Small RNA Diversity in Plants and its Impact in Development

MicroRNAs are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Both experimental and computational approaches have been used to identify miRNAs and their target genes. In plants, deep sequencing methods have recently allowed the analysis of small RNA diversity in different species and/or mutants. Most sequencing efforts have been concentrated on the identification of miRNAs and their mRNA targets have been predicted based on complementarity criteria. The recent demonstration that certain plant miRNAs could act partly via inhibition of protein translation certainly opens new fields of analysis for plant miRNA function on a broader group of targets. The roles of conserved miRNAs on target mRNA stability have been analysed in different species and defined common mechanisms in development and stress responses. In contrast, much less is known about expression patterns or functions of non-conserved miRNAs. In this review, we focus on the comparative analyses of plant small RNA diversity and the action of si/miRNAs in post-transcriptional regulation of some key genes involved in root development

siRNAs from miRNA sites mediate DNA methylation of target genes

Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give rise to two small RNA species, a 20- to 22-nt species and a 23- to 27-nt species, at the same site. Genetic analysis using small RNA pathway mutants reveals that the 20- to 22-nt small RNAs are typical miRNAs generated by DCL1 and are associated with Argonaute 1 (AGO1). In contrast, the accumulation of the 23- to 27-nt small RNAs from the miRNA-generating sites is dependent on DCL3, RDR2 and Pol IV, components of the typical heterochromatic small interfering RNA (hc-siRNA) pathway. We further demonstrate that these MIR-derived siRNAs associate with AGO4 and direct DNA methylation at some of their target loci in trans. In addition, we find that at the miRNA-generating sites, some conserved canonical MIR genes also produce siRNAs, which also induce DNA methylation at some of their target sites. Our systematic examination of published small RNA deep sequencing datasets of rice and moss suggests that this type of dual functional MIRs exist broadly in plants

Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control

Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined.Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3′UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21–23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants

A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development

Summary: RNA-dependent RNA polymerase 6 (RDR6) and suppressor of gene silencing 3 (SGS3) act together in post-transcriptional transgene silencing mediated by small interfering RNAs (siRNAs) and in biogenesis of various endogenous siRNAs including the tasiARFs, known regulators of auxin responses and plant development. Legumes, the third major crop family worldwide, has been widely improved through transgenic approaches. Here, we isolated rdr6 and sgs3 mutants in the model legume Medicago truncatula. Two sgs3 and one rdr6 alleles led to strong developmental defects and impaired biogenesis of tasiARFs. In contrast, the rdr6.1 homozygous plants produced sufficient amounts of tasiARFs to ensure proper development. High throughput sequencing of small RNAs from this specific mutant identified 354 potential MtRDR6 substrates, for which siRNA production was significantly reduced in the mutant. Among them, we found a large variety of novel phased loci corresponding to protein-encoding genes or transposable elements. Interestingly, measurement of GFP expression revealed that post-transcriptional transgene silencing was reduced in rdr6.1 roots. Hence, this novel mis-sense mutation, affecting a highly conserved amino acid residue in plant RDR6s, may be an interesting tool both to analyse endogenous pha-siRNA functions and to improve transgene expression, at least in legume species.Fil: Bustos Sanmamed, Maria del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina. Institut Des Sciences Du Végétal; FranciaFil: Hudik, Elodie. Institut Des Sciences Du Végétal; FranciaFil: Laffont, Carole. Institut Des Sciences Du Végétal; FranciaFil: Reynes, Christelle. Molécules Thérapeutiques In Silico; Francia. Université Paris Diderot - Paris 7; FranciaFil: Sallet, Erika. Laboratoire Des Interactions Plantes-microorganismes; FranciaFil: Wen, Jiangqi. The Samuel Roberts Noble Foundation; Estados UnidosFil: Mysore, Kirankumar S.. The Samuel Roberts Noble Foundation; Estados UnidosFil: Camproux, Anne Claude. Université Paris Diderot - Paris 7; Francia. Molécules Thérapeutiques In Silico; FranciaFil: Hartmann, Caroline. Institut Des Sciences Du Végétal; Francia. Université Paris Diderot - Paris 7; FranciaFil: Gouzy, Jérome. Laboratoire Des Interactions Plantes-microorganismes; FranciaFil: Frugier, Florian. Institut Des Sciences Du Végétal; FranciaFil: Crespi, Martin. Institut Des Sciences Du Végétal; FranciaFil: Lelandais Brière, Christine. Institut Des Sciences Du Végétal; Francia. Université Paris Diderot - Paris 7; Franci

Small RNA profiles in soybean primary root tips under water deficit

Background: Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling.Methods: Here we report miRNA profiles specifically from well-watered and water-stressed primary root tips (0 to 8 mm from the root apex) of soybean. Small RNA sequencing confirmed the expression of vastly diverse miRNA (303 individual miRNAs) population, and, importantly several conserved miRNAs were abundantly expressed in primary root tips.Results: Notably, 12 highly conserved miRNA families were differentially regulated in response to water-deficit; six were upregulated while six others were downregulated at least by one fold (log2) change. Differentially regulated soybean miRNAs are targeting genes include auxin response factors, Cu/Zn Superoxide dismutases, laccases and plantacyanin and several others.Conclusions: These results highlighted the importance of miRNAs in primary root tips both under control and water-deficit conditions; under control conditions, miRNAs could be important for cell division, cell elongation and maintenance of the root apical meristem activity including quiescent centre whereas under water stress differentially regulated miRNAs could decrease auxin signaling and oxidative stress as well as other metabolic processes that save energy and water.Peer reviewedBiochemistry and Molecular Biolog

Les ARN non-codants impliqués dans la réponse des plantes aux contraintes environnementales

Les ARN ne codant pas de protéines (ou ARNnc) ont émergé ces dernières années comme une part essentielle du transcriptome des cellules eucaryotes. Les approches récentes de génomique ont en effet permis de découvrir une grande variété d’ARNnc, de petite ou de grande taille, impliqués dans des réseaux de régulations moléculaires très complexes. Bien que de nombreux longs ARNnc soient régulés en réponse aux stresses abiotiques, leur fonction demeure mal comprise. Les petits ARN, quant à eux, sont des acteurs majeurs de la régulation génique aussi bien au niveau transcriptionnel que post-transcriptionnel. Ainsi, plusieurs d’entre eux jouent des rôles essentiels dans la réponse des plantes aux stresses. Dans cette revue, nous présenterons certains ARNnc associés aux contraintes environnementales (salinité, froid ou carence nutritionnelle) chez les végétaux. La compréhension des réseaux de régulations liés à ces ARN régulateurs devrait permettre de mettre en évidence de nouveaux mécanismes associés à l’adaptation des plantes à leur environnement

Les microARN : Une nouvelle classe de régulateurs de l’expression génique

Les microARN sont des ARN non codants de 21 à 25 nucléotides qui contrôlent l’expression génique au niveau post-trancriptionnel. Plusieurs centaines de gènes codant pour des microARN ont été identifiés chez les animaux, et une quarantaine chez les plantes. Certains de ces gènes sont conservés entre espèces et parfois même entre phylums. Ces microARN règlent l’expression génique en s’appariant avec des ARNm cibles dont ils sont partiellement complémentaires. Cette hybridation réprime la traduction de la protéine correspondante ou clive l’ARNm cible au milieu du site de fixation du microARN. Ce dernier mécanisme est très similaire à celui mis en oeuvre lors de l’interférence par l’ARN.MicroRNAs (miRs) are small non coding RNA, about 21-25 nucleotides in length, that direct post transcriptional regulation of gene expression through interaction with homologous mRNAs. Hundreds miR genes have been identified in animals and 40 in plants. Many of them are conserved between related species, and in some cases across phyla. Two mechanisms for regulation of gene expression by miRs have been reported. As described for lin-4 and let-7 miR of C.elegans, miRs can inhibit translation, which seems to represent the major mode of regulation in animals, or can direct cleavage of target mRNAs, which seems to represent the major mode of regulation in plants