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A Complex Small RNA Repertoire Is Generated by a Plant/Fungal-Like Machinery and Effected by a Metazoan-Like Argonaute in the Single-Cell Human Parasite Toxoplasma gondii

Braun, Laurence ; Cannella, Dominique ; Ortet, Philippe ; [et al.]

Public Library of Science (PLoS) ; 2010

In: PLoS Pathogens Vol. 6, No. 5 ( 2010-5-27), p. e1000920-

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In: PLoS Pathogens, Public Library of Science (PLoS), Vol. 6, No. 5 ( 2010-5-27), p. e1000920-

Type of Medium: Online Resource

ISSN: 1553-7374

URL: Article

DOI: 10.1371/journal.ppat.1000920

DOI: 10.1371/journal.ppat.1000920.g001

DOI: 10.1371/journal.ppat.1000920.g002

DOI: 10.1371/journal.ppat.1000920.g003

DOI: 10.1371/journal.ppat.1000920.g004

DOI: 10.1371/journal.ppat.1000920.g005

DOI: 10.1371/journal.ppat.1000920.g006

DOI: 10.1371/journal.ppat.1000920.g007

DOI: 10.1371/journal.ppat.1000920.g008

DOI: 10.1371/journal.ppat.1000920.t001

DOI: 10.1371/journal.ppat.1000920.s001

DOI: 10.1371/journal.ppat.1000920.s002

DOI: 10.1371/journal.ppat.1000920.s003

DOI: 10.1371/journal.ppat.1000920.s004

DOI: 10.1371/journal.ppat.1000920.s005

DOI: 10.1371/journal.ppat.1000920.s006

DOI: 10.1371/journal.ppat.1000920.s007

DOI: 10.1371/journal.ppat.1000920.s008

DOI: 10.1371/journal.ppat.1000920.s009

DOI: 10.1371/journal.ppat.1000920.s010

DOI: 10.1371/journal.ppat.1000920.s011

DOI: 10.1371/journal.ppat.1000920.s012

DOI: 10.1371/journal.ppat.1000920.s013

DOI: 10.1371/journal.ppat.1000920.s014

DOI: 10.1371/journal.ppat.1000920.s015

DOI: 10.1371/journal.ppat.1000920.s016

DOI: 10.1371/journal.ppat.1000920.s017

DOI: 10.1371/journal.ppat.1000920.s018

DOI: 10.1371/journal.ppat.1000920.s019

DOI: 10.1371/journal.ppat.1000920.s020

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2010

detail.hit.zdb_id: 2205412-1

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Corrigendum: Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins

Moissiard, Guillaume ; Parizotto, Eneida Abreu ; Himber, Christophe ; [et al.]

Cold Spring Harbor Laboratory ; 2016

In: RNA Vol. 22, No. 5 ( 2016-05), p. 810-810

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In: RNA, Cold Spring Harbor Laboratory, Vol. 22, No. 5 ( 2016-05), p. 810-810

Type of Medium: Online Resource

ISSN: 1355-8382 , 1469-9001

URL: Article

DOI: 10.1261/rna.056366.116

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2016

detail.hit.zdb_id: 1475737-0

SSG: 12

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Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins

Moissiard, Guillaume ; Parizotto, Eneida Abreu ; Himber, Christophe ; [et al.]

Cold Spring Harbor Laboratory ; 2007

In: RNA Vol. 13, No. 8 ( 2007-08), p. 1268-1278

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In: RNA, Cold Spring Harbor Laboratory, Vol. 13, No. 8 ( 2007-08), p. 1268-1278

Abstract: In plants, worms, and fungi, RNA-dependent RNA polymerases (RDRs) amplify the production of short-interfering RNAs (siRNAs) that mediate RNA silencing. In Arabidopsis , RDR6 is thought to copy endogenous and exogenous RNA templates into double-stranded RNAs (dsRNAs), which are subsequently processed into siRNAs by one or several of the four Dicer-like enzymes (DCL1→4). This reaction produces secondary siRNAs corresponding to sequences outside the primary targeted regions of a transcript, a phenomenon called transitivity. One recognized role of RDR6 is to strengthen the RNA silencing response mounted by plants against viruses. Accordingly, suppressor proteins deployed by viruses inhibit this defense. However, interactions between silencing suppressors and RDR6 have not yet been documented. Additionally, the mechanism underlying transitivity remains poorly understood. Here, we report how several viral silencing suppressors inhibit the RDR6-dependent amplification of virus-induced and transgene-induced gene silencing. Viral suppression of primary siRNA accumulation shows that transitivity can be initiated with minute amounts of DCL4-dependent 21-nucleotide (nt)-long siRNAs, whereas DCL3-dependent 24-nt siRNAs appear dispensable for this process. We further show that unidirectional (3→5′) transitivity requires the hierarchical and redundant functions of DCL4 and DCL2 acting downstream from RDR6 to produce 21- and 22-nt-long siRNAs, respectively. The 3→5′ transitive reaction is likely to be processive over 〉 750 nt, with secondary siRNA production progressively decreasing as the reaction proceeds toward the 5′-proximal region of target transcripts. Finally, we show that target cleavage by a primary small RNA and 3→5′ transitivity can be genetically uncoupled, and we provide in vivo evidence supporting a key role for priming in this specific reaction.

Type of Medium: Online Resource

ISSN: 1355-8382 , 1469-9001

URL: Article

DOI: 10.1261/rna.541307

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2007

detail.hit.zdb_id: 1475737-0

SSG: 12

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Corrigendum: Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins

Moissiard, Guillaume ; Parizotto, Eneida Abreu ; Himber, Christophe ; [et al.]

Cold Spring Harbor Laboratory ; 2016

In: RNA Vol. 22, No. 1 ( 2016-01), p. 162-165

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In: RNA, Cold Spring Harbor Laboratory, Vol. 22, No. 1 ( 2016-01), p. 162-165

Type of Medium: Online Resource

ISSN: 1355-8382 , 1469-9001

URL: Article

DOI: 10.1261/rna.055012.115

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2016

detail.hit.zdb_id: 1475737-0

SSG: 12

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Biochemical and genetic functional dissection of the P38 viral suppressor of RNA silencing

Iki, Taichiro ; Tschopp, Marie-Aude ; Voinnet, Olivier

Cold Spring Harbor Laboratory ; 2017

In: RNA Vol. 23, No. 5 ( 2017-05), p. 639-654

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In: RNA, Cold Spring Harbor Laboratory, Vol. 23, No. 5 ( 2017-05), p. 639-654

Abstract: Phytoviruses encode viral suppressors of RNA silencing (VSRs) to counteract the plant antiviral silencing response, which relies on virus-derived small interfering (si)RNAs processed by Dicer RNaseIII enzymes and subsequently loaded into ARGONAUTE (AGO) effector proteins. Here, a tobacco cell-free system was engineered to recapitulate the key steps of antiviral RNA silencing and, in particular, the most upstream double-stranded (ds)RNA processing reaction, not kinetically investigated thus far in the context of plant VSR studies. Comparative biochemical analyses of distinct VSRs in the reconstituted assay showed that in all cases tested, VSR interactions with siRNA duplexes inhibited the loading, but not the activity, of antiviral AGO1 and AGO2. Turnip crinkle virus P38 displayed the additional and unique property to bind both synthetic and RNA-dependent-RNA-polymerase-generated long dsRNAs, and inhibited the processing into siRNAs. Single amino acid substitutions in P38 could dissociate dsRNA-processing from AGO-loading inhibition in vitro and in vivo, illustrating dual-inhibitory strategies discriminatively deployed within a single viral protein, which, we further show, are bona fide suppressor functions that evolved independently of the conserved coat protein function of P38.

Type of Medium: Online Resource

ISSN: 1355-8382 , 1469-9001

URL: Article

DOI: 10.1261/rna.060434.116

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2017

detail.hit.zdb_id: 1475737-0

SSG: 12

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A Small-RNA Perspective on Gametogenesis, Fertilization, and Early Zygotic Development

Bourc’his, Déborah ; Voinnet, Olivier

American Association for the Advancement of Science (AAAS) ; 2010

In: Science Vol. 330, No. 6004 ( 2010-10-29), p. 617-622

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In: Science, American Association for the Advancement of Science (AAAS), Vol. 330, No. 6004 ( 2010-10-29), p. 617-622

Abstract: Transient populations of cis- and trans-acting small RNAs have recently emerged as key regulators of extensive epigenetic changes taking place during periconception, which encompasses gametogenesis, fertilization, and early zygotic development. These small RNAs are not only important to maintain genome integrity in the gametes and zygote, but they also actively contribute to assessing the compatibility of parental genomes at fertilization and to promoting long-term memory of the zygotic epigenetic landscape by affecting chromatin. Striking parallels exist in the biogenesis and modus operandi of these molecules among diverse taxa, unraveling universal themes of small-RNA–mediated epigenetic reprogramming during sexual reproduction.

Type of Medium: Online Resource

ISSN: 0036-8075 , 1095-9203

URL: Article

DOI: 10.1126/science.1194776

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: American Association for the Advancement of Science (AAAS)

Publication Date: 2010

detail.hit.zdb_id: 128410-1

detail.hit.zdb_id: 2066996-3

detail.hit.zdb_id: 2060783-0

SSG: 11

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Widespread Translational Inhibition by Plant miRNAs and siRNAs

Brodersen, Peter ; Sakvarelidze-Achard, Lali ; Bruun-Rasmussen, Marianne ; [et al.]

American Association for the Advancement of Science (AAAS) ; 2008

In: Science Vol. 320, No. 5880 ( 2008-05-30), p. 1185-1190

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In: Science, American Association for the Advancement of Science (AAAS), Vol. 320, No. 5880 ( 2008-05-30), p. 1185-1190

Abstract: High complementarity between plant microRNAs (miRNAs) and their messenger RNA targets is thought to cause silencing, prevalently by endonucleolytic cleavage. We have isolated Arabidopsis mutants defective in miRNA action. Their analysis provides evidence that plant miRNA–guided silencing has a widespread translational inhibitory component that is genetically separable from endonucleolytic cleavage. We further show that the same is true of silencing mediated by small interfering RNA (siRNA) populations. Translational repression is effected in part by the ARGONAUTE proteins AGO1 and AGO10. It also requires the activity of the microtubule-severing enzyme katanin, implicating cytoskeleton dynamics in miRNA action, as recently suggested from animal studies. Also as in animals, the decapping component VARICOSE (VCS)/Ge-1 is required for translational repression by miRNAs, which suggests that the underlying mechanisms in the two kingdoms are related.

Type of Medium: Online Resource

ISSN: 0036-8075 , 1095-9203

URL: Article

DOI: 10.1126/science.1159151

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: American Association for the Advancement of Science (AAAS)

Publication Date: 2008

detail.hit.zdb_id: 128410-1

detail.hit.zdb_id: 2066996-3

detail.hit.zdb_id: 2060783-0

SSG: 11

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An endogenous, systemic RNAi pathway in plants

Dunoyer, Patrice ; Brosnan, Christopher A ; Schott, Gregory ; [et al.]

Wiley ; 2010

In: The EMBO Journal Vol. 29, No. 10 ( 2010-5-19), p. 1699-1712

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In: The EMBO Journal, Wiley, Vol. 29, No. 10 ( 2010-5-19), p. 1699-1712

Type of Medium: Online Resource

ISSN: 0261-4189 , 1460-2075

URL: Article

DOI: 10.1038/emboj.2010.65

RVK:

WA 15000

Language: Unknown

Publisher: Wiley

Publication Date: 2010

detail.hit.zdb_id: 1467419-1

detail.hit.zdb_id: 586044-1

SSG: 12

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The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs in Arabidopsis

Bologna, Nicolas G. ; Voinnet, Olivier

Annual Reviews ; 2014

In: Annual Review of Plant Biology Vol. 65, No. 1 ( 2014-04-29), p. 473-503

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In: Annual Review of Plant Biology, Annual Reviews, Vol. 65, No. 1 ( 2014-04-29), p. 473-503

Abstract: In eukaryotic RNA silencing, RNase-III classes of enzymes in the Dicer family process double-stranded RNA of cellular or exogenous origin into small-RNA (sRNA) molecules. sRNAs are then loaded into effector proteins known as ARGONAUTEs (AGOs), which, as part of RNA-induced silencing complexes, target complementary RNA or DNA for silencing. Plants have evolved a large variety of pathways over the Dicer–AGO consortium, which most likely underpins part of their phenotypic plasticity. Dicer-like proteins produce all known classes of plant silencing sRNAs, which are invariably stabilized via 2′-O-methylation mediated by HUA ENHANCER 1 (HEN1), potentially amplified by the action of several RNA-dependent RNA polymerases, and function through a variety of AGO proteins. Here, we review the known characteristics and biochemical properties of the core silencing factors found in the model plant Arabidopsis thaliana. We also describe how interactions between these core factors and more specialized proteins allow the production of a plethora of silencing sRNAs involved in a large array of biological functions. We emphasize in particular the biogenesis and activities of silencing sRNAs of endogenous origin.

Type of Medium: Online Resource

ISSN: 1543-5008 , 1545-2123

URL: Issue

URL: Article

DOI: 10.1146/arplant.2014.65.issue-1

DOI: 10.1146/annurev-arplant-050213-035728

Language: English

Publisher: Annual Reviews

Publication Date: 2014

detail.hit.zdb_id: 2098209-4

SSG: 12

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ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data

Chen, Chong-Jian ; Servant, Nicolas ; Toedling, Joern ; [et al.]

Oxford University Press (OUP) ; 2012

In: Bioinformatics Vol. 28, No. 23 ( 2012-12-01), p. 3147-3149

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In: Bioinformatics, Oxford University Press (OUP), Vol. 28, No. 23 ( 2012-12-01), p. 3147-3149

Abstract: Summary: Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions. The ncPRO-seq pipeline supports input read sequences in fastq, fasta and color space format, as well as alignment results in BAM format, meaning that sRNA raw data from the three current major platforms (Roche-454, Illumina-Solexa and Life technologies-SOLiD) can be analyzed with this pipeline. The ncPRO-seq pipeline can be used to analyze read and alignment data, based on any sequenced genome, including mammals and plants. Availability: Source code, annotation files, manual and online version are available at http://ncpro.curie.fr/. Contact: bioinfo.ncproseq@curie.fr or cciaudo@ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online.

Type of Medium: Online Resource

ISSN: 1367-4803 , 1367-4811

URL: Article

DOI: 10.1093/bioinformatics/bts587

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2012

detail.hit.zdb_id: 1468345-3

SSG: 12

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