Two classes of endogenous small RNAs in<i>Tetrahymena thermophila</i>

Lee, Suzanne R.; Collins, Kathleen

doi:10.1101/gad.1377006

Cited by 94 publications

(131 citation statements)

References 31 publications

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“…Moreover, Chlamydomonas contains an assortment of siRNAs as well as miRNAs (Molnar et al 2007;Zhao et al 2007). Other unicellular organisms with relatively large nuclear genomes, such as the ciliate Tetrahymena thermophila and the social amoeba Dictyostelium discoideum, also show expansion of the core RNAi machinery and different classes of small RNAs (Lee and Collins 2006;Hinas et al 2007). These observations suggest that diversification of RNA-silencing components is not limited to multicellular lineages and appears to have been a common occurrence during the evolution of eukaryotes.…”

Section: Discussionmentioning

confidence: 99%

Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

Casas-Mollano¹,

Rohr²,

Kim

et al. 2008

Genetics

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Small RNA-guided gene silencing is an evolutionarily conserved process that operates by a variety of molecular mechanisms. In multicellular eukaryotes, the core components of RNA-mediated silencing have significantly expanded and diversified, resulting in partly distinct pathways for the epigenetic control of gene expression and genomic parasites. In contrast, many unicellular organisms with small nuclear genomes seem to have lost entirely the RNA-silencing machinery or have retained only a basic set of components. We report here that Chlamydomonas reinhardtii, a unicellular eukaryote with a relatively large nuclear genome, has undergone extensive duplication of Dicer and Argonaute polypeptides after the divergence of the green algae and land plant lineages. Chlamydomonas encodes three Dicers and three Argonautes with DICER-LIKE1 (DCL1) and ARGONAUTE1 being more divergent than the other paralogs. Interestingly, DCL1 is uniquely involved in the post-transcriptional silencing of retrotransposons such as TOC1. Moreover, on the basis of the subcellular distribution of TOC1 small RNAs and target transcripts, this pathway most likely operates in the nucleus. However, Chlamydomonas also relies on a DCL1-independent, transcriptional silencing mechanism(s) for the maintenance of transposon repression. Our results suggest that multiple, partly redundant epigenetic processes are involved in preventing transposon mobilization in this green alga.

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Section: Discussionmentioning

confidence: 99%

Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

Casas-Mollano¹,

Rohr²,

Kim

et al. 2008

Genetics

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“…This overall organization is maintained in Dicer-like proteins from animals (H. sapiens), fungi (Schyzosaccharomyces pombe), and plants (A. thaliana) (Figure 1) with the greatest variability associated with the presence or absence of the DSRM and/or of the PAZ domains. In Tetrahymena thermophila there are three Dicer-like sequences: Dcr2, which contains only the helicase and the two RNaseIII domains (Figure 1), and Dcr1 and Dcl1, which are more divergent (Lee and Collins 2006;Mochizuki and Gorovsky 2005). Indeed, Dcl1 only includes the RNaseIII motifs and a C-terminal DSRM.…”

Section: Phytophthora Infestansmentioning

confidence: 99%

“…For instance, a Piwi-like protein, Twi1, is required for the conjugation-induced accumulation of small RNAs involved in programmed DNA elimination in T. thermophila (Lee and Collins 2006;Liu et al 2004b). The D. melanogaster Piwi-like genes Aubergine and Piwi have been implicated in both transcriptional, partly associated with histone H3 lysine 9 (H3K9) methylation, and post-transcriptional gene silencing (Aravin et al 2004;Kavi et al 2005;PalBhadra et al 2004).…”

Section: Nature Of the Ancestral Rnai Machinerymentioning

confidence: 99%

“…This process requires small RNAs, termed scan RNAs, and components of the RNA machinery that direct H3K9 methylation of the chromatin associated with the sequences to be deleted (Garnier et al 2004;Liu et al 2004b;Mochizuki and Gorovsky 2005;Yao and Chao 2005). Many of the eliminated sequences appear to be derived from transposons (Lee and Collins 2006;Yao and Chao 2005) and RNA-mediated DNA elimination may have evolved as an extension of the role of the RNAi machinery in the transcriptional silencing of transposon/repetitive sequences. Interestingly, DNA diminution phenomena have also been observed in Ascaris worms and in some species of crustaceans and fish, although it is not known whether these processes are RNAi mediated.…”

Section: Additional (Derived?) Functions Of the 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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“…zoan, Tetrahymena thermophila, to direct developmentally programmed DNA elimination (Mochizuki et al 2002;Mochizuki and Gorovsky 2004;Lee and Collins 2006). PIWI-interacting RNAs (piRNAs) of 26-to 31-nt were discovered in mammalian germline cells (Aravin et al 2006;Girard et al 2006;Grivna et al 2006;Lau et al 2006) and zebrafish (Houwing et al 2007).…”

mentioning

confidence: 99%

A novel class of bacteria-induced small RNAs in Arabidopsis

Katiyar-Agarwal¹,

Gao²,

et al. 2007

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Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are essential regulatory molecules of many cellular processes. Arabidopsis has at least three classes of endogenous siRNAs-chromatin-associated siRNAs, trans-acting siRNAs (tasiRNAs), and natural antisense transcript (NAT)-associated siRNAs (nat-siRNAs)-all 20-25 nucleotides (nt) in length. Here, we identified a novel class of small RNAs, long siRNAs (lsiRNAs), which are 30-40 nt and share many common features with known siRNAs. The lsiRNAs identified so far are induced by pathogen infection or under specific growth conditions. One of the lsiRNAs, AtlsiRNA-1, is generated from SRRLK/AtRAP NAT pair and specifically induced by the bacterium Pseudomonas syringae carrying effector avrRpt2. Recently, 25-to 31-nt PIWI-interacting RNAs (piRNAs) and repeat-associated siRNAs (rasiRNAs) were identified in animal germline cells. In contrast to the biogenesis of piRNAs/rasiRNAs, which is dicer independent and requires PIWI subfamily proteins, generation of AtlsiRNA-1 requires DCL1, DCL4, and the ARGONAUTE subfamily protein AGO7. It also depends on HYL1, HEN1, HST1, RDR6, and Pol IV. Induction of AtlsiRNA-1 silences AtRAP, which encodes a RAP-domain protein involved in disease resistance. Our further analysis implies that AtlsiRNA-1 may destabilize target mRNA through decapping and XRN4-mediated 5-to-3 degradation.[Keywords: Long siRNAs (lsiRNAs); DCL1; AGO7; decapping; bacteria-induced] Supplemental material is available at http://www.genesdev.org. Small RNA-mediated gene silencing plays important roles in many cellular processes, including development, genome maintenance and integrity, and adaptive responses to biotic and abiotic stress in most eukaryotes. Small RNAs, usually 20-25 nucleotides (nt) in length, can be grouped into two classes on the basis of their origins: microRNAs (miRNAs) and small interfering RNAs (siRNAs). They guide heterochromatin formation, mRNA degradation, translational inhibition, and DNA elimination (Baulcombe 2004;Zamore and Haley 2005;Vazquez 2006). Rapid and phenomenal progress has been achieved in unraveling the components and mechanisms involved in the biogenesis and function of various small RNAs. In plants, small RNAs are highly diverse. In general, miRNAs in Arabidopsis are processed from singlestranded (ss) hairpin RNA precursors by an RNase IIItype enzyme Dicer-like (DCL) 1. A recent study shows that a couple of newly identified miRNAs are processed by DCL4 (Rajagopalan et al. 2006). The precursors of these miRNAs tend to have more complementarity within the foldback structure than that in most previously identified DCL1-dependent miRNAs. miRNAs are primarily associated with ARGONAUTE 1 (AGO1) to guide mRNA cleavage or translational inhibition. Endogenous siRNAs are usually processed from long doublestranded RNAs (dsRNAs). The generation of trans-acting siRNAs (tasiRNAs) is initiated by miRNAs, and requires DCL4 and RNA-dependent RNA polymerase (RDR) 6 for their biogenesis. Both miRNAs and tasiRNAs are 21-to 2...

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Two classes of endogenous small RNAs inTetrahymena thermophila

Cited by 94 publications

References 31 publications

Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

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

A novel class of bacteria-induced small RNAs in Arabidopsis

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