Short RNAs Can Identify New Candidate Transposable Element Families in Arabidopsis

Mette, Michael Florian; Winden, J. van der; Matzke, Marjori; Matzke, A. J. M.

doi:10.1104/pp.007047

Cited by 125 publications

(63 citation statements)

References 18 publications

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“…miRNAs posttranscriptionally down-regulate gene expression by cleavage or translational repression of target mRNAs. In plants, miRNAs were first found in 2002 [2][3][4][5]. To date, 4584 miRNAs have been identified in animals and plants (miRBase, http://microrna.sanger.ac.uk/, Release 9.2).…”

Section: Introductionmentioning

confidence: 99%

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

et al. 2007

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It has been shown that overexpression of MIR156b/c resulted in a bushy phenotype in maize and rice. Our results indicated that the MIR156b/c locus was highly conserved among cereals, but not in dicots and that genome duplication events played an important role in the evolution of the miR156 family. Genetic diversity investigation at the locus indicated that only $9% of nucleotide diversity observed in wild rice (O. rufigogon) was maintained in the cultivated rice and the neutral model was rejected (P < 0.05) based on Tajima's D and Fu and Li's D * and F * tests. To our knowledge, this is the first example of miRNA gene to be targeted by both natural and domestication selection in plants.

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Section: Introductionmentioning

confidence: 99%

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

et al. 2007

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“…There have been many studies to identify plant miRNAs and numerous miRNAs have been discovered in Arabidopsis and rice (Adai et al 2005;Bonnet et al 2004;Floyd and Bowman 2004;Jones-Rhoades and Bartel 2004;Li and Zhang 2005;Llave et al 2002;Mette et al 2002;Sunkar and Zhu 2004;Wang et al 2004a, b;Palatnik et al 2003;Park et al 2002;Reinhart et al 2002;Sunkar et al 2005;Wang et al 2004a, b). miRNAs have also been identified in other plant species, such as Nicotiana tabacum (Billoud et al 2005), Zea mays (Dezulian et al 2005), Sorghum bicolor (Bedell et al 2005), Populus Tuskan et al 2006), Gossypium hirsutum (Qiu et al 2007), Brassica napus ) and Vitis vinifera (Velasco et al 2007).…”

Section: Mirnas and Plant Defensementioning

confidence: 99%

Roles of microRNA in plant defense and virus offense interaction

Gan

Chi

et al. 2008

Plant Cell Rep

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MicroRNAs (miRNA) that are around 22 nucleotides long non-protein-coding RNAs, play key regulatory roles in plants. Recent research findings show that miRNAs are involved in plant defense and viral offense systems. Advances in understanding the mechanism of miRNA biogenesis and evolution are useful for elucidating the complicated roles they play in viral infection networks. In this paper a brief summary of evolution of plant antivirus defense is given and the function of miRNAs involved in plant-virus competition is highlighted. It is believed that miRNAs have several advantages over homology-dependent and siRNA-mediated gene silencing when they are applied biotechnologically to promote plant anti-virus defense. miRNA-mediated anti-virus pathway is an ancient mechanism with a promising future. However, using miRNAs as a powerful anti-virus tool will be better realized only if miRNA genomics and functions in plant viral infection are fully understood.

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“…miRNAs are processed from the dsRNA regions of short, z70-90 base pairs (bp), stem-loop (hairpin) RNA structures by the same endonuclease, Dicer (or Dicer-like in plants), which cleaves siRNAs from longer dsRNA sequences. A connection between TEs and miRNAs was more recently established when a number of miRNA genes were found to be derived from TE sequences (Mette et al 2002;Smalheiser and Torvik 2005;Borchert et al 2006;). …”

Section: Introductionmentioning

confidence: 99%

Dual coding of siRNAs and miRNAs by plant transposable elements

Piriyapongsa¹,

Jordan²

2008

RNA

260

226

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We recently proposed a specific model whereby miRNAs encoded from short nonautonomous DNA-type TEs known as MITEs evolved from corresponding ancestral full-length (autonomous) elements that originally encoded short interfering (siRNAs). Our miRNA-origins model predicts that evolutionary intermediates may exist as TEs that encode both siRNAs and miRNAs, and we analyzed Arabidopsis thaliana and Oryza sativa (rice) genomic sequence and expression data to test this prediction. We found a number of examples of individual plant TE insertions that encode both siRNAs and miRNAs. We show evidence that these dual coding TEs can be expressed as readthrough transcripts from the intronic regions of spliced RNA messages. These TE transcripts can fold to form the hairpin (stem-loop) structures characteristic of miRNA genes along with longer doublestranded RNA regions that typically are processed as siRNAs. Taken together with a recent study showing Drosha independent processing of miRNAs from Drosophila introns, our results indicate that ancestral miRNAs could have evolved from TEs prior to the full elaboration of the miRNA biogenesis pathway. Later, as the specific miRNA biogenesis pathway evolved, and numerous other expressed inverted repeat regions came to be recognized by the miRNA processing endonucleases, the host gene-related regulatory functions of miRNAs emerged. In this way, host genomes were afforded an additional level of regulatory complexity as a by-product of TE defense mechanisms. The siRNA-to-miRNA evolutionary transition is representative of a number of other regulatory mechanisms that evolved to silence TEs and were later co-opted to serve as regulators of host gene expression.

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Short RNAs Can Identify New Candidate Transposable Element Families in Arabidopsis

Cited by 125 publications

References 18 publications

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

Roles of microRNA in plant defense and virus offense interaction

Dual coding of siRNAs and miRNAs by plant transposable elements

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