Targeting Argonaute to chromatin

Wendte, Jered M.; Pikaard, Craig S.

doi:10.1101/gad.294900.116

Cited by 4 publications

(3 citation statements)

References 11 publications

(18 reference statements)

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“…Our results indicate that Pol V transcription is highly accurate, suggesting that accuracy is important for Pol V transcript function. Pol V makes RNAs at loci to be silenced by RNA-directed DNA methylation, and its transcripts are thought to provide scaffolds for the binding of siRNA-AGO complexes that then recruit additional chromatin modifying activities ( 11 , 37 ), consistent with studies in fission yeast and other organisms ( 40 ). A need for precise basepairing between siRNAs and Pol V transcripts might result in selective pressure to maintain Pol V fidelity.…”

Section: Discussionsupporting

confidence: 56%

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

Marasco

Lynch

et al. 2017

Nucleic Acids Research

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All eukaryotes have three essential nuclear multisubunit RNA polymerases, abbreviated as Pol I, Pol II and Pol III. Plants are remarkable in having two additional multisubunit RNA polymerases, Pol IV and Pol V, which synthesize noncoding RNAs that coordinate RNA-directed DNA methylation for silencing of transposons and a subset of genes. Based on their subunit compositions, Pols IV and V clearly evolved as specialized forms of Pol II, but their catalytic properties remain undefined. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is considerably more error-prone than Pols II or V, which may be tolerable in its synthesis of short RNAs that serve as precursors for siRNAs targeting non-identical members of transposon families. By contrast, Pol V exhibits high fidelity transcription, similar to Pol II, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci to which siRNA–Argonaute silencing complexes are recruited.

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Section: Discussionsupporting

confidence: 56%

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

Marasco

Lynch

et al. 2017

Nucleic Acids Research

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“…Our results indicate that Pol V transcription is also highly accurate, suggesting that accuracy is important for Pol V transcript function. Pol V makes RNAs at loci to be silenced by RNA-directed DNA methylation, and its transcripts are thought to provide scaffolds for the binding of siRNA-AGO complexes that then recruit additional chromatin modifying activities (11,34), consistent with studies in fission yeast and other organisms (37). A need for precise basepairing between siRNAs and Pol V transcripts might be a selective pressure for maintaining Pol V fidelity.…”

Section: Discussionsupporting

confidence: 52%

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

Marasco

Lynch

et al. 2017

Preprint

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Catalytic subunits of DNA-dependent RNA polymerases of bacteria, archaea and eukaryotes share hundreds of ultra-conserved amino acids. Remarkably, the plantspecific RNA silencing enzymes, Pol IV and Pol V differ from Pols I, II and III at ~140 of these positions, yet remain capable of RNA synthesis. Whether these amino acid changes in Pols IV and V alter their catalytic properties in comparison to Pol II, from which they evolved, is unknown. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is notably error-prone, which may be tolerable, or even beneficial, for biosynthesis of siRNAs targeting transposon families in trans. By contrast, Pol V exhibits high fidelity transcription, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci in order to recruit siRNA-Argonaute protein silencing complexes.

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“…In plants, de novo 5mC in all cytosine contexts requires DOMAINS REARRANGED METHYLATRANSFERASE 2 (DRM2) orthologs. DRM2-mediated de novo 5mC requires many plant factors of the so-called RNA-directed DNA methylation (RdDM) pathway, including RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3), producing 24-nt siRNAs, ARGONAUTE 4 (AGO4), as well as the plant-specific RNA polymerase IV (RNA Pol IV) and RNA Pol V proteins, acting in concert in transcriptional gene silencing (TGS) (reviewed in [ 34 , 35 , 36 ]). Maintenance of mCG is catalyzed by DNMT1 and DNA METHYLTRANSFERASE 1 (MET1) in animals and plants, respectively.…”

Section: A Plethora Of Sophisticated Epigenetic Pathways Dampen Tesmentioning

confidence: 99%

The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

Nicolau

Picault

Moissiard

2021

Cells

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Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.

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Targeting Argonaute to chromatin

Cited by 4 publications

References 11 publications

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

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