Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana

Alves-Junior, Leonardo; Niemeier, Sandra; Hauenschild, Arne; Rehmsmeier, Marc; Merkle, Thomas

doi:10.1093/nar/gkp272

Cited by 101 publications

(61 citation statements)

References 76 publications

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“…in concordance with the initial threshold used in [19]. Note that for the final set, the authors in [19] used a stricter 75% mfe cutoff. In Arabidopsis and using a 75% mfe threshold level, we obtained 2,967 unique targets transcripts for 218 miRNAs.…”

Section: Methodsmentioning

confidence: 89%

Comparative analysis of miRNAs and their targets across four plant species

Lenz

Walther

2011

BMC Res Notes

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BackgroundMicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs and their respective gene targets across four plant species: Arabidopsis thaliana (Ath), Medicago truncatula(Mtr), Brassica napus (Bna), and Chlamydomonas reinhardtii (Cre).ResultsmiRNAs were obtained from mirBase with 218 miRNAs for Ath, 375 for Mtr, 46 for Bna, and 73 for Cre, annotated for each species respectively. miRNA targets were obtained from available database annotations, bioinformatic predictions using RNAhybrid as well as predicted from an analysis of mRNA degradation products (degradome sequencing) aimed at identifying miRNA cleavage products. On average, and considering both experimental and bioinformatic predictions together, every miRNA was associated with about 46 unique gene transcripts with considerably variation across species. We observed a positive and linear correlation between the number miRNAs and the total number of transcripts across different plant species suggesting that the repertoire of miRNAs correlates with the size of the transcriptome of an organism. Conserved miRNA-target pairs were found to be associated with developmental processes and transcriptional regulation, while species-specific (in particular, Ath) pairs are involved in signal transduction and response to stress processes. Conserved miRNAs have more targets and higher expression values than non-conserved miRNAs. We found evidence for a conservation of not only the sequence of miRNAs, but their expression levels as well.ConclusionsOur results support the notion of a high birth and death rate of miRNAs and that miRNAs serve many species specific functions, while conserved miRNA are related mainly to developmental processes and transcriptional regulation with conservation operating at both the sequence and expression level.

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Section: Methodsmentioning

confidence: 89%

Comparative analysis of miRNAs and their targets across four plant species

Lenz

Walther

2011

BMC Res Notes

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“…, 2006; Fahlgren et al. , 2007; Alves‐Junior et al. , 2009) using more sophisticated algorithms that take into consideration further parameters such as the minimum free energy of the duplex, expression profiles of the putative targets in miRNA biogenesis mutants, and the position of the mismatches, as the pairing in the 5′ seed region of the miRNA and around the cleavage site (spanning nucleotides 10 and 11) appears to be the most important (Schwab et al.…”

Section: Discussionmentioning

confidence: 99%

“…, 2008). The only exception is from a recent study (Alves‐Junior et al. , 2009), in which a target of miR161 containing six GU wobbles and two mismatches was predicted and validated by 5′‐RACE PCR.…”

Section: Discussionmentioning

confidence: 99%

“…Using a system of penalty scoring that takes into account GU wobbles and bulges, and restricting the results to target sequences conserved between species, more targets could be predicted and validated (Jones- Rhoades and Bartel, 2004). Finally, additional targets have been found (Wang et al, 2004;Allen et al, 2005;Schwab et al, 2005;Rajagopalan et al, 2006;Fahlgren et al, 2007;Alves-Junior et al, 2009) using more sophisticated algorithms that take into consideration further parameters such as the minimum free energy of the duplex, expression profiles of the putative targets in miRNA biogenesis mutants, and the position of the mismatches, as the pairing in the 5¢ seed region of the miRNA and around the cleavage site (spanning nucleotides 10 and 11) appears to be the most important (Schwab et al, 2005;Mallory and Bouché , 2008). About 120 Arabidopsis miRNA/target mRNA duplexes have been validated by 5¢-RACE PCR since the discovery of miRNAs in plants (Table S1), and we found only six duplexes that exceed four mismatches in this list (if we consider GU as a mismatch).…”

Section: Discussionmentioning

confidence: 99%

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microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis

2010

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SUMMARY microRNA398 (miR398) is a conserved miRNA of plants that targets two of the three copper/zinc superoxide dismutases (SOD) of Arabidopsis (CSD1 and CSD2) by triggering cleavage or inhibiting translation of their mRNAs. We analysed the transcriptomes of mutants impaired in miR398 production, and found that the mRNAs encoding the copper chaperone for superoxide dismutase (CCS1), which delivers copper to CSD1 and CSD2 apoproteins in different cellular compartments, are undiscovered targets of miR398. We identified the cleavage site in CCS1 mRNAs by 5¢-RACE PCR. We further show that both CCS1 protein and mRNA levels are tightly linked to the quantities of miR398, which are themselves dependent on the copper content in the medium. We generated transgenic plants carrying a CCS1 mRNA version resistant to cleavage by miR398, and demonstrated that both CCS1 mRNAs and proteins accumulate in these plants when miR398 is abundant and copper limiting. Moreover, we show that one of the ten ARGONAUTE proteins of Arabidopsis (AGO10) is involved in miR398-directed translational inhibition of CCS1 mRNAs, as CCS1 protein, but not CCS1 mRNAs accumulates in ago10 (zll) mutants. Thus, miR398 mediates the cleavage and translational inhibition of mRNAs encoding CCS1, the chaperone protein that is essential for generating the mature copper/zinc SODs of Arabidopsis. Our results also imply that new targets that have not been identified by computing analyses have yet to be discovered, even for an extensively studied miRNA such as miR398.

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“…To date, large numbers of small RNAs have been identified by direct cloning and/or deep sequencing, with some targets being originally predicted via bioinformatics, based on either the perfect or nearly perfect sequence complementarity between a miRNA and the target mRNA or sequence conservation among different species in higher plants (Archak and Nagaraju, 2007; Alves-Junior et al, 2009). However, due to the existence of some mismatches in miRNA–target pairing, target prediction was subjected to challenge (Jones-Rhoades and Bartel, 2004).…”

Section: Introductionmentioning

confidence: 99%

Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis

Yang¹,

Wang²,

Yuan³

et al. 2013

Journal of Experimental Botany

183

132

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MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide RNAs that regulate gene expression at the transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress, and pathogen responses. miRNAs with their targets have been widely studied in model plants, but limited knowledge is available on the small RNA population of cotton (Gossypium hirsutum)—an important economic crop, and global identification of related targets through degradome sequencing has not been developed previously. In this study, small RNAs and their targets were identified during cotton somatic embryogenesis (SE) through high-throughput small RNA and degradome sequencing, comparing seedling hypocotyl and embryogenic callus (EC) of G. hirsutum YZ1. A total of 36 known miRNA families were found to be differentially expressed, of which 19 miRNA families were represented by 29 precursors. Twenty-five novel miRNAs were identified. A total of 234 transcripts in EC and 322 transcripts in control (CK) were found to be the targets of 23 and 30 known miRNA families, respectively, and 16 transcripts were targeted by eight novel miRNAs. Interestingly, four trans-acting small interfering RNAs (tas3-siRNAs) were also found in degradome libraries, three of which perfectly matched their precursors. Several targets were further validated via RNA ligase-mediated rapid amplification of 5’ cDNA ends (RLM 5’-RACE). The profiling of the miRNAs and their target genes provides new information on the miRNAs network during cotton SE.

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Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana

Cited by 101 publications

References 76 publications

Comparative analysis of miRNAs and their targets across four plant species

Comparative analysis of miRNAs and their targets across four plant species

microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis

Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis

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