<i>ARGONAUTE4</i>
            Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation

Zilberman, Daniel; Cao, Xiaofeng; Jacobsen, Steven E.

doi:10.1126/science.1079695

Cited by 945 publications

(769 citation statements)

References 20 publications

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“…Archaeplastida Chlamydomonas reinhardtii Rohr et al (2004) and Schroda (2006) Arabidopsis thaliana Llave et al (2002) and and Watson et al (2005) Direct b Matzke and Birchler (2005) and Zilberman et al (2003) Chan et al (2004) and Matzke and Birchler (2005) Chen ( Aspergillus nidulans Hammond and Keller (2005) among the RNAi-positive organisms listed in Table 1 is Giardia intestinalis that encodes a protein with a well-defined PIWI domain fused to a highly divergent PAZ domain. However, Giardia protein-encoding genes are notoriously fast-evolving compared with those of most other eukaryotes (Richards and Cavalier-Smith 2005), which might explain the poor conservation of the PAZ domain.…”

Section: Phytophthora Infestansmentioning

confidence: 99%

“…In plants, specific members of the Argonaute subfamily also show distinct activities. Arabidopsis Ago4 has been implicated in DNA and histone methylation whereas Ago1 is an RNA slicer and much more pleotropic in its functions (Baumberger and Baulcombe 2005;Matzke and Birchler 2005;Qi et al 2005;Zilberman et al 2003). Interestingly, in organisms that encode a single Ago-Piwi protein, such as S. pombe and T. brucei, its mutation results in defects in both transcriptional and post-transcriptional silencing (Shi et al 2004;Sigova et al 2004).…”

Section: Nature Of the Ancestral Rnai Machinerymentioning

confidence: 99%

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On the origin and functions of RNA-mediated silencing: from protists to man

2006

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Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways. We have examined the taxonomic distribution and the phylogenetic relationship of key components of the RNA interference (RNAi) machinery in members of five eukaryotic supergroups. On the basis of the parsimony principle, our analyses suggest that a relatively complex RNAi machinery was already present in the last common ancestor of eukaryotes and consisted, at a minimum, of one Argonautelike polypeptide, one Piwi-like protein, one Dicer, and one RNAdependent RNA polymerase. As proposed before, the ancestral (but non-essential) role of these components may have been in defense responses against genomic parasites such as transposable elements and viruses. From a mechanistic perspective, the RNAi machinery in the eukaryotic ancestor may have been capable of both small-RNA-guided transcript degradation as well as transcriptional repression, most likely through histone modifications. Both roles appear to be widespread among living eukaryotes and this diversification of function could account for the evolutionary conservation of duplicated Argonaute-Piwi proteins. In contrast, additional RNAi-mediated pathways such as RNA-directed DNA methylation, programmed genome rearrangements, meiotic silencing by unpaired DNA, and miRNA-mediated gene regulation may have evolved independently in specific lineages.

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Section: Phytophthora Infestansmentioning

confidence: 99%

Section: Nature Of the Ancestral Rnai Machinerymentioning

confidence: 99%

On the origin and functions of RNA-mediated silencing: from protists to man

2006

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“…The involvement of RISC in this pathway is suggested by the requirement for argonaute family members. For example, in Arabidopsis, mutant argonaute 4 protein diminishes methylation of the gene SUPERMAN, which defines boundaries between carpels and stamens 13,37 .…”

Section: Rna-directed Dna Read-outmentioning

confidence: 99%

The four Rs of RNA-directed evolution

Herbert

2003

Nat Genet

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The read-out of genetic information in eukaryotes is not only more complex than previously realized, but also more dynamic. Much of the information is 'soft-wired' , with extensive RNA processing necessary to generate phenotypes 10 . A subset of the RNA, referred to here as coRNA ( Fig. 1), coordinates the read-out of genetic information and reconciles regulatory inputs. For each cell type, the sum of these interactions defines a distinct RNA profile or ribotype 10 . RNA-based processes also facilitate replication of ribotypes in subsequent generations. The flexibility of these programs allows soft-wired organisms to evolve in a more rapid and dynamic way than 'hard-wired' organisms constrained by DNA mutation 10 . Together, the actions of reading, 'riting, 'rithmetic and replication constitute the four Rs of RNA-directed evolution. Here, we describe roles for coRNAs and SATs (Fig. 2) in these events. RNA-directed RNA readoutRNA coregulates the sequence-specific read-out of genetic information from RNA by targeting the evolutionarily conserved machinery of RNA interference (RNAi) 11 and translational repression. RNAi leading to post-transcriptional gene silencing (PTGS) is induced by doublestranded RNA (dsRNA) arising from infection by dsRNA viruses, senseantisense transcription pairs, transcription of inverted repeats and delivery of dsRNAs manufactured in vitro 12 . Both endogenous and exogenous dsRNAs are processed cytoplasmically by RNase III dicer paralogs into small interfering RNAs (siRNAs) that are 21-25 bases long 12,13 . These siRNAs are incorporated into an RNA-induced silencing complex (RISC) that targets any RNA with a sequence complementary to the siRNA 12,14 . The target RNA is cleaved by RISC, which has endonucleolytic and presumed exonucleolytic activity 12,15 . Each cycle results in the destruction of the target RNA and the regeneration of an active RISC 16,17 .In Neurospora crassa 18,19 , plants 20 , Schizosaccharomyces pombe 21 and Caenorhabditis elegans 22 , but not in flies, humans or mouse oocyctes 18,19,23,24 , PTGS can also be initiated by an RNA-dependent RNA polymerase (RdRP) that synthesizes complementary RNA from highly expressed transcripts to generate dsRNA. This process can spread from the 3´ to the 5´ end of the mRNA, leading to progressive silencing of a gene and other mRNAs with exons in common (transitive RNAi) 18,22 . From the evolutionary viewpoint, transitive RNAi favors the generation of new phenotypes, as related genes in species with polyploid genomes will escape cosuppression by sequence divergence, resulting in altered function or expression.The number of dicer paralogs also differs between species. Arabidopsis, which has at least four dicer family members, seems to use different enzymes to defend against viruses and to process endogenously produced dsRNA 13,25 . In humans, mice and worms, there is only one dicer ortholog, suggesting that any pathway-specific functions are guided by ancillary regulatory proteins associated with RISC. These ancillary proteins include me...

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“…Indeed, diVerent members of the AGO, Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) families of proteins are required for the two processes. AGO1, DCL1, DCL4, and RDR6 act in the PTGS/miRNA/tasiRNA pathway (Peragine et al 2004;Vaucheret et al 2004;Vazquez et al 2004;Gasciolli et al 2005;Xie et al 2005;Yoshikawa et al 2005), whereas AGO4, DCL3, and RDR2 act in the TGS pathway (Zilberman et al 2003;Chan et al 2004;Xie et al 2004). Some cellular components act in both TGS and PTGS pathways, although to diVerent extents.…”

Section: Introductionmentioning

confidence: 99%

A single transgene locus triggers both transcriptional and post-transcriptional silencing through double-stranded RNA production

Mourrain

Blokland

Kooter

et al. 2006

Planta

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Silencing of a target locus by an unlinked silencing locus can result from transcription inhibition (transcriptional gene silencing; TGS) or mRNA degradation (post-transcriptional gene silencing; PTGS), owing to the production of double-stranded RNA (dsRNA) corresponding to promoter or transcribed sequences, respectively. The involvement of distinct cellular components in each process suggests that dsRNA-induced TGS and PTGS likely result from the diversiWcation of an ancient common mechanism. However, a strict comparison of TGS and PTGS has been diYcult to achieve because it generally relies on the analysis of distinct silencing loci. We describe a single transgene locus that triggers both TGS and PTGS, owing to the production of dsRNA corresponding to promoter and transcribed sequences of diVerent target genes. We describe mutants and epigenetic variants derived from this locus and propose a model for the production of dsRNA. Also, we show that PTGS, but not TGS, is graft-transmissible, which together with the sensitivity of PTGS, but not TGS, to RNA viruses that replicate in the cytoplasm, suggest that the nuclear compartmentalization of TGS is responsible for cell-autonomy. In contrast, we contribute local and systemic traYcking of silencing signals and sensitivity to viruses to the cytoplasmic steps of PTGS and to ampliWcation steps that require high levels of target mRNAs.

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ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation

Cited by 945 publications

References 20 publications

On the origin and functions of RNA-mediated silencing: from protists to man

On the origin and functions of RNA-mediated silencing: from protists to man

The four Rs of RNA-directed evolution

A single transgene locus triggers both transcriptional and post-transcriptional silencing through double-stranded RNA production

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