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53
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
- Cell
, 2005
"... In higher eukaryotes, miRNAs and siRNAs guide translational inhibition, mRNA cleavage, or chromatin regulation. We found that the antisense overlapping gene pair of D 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), a stress-related gene, and SRO5, a gene of unknown function, generates two types of ..."
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Cited by 101 (2 self)
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In higher eukaryotes, miRNAs and siRNAs guide translational inhibition, mRNA cleavage, or chromatin regulation. We found that the antisense overlapping gene pair of D 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), a stress-related gene, and SRO5, a gene of unknown function, generates two types of siRNAs. When both transcripts are present, a 24-nt siRNA is formed by a biogenesis pathway dependent on DCL2, RDR6, SGS3, and NRPD1A. Initial cleavage of the P5CDH transcript guided by the 24-nt siRNA establishes a phase for the subsequent generation of 21-nt siRNAs by DCL1 and further cleavage of P5CDH transcripts. The expression of SRO5 is induced by salt, and this induction is required to initiate siRNA formation. Our data suggest that the P5CDH and SRO5 proteins are also functionally related, and that the P5CDH-SRO5 gene pair defines a mode of siRNA function and biogenesis that may be applied to other natural cis-antisense gene pairs in eukaryotic genomes.
Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation.
- Cell
, 2008
"... SUMMARY Trans-acting siRNA form through a refined RNAi mechanism in plants. miRNA-guided cleavage triggers entry of precursor transcripts into an RNA-DEPENDENT RNA POLYMERASE6 pathway, and sets the register for phased tasiRNA formation by DICER-LIKE4. Here, we show that miR390-ARGONAUTE7 complexes ..."
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Cited by 42 (3 self)
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SUMMARY Trans-acting siRNA form through a refined RNAi mechanism in plants. miRNA-guided cleavage triggers entry of precursor transcripts into an RNA-DEPENDENT RNA POLYMERASE6 pathway, and sets the register for phased tasiRNA formation by DICER-LIKE4. Here, we show that miR390-ARGONAUTE7 complexes function in distinct cleavage or noncleavage modes at two target sites in TAS3a transcripts. The AGO7 cleavage, but not the noncleavage, function could be provided by AGO1, the dominant miRNA-associated AGO, but only when AGO1 was guided to a modified target site through an alternate miRNA. AGO7 was highly selective for interaction with miR390, and miR390 in turn was excluded from association with AGO1 due entirely to an incompatible 5 0 adenosine. Analysis of AGO1, AGO2, and AGO7 revealed a potent 5 0 nucleotide discrimination function for some, although not all, ARGONAUTEs. miR390 and AGO7, therefore, evolved as a highly specific miRNA guide/effector protein pair to function at two distinct tasiRNA biogenesis steps.
Evolutionary Patterns of Non-Coding RNAs
, 2005
"... A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Ne ..."
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Cited by 22 (7 self)
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A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this “Modern RNA World ” and its components. In this contribution we attempt to provide at least a cursory overview of the diversity of non-coding RNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates, studies of the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution
Origins and evolution of microRNA genes in plant species.
- Genome Biol. Evol.,
, 2012
"... Abstract MicroRNAs (miRNAs) are among the most important regulatory elements of gene expression in animals and plants. However, their origin and evolutionary dynamics have not been studied systematically. In this paper, we identified putative miRNA genes in 11 plant species using the bioinformatic ..."
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Cited by 18 (0 self)
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Abstract MicroRNAs (miRNAs) are among the most important regulatory elements of gene expression in animals and plants. However, their origin and evolutionary dynamics have not been studied systematically. In this paper, we identified putative miRNA genes in 11 plant species using the bioinformatic technique and examined their evolutionary changes. Our homology search indicated that no miRNA gene is currently shared between green algae and land plants. The number of miRNA genes has increased substantially in the land plant lineage, but after the divergence of eudicots and monocots, the number has changed in a lineage-specific manner. We found that miRNA genes have originated mainly by duplication of preexisting miRNA genes or protein-coding genes. Transposable elements also seem to have contributed to the generation of speciesspecific miRNA genes. The relative importance of these mechanisms in plants is quite different from that in Drosophila species, where the formation of hairpin structures in the genomes seems to be a major source of miRNA genes. This difference in the origin of miRNA genes between plants and Drosophila may be explained by the difference in the binding to target mRNAs between plants and animals. We also found that young miRNA genes are less conserved than old genes in plants as well as in Drosophila species. Yet, nearly half of the gene families in the ancestor of flowering plants have been lost in at least one species examined. This indicates that the repertoires of miRNA genes have changed more dynamically than previously thought during plant evolution.
Primate microRNAs miR-220 and miR-492 lie within processed pseudogenes
- J. Heredity
, 2006
"... MicroRNAs (miRNAs) are a new and abundant class of small, noncoding RNAs. To date, the evolutionary history of most of these loci appears to be marked by duplication and di-vergence. The ultimate origin of miRNAs remains an open question. A survey of the genomic context of more than 300 human miRNA ..."
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Cited by 14 (0 self)
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MicroRNAs (miRNAs) are a new and abundant class of small, noncoding RNAs. To date, the evolutionary history of most of these loci appears to be marked by duplication and di-vergence. The ultimate origin of miRNAs remains an open question. A survey of the genomic context of more than 300 human miRNA loci revealed that two primate-specific miRNAs, miR-220 and miR-492, each lie within a processed pseudogene. In silico and in vitro examinations of these two loci suggest that this is a rare phenomenon requiring the juxtaposition of a specific combination of factors. Thus it appears that, while processed pseudogenes are good candi-dates for miRNA incubators, it is unlikely that more than a very small percentage of new miRNAs arise this way. MicroRNAs (miRNAs) are an abundant class of small, non-coding RNAs. First reported in Caenorhabditis elegans just over
Plant microRNAs and development
- Int. J. Dev. Biol
, 2005
"... ABSTRACT MicroRNAs (miRNAs) act as negative regulators of gene expression in eukaryotes, a discovery that has opened an expanding field of biological research. Plant miRNAs are known to repress gene expression posttranscriptionally, mainly by guiding cleavage but also by attenuating the translation ..."
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Cited by 7 (0 self)
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ABSTRACT MicroRNAs (miRNAs) act as negative regulators of gene expression in eukaryotes, a discovery that has opened an expanding field of biological research. Plant miRNAs are known to repress gene expression posttranscriptionally, mainly by guiding cleavage but also by attenuating the translation of target transcripts. In addition, it has been shown that plant miRNAs can also act at the transcriptional level by directing the methylation of target chromosomal loci. Genetic and biochemical approaches are quickly broadening our knowledge of the biogenesis and function of plant miRNAs. Computational approaches have uncovered an unexpectedly large number of miRNAs and their targets in plants. The targets of plant miRNAs often belong to families of transcription factors involved in the control of developmental processes. We review the status of research in this dynamic field, summarizing recent advances in our understanding of the biogenesis and mechanism of action of plant miRNAs, as well as in the developmental processes they regulate.
Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana
, 2010
"... In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances ..."
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Cited by 4 (0 self)
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In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing initiated by other classes of plant small RNAs (sRNAs) than siRNAs can extend has been less clear. Using a system based on the silencing of the CH42 gene, we have tracked the mobility of silencing signals initiated in phloem companion cells by artificial microRNAs (miRNA) and transacting siRNA (tasiRNA) that have the same primary sequence. In this system, both the ta-siRNA and the miRNA act at a distance. Non-autonomous effects of the miRNA can be triggered by several different miRNA precursors deployed as backbones. While the tasiRNA also acts non-autonomously, it has a much greater range than the miRNA or hairpinderived siRNAs directed against CH42, indicating that biogenesis can determine the non-autonomous effects of sRNAs. In agreement with this hypothesis, the silencing signals initiated by different sRNAs differ in their genetic requirements.
Conference summary
- In Marketing Science Institute Conference on Big Data
, 2012
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RNA silencing pathways in plants
, 2004
"... In one of the first described examples of RNA silenc-ing there was coordinate suppression (cosuppression) of a transgene and an endogenous gene. Petunia plants with a flower pigment transgene (chalcone synthase [CS]) had white flowers because the transgene and the endogenous gene were silenced (Napo ..."
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Cited by 2 (0 self)
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In one of the first described examples of RNA silenc-ing there was coordinate suppression (cosuppression) of a transgene and an endogenous gene. Petunia plants with a flower pigment transgene (chalcone synthase [CS]) had white flowers because the transgene and the endogenous gene were silenced (Napoli et al. 1990; van der Krol et al. 1990). There was no reduction in the transcription of the endogenous gene and it seemed likely that an RNA turnover mechanism was specifically targeted at CS RNA (van Blokland et al. 1994). In this and in other cosup-pression systems, the target RNA had a nucleotide se-quence that was identical to the transgene. When these findings were first described, it was not understood how such cosuppression could have such sequence specificity. However, based on discoveries in animal and plant sys-tems, it is now apparent that cosuppression is an RNA si-lencing process (Baulcombe 2004) in which RNA and DNA sequences are targeted specifically depending on the nucleotide sequence. The defining feature of RNA silencing is the involve-ment of long double-stranded (ds) RNA, which is pro-cessed by an RNAse III-type enzyme (Dicer) into short (21–25-nucleotide) interfering (si) RNAs that initially ex-ist in a ds form with two nucleotide overhangs at the 3´ ends. These short RNAs are separated into a single-stranded (ss) form that guides effector complexes of si-lencing to a target RNA by Watson–Crick base pairing. Proteins of the Argonaute class are key components of these effector complexes. They bind siRNAs (Song et al.
