CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thaliana

Park, Wonkeun; Li, Junjie; Song, Rentao; Messing, Joachim; Chen, Xuemei

doi:10.1016/s0960-9822(02)01017-5

Cited by 1,143 publications

(968 citation statements)

References 53 publications

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“…The identification of target genes for miRNAs is an important step in understanding the regulation of miRNA by structural genes. It is well understood that miRNAs and their counterpart target genes have perfect or near-perfect complementarities; computational identification coupled with experimental results have been successful in proving this in plants (Llave et al, 2002a;Park et al, 2002;Reinhart et al, 2002;Rhoades et al, 2002;Song et al, 2009). BLAST search analysis allowing for 1-4 nt mismatches without gaps for 186 miRNA could identify a total of 66 candidate target genes in B. rapa for 33 miRNA families.…”

Section: Discussionmentioning

confidence: 99%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20 th position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

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Section: Discussionmentioning

confidence: 99%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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“…In plants, miRNA genes have been readily discovered based on their cross species sequence conservation and stem-loop structures in completely sequenced genomes of Arabidopsis and rice [8,16,17]. Recently, rice specific or monocot specific microRNAs have been identified which suggests the differentiated evolution of microRNAs in individual plant genome [18,19].…”

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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“…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%

“…Indeed, the vast majority of the predicted or verified miRNA targets encode members of large families of transcription factors that regulate development [15]. Mutants that lack miRNA pathway proteins, such as DICER-LIKE 1 (DCL1), ARGONAUTE 1 (AGO1) and HUA ENHANCER 1 (HEN1), exhibit morphological defects in Arabidopsis and rice, suggesting an important role for miRNA in plant development [8,14,[16][17][18][19][20]. Recently, more and more plant miRNAs have been reported for their specialized developmental functions, such as miR159, miR-JAW, miR160, miR162, miR165/166, miR168, and miR172.…”

Section: Introductionmentioning

confidence: 99%

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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CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thaliana

Cited by 1,143 publications

References 53 publications

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Molecular evolution of the rice miR395 gene family

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

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