Finding MicroRNA Targets in Plants: Current Status and Perspectives

Ding, Jiandong; Zhou, Shuigeng; Guan, Jihong

doi:10.1016/j.gpb.2012.09.003

Cited by 51 publications

(33 citation statements)

References 133 publications

(153 reference statements)

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“…These particular tools were tailored to predict miRNA targets in plants based on specific plant miRNA–target pairing (Ding et al . ). Experimental approaches such as Northern blot and RT‐qPCR were used to validate and quantify the expression of predicted miRNA targets.…”

Section: Potential Mirna Function In Fruit Treesmentioning

confidence: 97%

MicroRNAs in fruit trees: discovery, diversity and future research directions

et al. 2014

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Since the first description of microRNAs (miRNAs) 20 years ago, the number of miRNAs identified in different eukaryotic organisms has exploded, largely due to the recent advances in DNA sequencing technologies. Functional studies, mostly from model species, have revealed that miRNAs are major post-transcriptional regulators of gene expression in eukaryotes. In plants, they are implicated in fundamental biological processes, from plant development and morphogenesis, to regulation of plant pathogen and abiotic stress responses. Although a substantial number of miRNAs have been identified in fruit trees to date, their functions remain largely uncharacterised. The present review aims to summarise the progress made in miRNA research in fruit trees, focusing specifically on the economically important species Prunus persica, Malus domestica, Citrus spp, and Vitis vinifera. We also discuss future miRNA research prospects in these plants and highlight potential applications of miRNAs in the on-going improvement of fruit trees.

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Section: Potential Mirna Function In Fruit Treesmentioning

confidence: 97%

MicroRNAs in fruit trees: discovery, diversity and future research directions

et al. 2014

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“…Plant miRNAs are approximately 21 nt-long small regulatory RNAs that are derived from the processing of longer primary miRNA transcripts [115,116]. miRNAs recognize their mRNA targets based on imperfect sequence complementation.…”

Section: Post-transcriptional Regulationmentioning

confidence: 99%

Cold Signaling and Cold Response in Plants

Miura

Furumoto

2013

IJMS

415

295

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Plants are constantly exposed to a variety of environmental stresses. Freezing or extremely low temperature constitutes a key factor influencing plant growth, development and crop productivity. Plants have evolved a mechanism to enhance tolerance to freezing during exposure to periods of low, but non-freezing temperatures. This phenomenon is called cold acclimation. During cold acclimation, plants develop several mechanisms to minimize potential damages caused by low temperature. Cold response is highly complex process that involves an array of physiological and biochemical modifications. Furthermore, alterations of the expression patterns of many genes, proteins and metabolites in response to cold stress have been reported. Recent studies demonstrate that post-transcriptional and post-translational regulations play a role in the regulation of cold signaling. In this review article, recent advances in cold stress signaling and tolerance are highlighted.

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“…These include Targetscan, miRanda, DIANAmicroT, PicTAR, whose predictions were integrated into the miRBase, the central annotation database for miRNAs (Kozomara and Griffiths-Jones, 2014) and were also repeatedly evaluated in benchmark studies Ding et al, 2012a;Majoros et al, 2013;Peterson et al, 2014;Xu et al, 2014a). We add to these also MIRZA as it is one of the most recent algorithms, which in many aspects outperforms the other ones (Gumienny and Zavolan, 2015).…”

Section: Common Target Prediction Toolsmentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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Finding MicroRNA Targets in Plants: Current Status and Perspectives

Cited by 51 publications

References 133 publications

MicroRNAs in fruit trees: discovery, diversity and future research directions

MicroRNAs in fruit trees: discovery, diversity and future research directions

Cold Signaling and Cold Response in Plants

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

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