Sequence and Expression Differences Underlie Functional Specialization of Arabidopsis MicroRNAs miR159 and miR319

Palatnik, Javier F.; Wollmann, Heike; Schommer, Carla; Schwab, Rebecca; Boisbouvier, Jérôme; Rodríguez, Ramiro E.; Warthmann, Norman; Allen, Edwards; Dezulian, Tobias; Huson, Daniel H.; Carrington, James C.; Weigel, Detlef

doi:10.1016/j.devcel.2007.04.012

Cited by 362 publications

(337 citation statements)

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“…It has been previously shown that the miR159 and miR319 families are related in sequence and targets but that divergent expression and slight sequence variation allows for specific biological functions for these distinct miRNAs (Palatnik et al, 2007). After our sequence analysis of A. coerulea, it is not possible to determine conclusively if 2183893560 and 2185799162 encode miR159 and/or miR319.…”

Section: Mir159/319mentioning

confidence: 92%

“…The fact that miR529 appears to be closely related to miR156 raises the possibility that it may have been lost without ill effect, possibility due to some redundancy with miR156. Before this hypothesis is tested, detailed work comparing miR156 and miR529 and their target specificity, similar to Palatnik et al (2007) where they determined that subtle sequence and expression differences in the related miR159 and miR319 families led to distinct functions, needs to be performed.…”

Section: Mir529mentioning

confidence: 99%

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Identification of conserved Aquilegia coerulea microRNAs and their targets

Puzey

Kramer

2009

Gene

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Aquilegia is an emerging model organism that is phylogenetically intermediate between the core eudicot and monocot models Arabidopsis and Oryza. In this study, we have used a comparative genomics approach to identify 45 Aquilegia microRNAs that comprise 20 separate plant microRNA families. We have predicted 85 targets of these newly identified Aquilegia microRNAs, including transcription factors and loci involved in metabolism, stress responses, transport, and auxin signaling. microRNA families from 16 plant species and the newly identified microRNAs from Aquilegia were analyzed in a phylogenetic context revealing 40 distantly conserved microRNA families. In addition to these highly conserved plant microRNA families, several families with disjointed phylogenetic distribution were identified. This study provides a phylogenetically important dataset for plant microRNA evolution studies. The current study is the first to identify miRNAs in a lower eudicot in which comprehensive genomic resources are becoming available. 16 plant species and the newly identified microRNAs from Aquilegia were analyzed in a phylogenetic context revealing 40 distantly conserved microRNA families. In addition to these highly conserved plant microRNA families, several families with disjointed phylogenetic distribution were identified. This study provides a phylogenetically important dataset for plant microRNA evolution studies. The current study is the first to identify miRNAs in a lower eudicot in which comprehensive genomic resources are becoming available.

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Section: Mir159/319mentioning

confidence: 92%

Section: Mir529mentioning

confidence: 99%

Identification of conserved Aquilegia coerulea microRNAs and their targets

Puzey

Kramer

2009

Gene

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“…A possible mechanism could involve stimulation of DUO1 turnover via miR159-mediated regulation since the DUO1 transcript contains a functional miR159 binding site (Palatnik et al, 2007). Borges et al (2011) found that miR159a was significantly enriched in sperm cells and miR159-guided cleavage products as well as noncanonical products were detected in wild-type inflorescences and pollen Allen et al, 2010).…”

Section: Daz1 and Daz2 Are Required For Sperm Cell Differentiation Anmentioning

confidence: 99%

An EAR-Dependent Regulatory Module Promotes Male Germ Cell Division and Sperm Fertility in Arabidopsis

et al. 2014

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The production of the sperm cells in angiosperms requires coordination of cell division and cell differentiation. In Arabidopsis thaliana, the germline-specific MYB protein DUO1 integrates these processes, but the regulatory hierarchy in which DUO1 functions is unknown. Here, we identify an essential role for two germline-specific DUO1 target genes, DAZ1 and DAZ2, which encode EAR motif-containing C 2 H 2 -type zinc finger proteins. We show that DAZ1/DAZ2 are required for germ cell division and for the proper accumulation of mitotic cyclins. Importantly, DAZ1/DAZ2 are sufficient to promote G2-to M-phase transition and germ cell division in the absence of DUO1. DAZ1/DAZ2 are also required for DUO1-dependent cell differentiation and are essential for gamete fusion at fertilization. We demonstrate that the two EAR motifs in DAZ1/DAZ2 mediate their function in the male germline and are required for transcriptional repression and for physical interaction with the corepressor TOPLESS. Our findings uncover an essential module in a regulatory hierarchy that drives mitotic transition in male germ cells and implicates gene repression pathways in sperm cell formation and fertility.

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“…However, with the modified structure, the 21-paired-base rule would cause DCL1 to release a 21-nt miR173; in Fig. 2A, this modified construct is termed MIR173 21 , and the unmodified construct is termed MIR173 22 .…”

mentioning

confidence: 99%

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

Chen

Patel

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

465

478

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The effect of RNA silencing in plants can be amplified if the production of secondary small interfering RNAs (siRNAs) is triggered by the interaction of microRNAs (miRNAs) or siRNAs with a long target RNA. miRNA and siRNA interactions are not all equivalent, however; most of them do not trigger secondary siRNA production.Here we use bioinformatics to show that the secondary siRNA triggers are miRNAs and transacting siRNAs of 22 nt, rather than the more typical 21-nt length. Agrobacterium-mediated transient expression in Nicotiana benthamiana confirms that the siRNAinitiating miRNAs, miR173 and miR828, are effective as triggers only if expressed in a 22-nt form and, conversely, that increasing the length of miR319 from 21 to 22 nt converts it to an siRNA trigger. We also predicted and validated that the 22-nt miR771 is a secondary siRNA trigger. Our data demonstrate that the function of small RNAs is influenced by size, and that a length of 22 nt facilitates the triggering of secondary siRNA production.gene silencing | microRNA | transacting siRNA S mall silencing RNAs (sRNAs) in plants and animals, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play important roles in the development and the response to pathogens and stresses. These RNAs are also valuable tools in functional genomics and biotechnology. The sRNAs associate with ARGONAUTE (AGO) and other proteins in silencing effector complexes, and they bind to a target nucleic acid via Watson-Crick base pairing. In most instances, the silencing is a direct consequence of this interaction, and the AGO effector mediates RNA-mediated DNA or histone methylation, endonucleolytic RNA cleavage, or translational inhibition. In a few instances, an sRNA interaction also triggers the production of secondary siRNAs. The targeted RNA is converted into double-stranded RNA (dsRNA) by RNA-DEPENDENT RNA POLYMERASEs (RDRs), which is then cleaved into the secondary siRNAs by DICER-LIKE (DCL) nucleases (1). Several proteins are known to be required for this process, but until now, the reason why most sRNA interactions do not result in secondary siRNA production was unclear.The transacting siRNA (tasiRNA) pathway in plants involves secondary siRNA production (2). Noncoding transcripts encoded by TAS1-4 genes serve as the precursors of tasiRNAs (3-5). After miRNA-directed cleavage, part of the remaining transcript is converted into dsRNA by RDR6. DCL4 then cleaves the dsRNA and generates tasiRNAs in a 21-nt phase relative to positions 10 and 11 of the miRNA that defines the site of targeted cleavage. TAS1 and TAS2 are targets of miR173, and their tasiRNAs in turn can target mRNAs for pentatricopeptide repeat (PPR) proteins. In one instance, a small sRNA cascade is initiated by miR173 (6, 7), because a TAS2-derived tasiRNA can itself initiate secondary siRNA production on several PPR mRNAs. The initiator of TAS3 tasiRNA is miR390 (3,8), and the TAS3 targets are AUXIN RESPONSE FACTOR mRNAs that influence the change from juvenile phase to adult phase, leaf morphology,...

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Sequence and Expression Differences Underlie Functional Specialization of Arabidopsis MicroRNAs miR159 and miR319

Cited by 362 publications

References 44 publications

Identification of conserved Aquilegia coerulea microRNAs and their targets

Identification of conserved Aquilegia coerulea microRNAs and their targets

An EAR-Dependent Regulatory Module Promotes Male Germ Cell Division and Sperm Fertility in Arabidopsis

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

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