The biosynthetic pathways and biological scopes of plant small RNAs

Vazquez, Franck; Legrand, Sylvain; Windels, David

doi:10.1016/j.tplants.2010.04.001

Cited by 137 publications

(103 citation statements)

References 113 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Arabidopsis ta-siRNAs are secondary siRNAs arising from noncoding transcripts that depend on DCL1, DCL4, RDR6, and SGS3 proteins for their biogenesis (Voinnet, 2009;Vazquez et al, 2010). No accumulation of AFB2 3#D2(+) and AFB3 3#D2(2) was detectable in the deficiency mutants rdr6-15 and sgs3-13; whereas, their accumulation in the deficiency mutants rdr1-1, rdr2-2, rdr3a-2, rdr3b-2, and rdr3c-1 was comparable to that of wild type ( Fig.…”

Section: Resultsmentioning

confidence: 99%

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

et al. 2011

Self Cite

View full text Add to dashboard Cite

The phytohormone auxin is a key regulator of plant growth and development that exerts its functions through F-box receptors. Arabidopsis (Arabidopsis thaliana) has four partially redundant of these receptors that comprise the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX1 auxin receptor (TAAR) clade. Recent studies have shown that the microRNA miR393 regulates the expression of different sets of TAAR genes following pathogen infection or nitrate treatment. Here we report that miR393 helps regulate auxin-related development of leaves. We found that AtMIR393B is the predominant source for miR393 in all aerial organs and that miR393 down-regulates all four TAAR genes by guiding the cleavage of their mRNAs. A mutant unable to produce miR393 shows developmental abnormalities of leaves and cotyledons reminiscent of enhanced auxin perception by TAARs. Interestingly, miR393 initiates the biogenesis of secondary siRNAs from the transcripts of at least two of the four TAAR genes. Our results indicate that these siRNAs, which we call siTAARs, help regulate the expression of TAAR genes as well as several unrelated genes by guiding the cleavage of their mRNAs. Thus, miR393 and possibly siTAARs regulate auxin perception and certain auxin-related aspects of leaf development.

show abstract

Section: Resultsmentioning

confidence: 99%

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…Apart from these aspects, the evolution of miRNA processing and functional diversification also underscores the dynamic nature of miRNA-based regulation in complex regulatory networks (Allen et al, 2004;Cuperus et al, 2011). The miRNA genes were suggested to originate from inverted repeats that could form self-complementary regions, such as the nonautonomous transposons containing flanking terminal inverted repeats (Allen et al, 2004;Vazquez et al, 2010;Cuperus et al, 2011). During evolutionary history, new miRNA families were spawned, and some might have been lost at a high frequency.…”

Section: Mirna Dynamics: An Evolutionary Perspectivementioning

confidence: 99%

The Regulatory Activities of Plant MicroRNAs: A More Dynamic Perspective

et al. 2011

View full text Add to dashboard Cite

Twenty years have elapsed since the discovery of a microRNA (miRNA) gene in Caenorhabditis elegans. Based on growing research progress, we are approaching the nature of this small RNA species, which seemed to be mysterious before. The regulatory activities of miRNAs have been extensively studied through target identification and physiological and phenotypic assays by using bioinformatic, genetic, and biochemical approaches. However, recent evidence points to the fact that the effective levels of miRNAs are determined by transcription, processing, miRNAinduced silencing complex loading, action, turnover use, and decay. Each process is affected by certain factors, such as genomic modifications, RNA editing, miRNA-induced silencing complex loading competition, target abundance and complementarity, and spatiotemporal effects, thus conferring a highly dynamic feature to miRNA activities. To maintain steady-state levels of the functional miRNAs, thus ensuring a normal physiological and biochemical status, plants employ several exquisite strategies, such as feedback regulation and a buffering system, to minimize the influence of external signal fluctuations. In this review, we raise the notion that a more dynamic picture of miRNA activities should be drawn to construct comprehensive miRNA-mediated networks in plants.MicroRNAs (miRNAs), approximately 21 nucleotides in length, were identified as a small RNA (sRNA) species with essential regulatory roles in various biological processes (Carrington and Ambros, 2003). The transcription of most miRNA genes is guided by RNA polymerase II Xie et al., 2005). Following transcription, the single-stranded RNAs with internal stem-loop structures are then recognized by Drosha and Dicer in animals (Kim et al., 2009a) or Dicer-Like1 (DCL1) in plants (Voinnet, 2009) for sequential cleavage, converting the primary microRNAs (pri-miRNAs) to the precursor microRNAs (pre-miRNAs) and finally to the miRNA/miRNA* duplexes. After dissociation from the duplexes, the miRNAs are incorporated into Argonaute (AGO)-associated micro-RNA-induced silencing complexes (miRISCs; preferentially AGO1-associated miRISCs). Although the sophisticated model of miRNA biogenesis is seemingly settled for each step, there exist many key nodes that influence the final activity of a miRNA gene. The transcription of miRNA genes is under the rigorous surveillance of many cis-and trans-factors, such as chromatin marks and specific transcription factors (TFs). The processing efficiency of the miRNA precursors is basically determined by their own sequences and structures and is regulated in a spatiotemporal manner (Davis and Hata, 2009;Cuperus et al., 2011;Zhu et al., 2011). Furthermore, the sorting of miRNAs into specific AGO complexes should not be oversimplified, since not all the miRNAs are uniformly loaded into AGO1-associated miRISCs. Additionally, loading competition between miRNAs and other sRNAs occurs in planta.In plants, miRNAs guide the miRISCs to target transcripts containing highly complementary recognition ...

show abstract

“…So far, little is known about how deposition of specific CTD phosphoserine marks affects the transcription and stability of noncoding RNAs. Two major classes of plant small noncoding RNAs are microRNAs (miRNAs) and short interfering RNAs (siRNAs) that posttranscriptionally regulate a broad range of biological functions (see reviews in Xie et al, 2004Xie et al, , 2010Voinnet, 2009;Vazquez et al, 2010). The siRNA family is comprised of trans-acting siRNAs (ta-siRNAs), natural-antisense transcriptderived siRNAs (nat-siRNAs), and repeat-associated siRNAs (rasiRNAs).…”

Section: Introductionmentioning

confidence: 99%

CDKF;1 and CDKD Protein Kinases Regulate Phosphorylation of Serine Residues in the C-Terminal Domain of Arabidopsis RNA Polymerase II

et al. 2012

View full text Add to dashboard Cite

Phosphorylation of conserved Y 1 S 2 P 3 T 4 S 5 P 6 S 7 repeats in the C-terminal domain of largest subunit of RNA polymerase II (RNAPII CTD) plays a central role in the regulation of transcription and cotranscriptional RNA processing. Here, we show that Ser phosphorylation of Arabidopsis thaliana RNAPII CTD is governed by CYCLIN-DEPENDENT KINASE F;1 (CDKF;1), a unique plant-specific CTD S 7 -kinase. CDKF;1 is required for in vivo activation of functionally redundant CYCLIN-DEPENDENT KINASE Ds (CDKDs), which are major CTD S 5 -kinases that also phosphorylate in vitro the S 2 and S 7 CTD residues. Inactivation of CDKF;1 causes extreme dwarfism and sterility. Inhibition of CTD S 7 -phosphorylation in germinating cdkf;1 seedlings is accompanied by 39-polyadenylation defects of pre-microRNAs and transcripts encoding key regulators of small RNA biogenesis pathways. The cdkf;1 mutation also decreases the levels of both precursor and mature small RNAs without causing global downregulation of the protein-coding transcriptome and enhances the removal of introns that carry premicroRNA stem-loops. A triple cdkd knockout mutant is not viable, but a combination of null and weak cdkd;3 alleles in a triple cdkd123* mutant permits semidwarf growth. Germinating cdkd123* seedlings show reduced CTD S 5 -phosphorylation, accumulation of uncapped precursor microRNAs, and a parallel decrease in mature microRNA. During later development of cdkd123* seedlings, however, S 7 -phosphorylation and unprocessed small RNA levels decline similarly as in the cdkf;1 mutant. Taken together, cotranscriptional processing and stability of a set of small RNAs and transcripts involved in their biogenesis are sensitive to changes in the phosphorylation of RNAPII CTD by CDKF;1 and CDKDs.

show abstract

The biosynthetic pathways and biological scopes of plant small RNAs

Cited by 137 publications

References 113 publications

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

The Regulatory Activities of Plant MicroRNAs: A More Dynamic Perspective

CDKF;1 and CDKD Protein Kinases Regulate Phosphorylation of Serine Residues in the C-Terminal Domain of Arabidopsis RNA Polymerase II

Contact Info

Product

Resources

About