Biochemical Evidence for Translational Repression by <i>Arabidopsis</i> MicroRNAs

Lanet, Elodie; Delannoy, Étienne; Sormani, Rodnay; Floris, Maïna; Brodersen, Peter; Crété, Patrice; Voinnet, Olivier; Robaglia, Christophe

doi:10.1105/tpc.108.063412

Cited by 283 publications

(220 citation statements)

References 34 publications

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“…For instance, imprecise excision of the mature miRNAs could result in functionally variable, or inert, miRNAs, as the miRNA sequence is important for selection of the miRNA over the miRNA* and sorting into functional AGO complexes (Mi et al, 2008;Montgomery et al, 2008a;Eamens et al, 2009;Ebhardt et al, 2010). Alternatively, young miRNAs could function primarily through nondegradative mechanisms that cannot be assayed by measuring target transcript abundance (Brodersen et al, 2008;Lanet et al, 2009). While this cannot be ruled out, it is difficult to explain why such a preference would exist.…”

Section: Is the Formation Of New Mirna Genes A Selective Or Neutral Pmentioning

confidence: 99%

Evolution and Functional Diversification of MIRNA Genes

2011

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MicroRNAs (miRNAs) are small regulatory RNAs found in diverse eukaryotic lineages. In plants, a minority of annotated MIRNA gene families are conserved between plant families, while the majority are family-or species-specific, suggesting that most known MIRNA genes arose relatively recently in evolutionary time. Given the high proportion of young MIRNA genes in plant species, new MIRNA families are likely spawned and then lost frequently. Unlike highly conserved, ancient miRNAs, young miRNAs are often weakly expressed, processed imprecisely, lack targets, and display patterns of neutral variation, suggesting that young MIRNA loci tend to evolve neutrally. Genome-wide analyses from several plant species have revealed that variation in miRNA foldback expression, structure, processing efficiency, and miRNA size have resulted in the unique functionality of MIRNA loci and resulting miRNAs. Additionally, some miRNAs have evolved specific properties and functions that regulate other transcriptional or posttranscriptional silencing pathways. The evolution of miRNA processing and functional diversity underscores the dynamic nature of miRNA-based regulation in complex regulatory networks.

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Section: Is the Formation Of New Mirna Genes A Selective Or Neutral Pmentioning

confidence: 99%

Evolution and Functional Diversification of MIRNA Genes

2011

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“…More direct biochemical evidence for translational repression came from the observation that some, though not all, miRNAs are associated with polysomes, and so is the AGO1 protein, a component of the silencing effector complex. Inhibiting the slicing function of AGO1 yields an increase in mRNA level, but no increase in protein, suggesting that the miRNA continues to repress translation (Lanet et al, 2009).…”

Section: Mirnasmentioning

confidence: 99%

Translational Regulation of Cytoplasmic mRNAs

Roy

Arnim

2013

The Arabidopsis Book

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Translation of the coding potential of a messenger RNA into a protein molecule is a fundamental process in all living cells and consumes a large fraction of metabolites and energy resources in growing cells. Moreover, translation has emerged as an important control point in the regulation of gene expression. At the level of gene regulation, translational control is utilized to support the specific life histories of plants, in particular their responses to the abiotic environment and to metabolites. This review summarizes the diversity of translational control mechanisms in the plant cytoplasm, focusing on specific cases where mechanisms of translational control have evolved to complement or eclipse other levels of gene regulation. We begin by introducing essential features of the translation apparatus. We summarize early evidence for translational control from the pre-Arabidopsis era. Next, we review evidence for translation control in response to stress, to metabolites, and in development. The following section emphasizes RNA sequence elements and biochemical processes that regulate translation. We close with a chapter on the role of signaling pathways that impinge on translation.

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“…These include the forkhead-associated domain containing protein dawdle (DDL) and the components of the nuclear cap binding complex abscisic acid ABA hypersensitive 1 (ABH1)/Cap-Binding Protein (CBP) 80 and CBP20 (12)(13)(14)(15). Processed miRNAs subsequently associate with one of the ten Arabidopsis argonaute (AGO) proteins to regulate their target mRNAs by transcript cleavage and/or inhibition of translation (16)(17)(18)(19)(20)(21)(22) until the miRNA is degraded by specific sRNA degradation nuclease (SDN) proteins (23).…”

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confidence: 99%

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

Laubinger

Zeller

Henz

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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In Arabidopsis thaliana, four different dicer-like (DCL) proteins have distinct but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and siRNAs from longer, noncoding precursor RNAs. To analyze the impact of different components of the small RNA biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in small RNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most primiRNAs, in two tissues and several stress conditions. Our analysis revealed a surprising number of common targets in dcl1 and dcl2 dcl3 dcl4 triple mutants. Furthermore, our results suggest that the DCL1 is not only involved in miRNA action but also contributes to silencing of a subset of transposons, apparently through an effect on DNA methylation.ike other plants, the widely used model species Arabidopsis thaliana produces a complex population of small RNAs (sRNAs). These sRNAs come in two major flavors: microRNAs (miRNAs), most of which are 20-22 nt long, and siRNAs, with a typical length of 23-24 nt. Most sRNAs are derived from longer precursor RNAs, which are either dsRNA molecules or ssRNA molecules that form a self-complementary fold-back structure. These RNAs are processed to sRNAs by four different dicer-like (DCL) proteins, DCL1, DCL2, DCL3, and DCL4 (reviewed in ref. 1).DCL1 is mainly involved in the generation of miRNAs, which are derived from longer primary miRNA (pri-miRNA) transcripts that are transcribed by polymerase II (polII) (2). PrimiRNAs are first trimmed by DCL1 to precursor miRNAs (pre-miRNAs), from which DCL1 further excises the miRNA/ miRNA* duplexes (3). DCL1 interacts with the dsRNA binding protein hyponastic leaves 1 (HYL1) and the zinc-finger protein serrate (SE) (4-10). Formation of this complex occurs in nuclear dicing bodies and is required for accurate processing activity of DCL1 (10, 11). The core miRNA biogenesis machinery probably acts in concert with associated factors that ensure proper processing of pri-miRNAs. These include the forkhead-associated domain containing protein dawdle (DDL) and the components of the nuclear cap binding complex abscisic acid ABA hypersensitive 1 (ABH1)/Cap-Binding Protein (CBP) . Processed miRNAs subsequently associate with one of the ten Arabidopsis argonaute (AGO) proteins to regulate their target mRNAs by transcript cleavage and/or inhibition of translation (16-22) until the miRNA is degraded by specific sRNA degradation nuclease (SDN) proteins (23).Other classes of sRNAs are mainly produced by DCL2, DCL3, and DCL4. SiRNAs derived from natural antisense transcripts (nat-siRNAs) are generated by DCL1 and DCL2 (24). DCL4 mainly acts in the biogenesis of transacting siRNAs (tasiRNAs) and in the generation of mobile siRNAs that communicate silencing effects between cells, but DCL4 also generates miRNAs from almost perfectly complementary miRNA fold backs (25-29). DCL3 acts in concert with RNA-dependent RNA polymerase 2 (RDR2) to generate heterochromatic...

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Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs

Cited by 283 publications

References 34 publications

Evolution and Functional Diversification of MIRNA Genes

Evolution and Functional Diversification of MIRNA Genes

Translational Regulation of Cytoplasmic mRNAs

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

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