MicroRNAs in plants

Reinhart, Brenda J.; Weinstein, Earl G.; Rhoades, Matthew W.; Bartel, Bonnie; Bartel, David P.

doi:10.1101/gad.1004402

Cited by 1,899 publications

(1,520 citation statements)

References 54 publications

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“…S2). A similar situation is observed when Dicer and DCL1 are depleted in human cell-lines and Arabidopsis thaliana , respectively [59–61]. We speculate that the presence of low levels of miRNAs in DrnB depleted cells is due to processing by DrnA.…”

Section: Resultssupporting

confidence: 78%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.

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Section: Resultssupporting

confidence: 78%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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“…The mature miRNA sequence in each locus is predicted to pair with a nearby genomic segment, forming a dsRNA stem-loop structure, which is contained in miRNA precursors (pri-miRNA and pre-miRNA) and is required for Dicer processing. The mature miRNA can then be processed from either the 5' or the 3' arm of this structure [9]. This type of multiple loci phenomenon has been widely observed in plants and animals [9,[29][30][31].…”

Section: Introductionmentioning

confidence: 93%

“…These are generated by RNase III-like enzymes from long primary transcripts encoded in intergenic regions (IGRs) or introns of the mRNA primary transcripts [5,[7][8][9]. Mature miRNAs can downregulate gene expression by pairing with messages of protein-coding genes to promote mRNA cleavage, or repression of productive translation upon incorporation into a ribonucleoprotein complex (miRNP) similar to the RNA-induced silencing complex (RISC) [10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

“…The mature miRNA can then be processed from either the 5' or the 3' arm of this structure [9]. This type of multiple loci phenomenon has been widely observed in plants and animals [9,[29][30][31]. Although recent research has demonstrated that nearly all the miRNA genes of Arabidopsis are expressed [32], little is known, in plants, about whether the expression or function is different among members within the same miRNA family.…”

Section: Introductionmentioning

confidence: 99%

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Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

Jiang

Yin

et al. 2006

Cell Res

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To understand the expansion of multicopy microRNA (miRNA) families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miR160 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.

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“…The 20-22 nt miRNAs, also called mature miRNAs, are usually located at the stem region of larger precursors, or miRNA genes. In plants, the sizes of miRNA precursors range from 60 to a few hundred nt [5,8]. Mature miRNAs are processed from their precursors by Dicer-like enzymes [9,10].…”

Section: Introductionmentioning

confidence: 99%

Molecular evolution of the rice miR395 gene family

et al. 2005

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MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.

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MicroRNAs in plants

Cited by 1,899 publications

References 54 publications

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

Molecular evolution of the rice miR395 gene family

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