Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

Mi, Shijun; Cai, Tao; Hu, Yugang; Chen, Yemiao; Hodges, Emily; Ni, Fangrui; Wu, Liang; Li, Shan; Zhou, Huanyu; Long, Chengzu; Chen, She; Hannon, Gregory J.; Qi, Yijun

doi:10.1016/j.cell.2008.02.034

Cited by 1,179 publications

(1,325 citation statements)

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“…It is suggested that the difference in size of the identified miRNAs within different families might offer unique functions for the regulation of miRNA biogenesis or gene expression in plants. It is reported that uracil is more represented at the 5′ side of mature miRNAs; the percentage of representation of mature miRNAs having U at the 5′ side of the stem loop is 66.67%, followed by A (14.52%), C (9.68%), and G (9.14%); this is consistent with previous findings (Mi et al, 2008;Montgomery et al, 2008;Takeda et al, 2008;Zhang et al, 2008). It is speculated that the strong bias of uracil in the first 5′ nucleotide position is due to its important role in the recognition of the miRNA by argonaute1 (Zhang et al, 2006b Table 1 and Fig.…”

Section: Resultssupporting

confidence: 92%

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: Resultssupporting

confidence: 92%

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 contrast to AGO7, AGO2 efficiently incorporated the miR390/miR390* mutant with the flipped central 3-nt ( Supplementary Fig S1 online), suggesting that AGO2 does not inspect the central region for RISC assembly. This is consistent with the previous finding that AGO2 incorporates a wide variety of 5 0 -A small RNAs including viral siRNAs [22][23][24]. miR390/miR390* duplex has two mismatches: a G-U wobble in the seed region (guide position 3) and a G-A mismatch in the central region (guide position 11).…”

Section: Ago7 Inspects the Central Region Of Mir390 Duplexsupporting

confidence: 92%

Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly

2013

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Plant ARGONAUTE7 (AGO7) assembles RNA-induced silencing complex (RISC) specifically with miR390 and regulates the auxinsignalling pathway via production of TAS3 trans-acting siRNAs (tasiRNAs). However, how AGO7 discerns miR390 among other miRNAs remains unclear. Here, we show that the 5 0 adenosine of miR390 and the central region of miR390/miR390* duplex are critical for the specific interaction with AGO7. Furthermore, despite the existence of mismatches in the seed and central regions of the duplex, cleavage of the miR390* strand is required for maturation of AGO7-RISC. These findings suggest that AGO7 uses multiple checkpoints to select miR390, thereby circumventing promiscuous tasiRNA production.

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“…In Arabidopsis, 21-nt sRNAs are produced by DCL4, 24-nt sRNAs by DCL 2 or DCL 3, and DCL1 produces miRNAs that are 22 nucleotides in length [27,40]. In this study a large percentage of the sRNAs had read lengths of 20-24 nucleotides, which is typical for DICER-processed sRNA products [24][25][26].…”

Section: Discussionmentioning

confidence: 92%

“…Aspergillus flavus produces AfB 1 and AfB 2 , and A. parasiticus single-stranded RNA and are mostly processed by DCL1 into 19-24 nucleotides in Arabidopsis, whereas siRNAs are derived from dsRNA and cleaved into 20-24 nucleotides by DCL2, DCL3 or DCL4 [24][25][26]. In Arabidopsis, loading of sRNAs onto a specific AGO depends on the nucleotide at the 5 -terminal end of the sRNA, for example, miRNAs with a uridine (U) at their 5 end are predominantly associated with AGO1, and miRNAs that start with an adenosine (A) are predominantly associated with AGO2 and AGO4 [27].…”

Section: Introductionmentioning

confidence: 99%

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

et al. 2017

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Power, Imana L.; Dang, Phat M.; Sobolev, Victor S.; Orner, Valerie; Powell, Joseph L.; Lamb, Marshall C.; and Arias, Renée S., "Characterization of small RNA populations in non-transgenic andaflatoxin-reducing-transformed peanut" (2017 t r a c tAflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B 1 than the controls. The objective was to determine the putative involvement of the small RNA populations in aflatoxin reduction. In total, 41 known microRNA (miRNA) families and many novel miRNAs were identified. Among those, 89 known and 10 novel miRNAs were differentially expressed in the transformed lines. We furthermore found two small interfering RNAs derived from the inverted repeat, and 39 sRNAs that mapped without mismatches to the genome of A. flavus and were present only in the transformed lines. This information will increase our understanding of the effectiveness of RNAi and enable the possible improvement of the RNAi technology for the control of aflatoxins.

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Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

Cited by 1,179 publications

References 56 publications

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

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

Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

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