno MA, Vaten A, Thitamadee S, Campilho A, Sebastian J, Bowman JL, Helariutta Y, Benfey PN: Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature. 2010, 465: 316-321. 10.1038/nature08977.PubMedPubMed CentralView ArticleGoogle Scholar
- Schwab R, Maizel A, Ruiz-Ferrer V, Garcia D, Bayer M, Crespi M, Voinnet O, Martienssen RA: Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana. PLoS ONE. 2009, 4: e5980-10.1371/journal.pone.0005980.PubMedPubMed CentralView ArticleGoogle Scholar
- Chitwood DH, Nogueira FTS, Howell MD, Montgomery TA, Carrington JC, Timmermans MCP: Pattern formation via small RNA mobility. Genes Dev. 2009, 23: 549-554. 10.1101/gad.1770009.PubMedPubMed CentralView ArticleGoogle Scholar
- Vazquez F, Legrand S, Windels D: The biosynthetic pathways and biological scopes of plant small RNAs. Trends Plant Sci. 2010, 15: 337-345. 10.1016/j.tplants.2010.04.001.PubMedView ArticleGoogle Scholar
- Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS: Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell. 2005, 120: 613-622. 10.1016/j.cell.2005.02.007.PubMedView ArticleGoogle Scholar
- Herr AJ, Jensen MB, Dalmay T, Baulcombe D: RNA polymerase IV directs silencing of endogenous DNA. Science. 2005, 308: 118-120. 10.1126/science.1106910.PubMedView ArticleGoogle Scholar
- Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE: Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci USA. 2007, 104: 4536-4541. 10.1073/pnas.0611456104.PubMedPubMed CentralView ArticleGoogle Scholar
- Mosher RA, Schwach F, Studhollme D, Baulcombe DC: PolIVb influences RNA-directed DNA-methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA. 2008, 105: 3145-3150. 10.1073/pnas.0709632105.PubMedPubMed CentralView ArticleGoogle Scholar
- Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y: DNA methylation mediated by a microRNA pathway. Mol Cell. 2010, 38: 465-475. 10.1016/j.molcel.2010.03.008.PubMedView ArticleGoogle Scholar
- Mlotshwa S, Voinnet O, Mette MF, Matzke M, Vaucheret H, Ding SW, Pruss G, Vance VB: RNA silencing and the mobile silencing signal. Plant Cell. 2002, 14 (Suppl): S289-S301.PubMedPubMed CentralGoogle Scholar
- Slotkin RK, Freeling M, Lisch D: Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet. 2005, 37: 641-644. 10.1038/ng1576.PubMedView ArticleGoogle Scholar
- Lisch D: Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol. 2009, 60: 43-66. 10.1146/annurev.arplant.59.032607.092744.PubMedView ArticleGoogle Scholar
- Martin-Hernandez AM, Baulcombe DC: Tobacco rattle virus 16-kilodalton protein encodes a suppressor of RNA silencing that allows transient viral entry in meristems. J Virol. 2008, 82: 4064-4071. 10.1128/JVI.02438-07.PubMedPubMed CentralView ArticleGoogle Scholar
- Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu J-K: Endogenous siRNAs derived from a pair of natural cis-Antisense Transcripts regulate salt tolerance in Arabidopsis. Cell. 2005, 123: 1279-1291. 10.1016/j.cell.2005.11.035.PubMedPubMed CentralView ArticleGoogle Scholar
- Baurle I, Smith LMA, Baulcombe DC, Dean C: Widespread role for the flowering time regulators FCA and FPA in siRNA-directed chromatin silencing. Science. 2007, 318: 109-112. 10.1126/science.1146565.PubMedView ArticleGoogle Scholar
- Katiyar-Agarwal S, Morgan RA, Dahlbeck D, Borsani O, Villegas A, Zhu J, Staskawicz BJ, Jin H: A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci USA. 2006, 103: 18002-18007. 10.1073/pnas.0608258103.PubMedPubMed CentralView ArticleGoogle Scholar
- Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC: Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature. 2009, 460: 283-286. 10.1038/nature08084.PubMedView ArticleGoogle Scholar
- Whittle CA, Otto SP, Johnston MO, Krochko JE: Adaptive epigenetic memory of ancestral temperature regime in Arabidopsis thaliana. Botany. 2009, 87: 650-657. 10.1139/B09-030.View ArticleGoogle Scholar