Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

Kumar, Dharmender; Singh, Dharmendra; Kanodia, Pulkit; Prabhu, K. V.; Kumar, Manish; Mukhopadhyay, Kunal

doi:10.1155/2014/570176

Cited by 31 publications

(27 citation statements)

References 70 publications

(91 reference statements)

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“…Interestingly, some predicted mirtron-like miRNAs (miR-1225 and miR-1228) are splicing-independent (simtrons) and their biogenesis involves Drosha but neither DGCR8 nor Dicer (Havens et al, 2012). Other non-canonical substrates can be, for example, 5 '-Capped RNAs (Xie et al, 2013), SINE repeat-derived, (Babiarz et al, 2008;Castellano and Stebbing, 2013), small vault RNA (svtRNA2-1a) (Minones-Moyano et al, 2013), or RNase III transcripts (Maurin et al, 2012) including annotated RNAs such as snoRNAs (Ender et al, 2008;Burroughs et al, 2011;Li et al, 2012), 7SL RNA (Ren et al, 2012, tRNA fragments (Maniataki and Mourelatos, 2005a;Haussecker et al, 2010;Burroughs et al, 2011;Maute et al, 2013;Kumar et al, 2014;Venkatesh et al, 2016). Non-canonical miRNAs can be also produced from viral RNAs (Li et al, 2009c;Xu et al, 2009;Bogerd et al, 2010;Kincaid et al, 2014).…”

Section: Additional Small Rnas Associated With Ago Proteinsmentioning

confidence: 99%

“…The high complementarity interactions are also easier to predict and this predictive value is being used for identification of putative plant miRNA targets. (Rhoades et al, 2002;Bonnet et al, 2010;Kumar et al, 2014). While animal miRNA binding sites are typically localized to 3'UTRs, plant miRNA recognition sites can be found in 5'UTRs, ORFs, or 3' UTRS as well as in non-coding RNAs (e.g.…”

Section: Modes Of Mirna Action In Plant Cellsmentioning

confidence: 99%

“…A specific plant-miRNA-target analysis server is psRNATarget: a plant small RNA target analysis server (Dai and Zhao, 2011), which can be used not only for miRNAs but also for other plant small RNA analysis (Guzman et al, 2013;Huang et al, 2014b;Kumar et al, 2014). Other authors use general target prediction algorithms such as Miranda or RNAhybrid either alone (Shweta and Khan, 2014) or in more complex arrangements (Kurubanjerdjit et al, 2013).…”

Section: Target Prediction For Plant Mirnasmentioning

confidence: 99%

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

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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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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Section: Additional Small Rnas Associated With Ago Proteinsmentioning

confidence: 99%

Section: Modes Of Mirna Action In Plant Cellsmentioning

confidence: 99%

Section: Target Prediction For Plant Mirnasmentioning

confidence: 99%

See 1 more Smart Citation

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

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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“…To date, miRNA-based regulation of several plant genes in response to biotic and abiotic stresses has been shown with several studies (Kantar et al 2011a; Hackenberg et al 2014; Kumar et al 2014a; Wang et al 2014). During the miRNA-based stress regulation, alterations in gene expression can be achieved by direct targeting of the gene transcripts.…”

Section: Mirnas As Regulatory Keystones In Cropsmentioning

confidence: 99%

Abiotic stress miRNomes in the Triticeae

Alptekin

Langridge

Budak

2016

Funct Integr Genomics

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The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.

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“…A number of miRNA families have now been identified in wheat, and about twenty miRNA families are conserved in diverse plant species (Yao et al, 2007;Feng et al, 2014;Han et al, 2014;Kumar et al, 2014;Sun et al, 2014). Of these, miR408 contains 21 nucleotides and has been annotated in more than 30 plant species to date, indicating a high level of conservation in different plant species (Axtell and Bowman, 2008;Kozomara and Griffiths-Jones, 2011).…”

mentioning

confidence: 99%

The tae-miR408-Mediated Control of TaTOC1 Genes Transcription Is Required for the Regulation of Heading Time in Wheat

Zhao

Hong

et al. 2016

Plant Physiol.

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ORCID IDs: 0000-0002-1560-7935 (J.Y.W.); 0000-0002-3129-5206 (X.S.Z.).Timing of flowering is not only an interesting topic in developmental biology, but it also plays a significant role in agriculture for its effects on the maturation time of seed. The hexaploid wheat (Triticum aestivum) is one of the most important crop species whose flowering time, i.e. heading time, greatly influences yield. However, it remains unclear whether and how microRNAs regulate heading time in it. In our current study, we identified the tae-miR408 in wheat and its targets in vivo, including Triticum aestivum TIMING OF CAB EXPRESSION-A1 (TaTOC-A1), TaTOC-B1, and TaTOC-D1. The tae-miR408 levels were reciprocal to those of TaTOC1s under long-day and short-day conditions. Wheat plants with a knockdown of TaTOC1s via RNA interference and overexpression of tae-miR408 showed early-heading phenotype. Furthermore, TaTOC1s expression was down-regulated by the tae-miR408 in the hexaploid wheat. In addition, other important agronomic traits in wheat, such as plant height and flag leaf angle, were regulated by both tae-miR408 and TaTOC1s. Thus, our results suggested that the tae-miR408 functions in the wheat heading time by mediating TaTOC1s expression, and the study provides important new information on the mechanism underlying heading time regulation in wheat.

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Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

Cited by 31 publications

References 70 publications

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

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

Abiotic stress miRNomes in the Triticeae

The tae-miR408-Mediated Control of TaTOC1 Genes Transcription Is Required for the Regulation of Heading Time in Wheat

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