Computational identification of plant microRNAs and their targets, including a stress-induced miRNA.

By M. Jones-Rhoades, David P. Bartel. Molecules and Cells, 2004

2,303 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/da380e31e96d734fa4d6db9abf89064342fb0729

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In Plant Science

Citations in the corpus

Plant microRNA: a small regulatory molecule with big impact. (2006, methodology): “miRNA conservation has also been observed in plants (Llave et al., 2002; Reinhart et al., 2002; Sunkar and Zhu, 2004; Wang et al., 2004; Jones-Rhoades and Bartel, 2004; Bonnet et al., 2004a,b; Adai et al., 2005; Axtell and Bartel, 2005), however, only mature plant miRNAs are conserved, unlike the co”
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes (2007, methodology): “miR393 targets mRNAs encoding the auxin receptor, TRANSPORT INHIBITOR RESPONSE1 (TIR1), and related proteins [18,43].”
A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence (2008, background): “In plants, miRNA targets can be predicted with relatively high confidence because of the extensive base pairing between plant miRNAs and their target mRNAs (1).”
PMRD: plant microRNA database (2009, background): “Jones-Rhoades et al. ( 8 ) developed comparative genomic approaches to systematically identify both miRNAs and target genes, which enlarged the miRNAs family and the number of target genes in A. thaliana.”
Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends (2008, methodology): “Next, we searched our libraries for a list of 124 previously predicted but yet to be validated targets of miRNA”
A miRNA involved in phosphate-starvation response in Arabidopsis. (2005, background): “Recently, it was shown that miR395 is induced by sulfate starvation and that its predicted target gene, ATP sulfurylase, is reduced in low sulfate conditions [6].”
MicroRNA Directs mRNA Cleavage of the Transcription Factor NAC1 to Downregulate Auxin Signals for Arabidopsis Lateral Root Development (2005, background): “Subsequent computational analyses by three independent groups increased the number of potential Arabidopsis miRNAs to more than 100 (Bonnet et al., 2004; Jones-Rhoades and Bartel, 2004; Wang et al., 2004).”
RNA silencing in plants (2004, background): “A further important difference is that the plant miRNAs are more perfectly paired to their target RNA and use RNA cleavage rather than translation suppression as the primary silencing mechanis”
Genome Structure of the Legume, Lotus japonicus (2008, background): “A stem-loop structure was searched within a distance of 500 nucleotides from the coding region of the mature miRNA based on the finding that the longest Arabidopsis thaliana precursor sequences identified to date are 411 nucleotides long.(23) Target genes of the miRNA candidates were searched in the”
Auxin: regulation, action, and interaction. (2005, background): “Moreover, miR393 targets mRNAs encoding TIR1 and the three most closely related F-box proteins (Jones-Rhoades and Bartel, 2004; Sunkar and Zhu, 2004).”
miR394 and its target gene LCR are involved in cold stress response in Arabidopsis (2016, neutral): “The biological roles and regulatory networks in plant response to cold stress remain to be elusive. miR394 is one of the highly conserved miRNAs existing in many monocot and dicot plant species (Jones-Rhoades and Bartel, 2004, Huang et al., 2010; Ni et al., 2012; Zhou et al., 2012b).”