Computational identification of miRNA genes and their targets in mulberry

Huang, Yong; Zou, Quan; Wang, Z. B.

doi:10.1134/s1021443714040104

Cited by 9 publications

(2 citation statements)

References 28 publications

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“…Some authors even use for searching sequence similarity between a plant miRNA and mRNAs the Basic Local Alignment Search Tool algorithm (Huang et al, 2014a). 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;. 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%

Introduction to RNAi and miRNA pathways

Svoboda¹

2020

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edge hereby that the contents have been produced under a contract with EFSA (OC/EFSA/ GMO/2015/01-CT 01) and that the opinions expressed are those of the contractor only and do not represent EFSA's official position.Regarding the conversion, the original text was reorganized into twelve chapters, which were reformatted and revised in order to remove copyrighted material from third parties and provide a introductory parts for stand alone chapters. Nine of the chapters focus on small RNA pathways in animals (mammals, birds, fish, arthropods, nematodes, molluscs, and annelids) and plants. The remaining three chapters include a general introduction and reviews of important phenomena -off-targeting and extracellular small RNAs. I hope that this collection will serve as a useful source for many.

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Section: Target Prediction For Plant Mirnasmentioning

confidence: 99%

Introduction to RNAi and miRNA pathways

Svoboda¹

2020

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“…Some authors even use for searching sequence similarity between a plant miRNA and mRNAs the Basic Local Alignment Search Tool algorithm (Huang et al, 2014a). 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%

Specificity of targeting in RNAi and miRNA pathways

Svoboda¹

2020

Introduction to RNAi and miRNA Pathways

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This review systematically covers sequence-specific gene regulation by miRNAs and dsRNA-derived siRNAs in animals and plants from the perspective of target RNA recognition, potential for non-target (off-target) effects, and reliable determination of biological effects of small RNAs in animals and plants. I will review sequence complementarity between target RNA and small RNA (siRNA or miRNA), including tolerance to mismatches, parameters influencing sequence complementarity (and target recognition and repression) and discuss specificity of targeting by miRNAs and off-targeting by siRNAs. In addition, I will discuss reliable identification of target RNAs (and, eventually, biological effects). Accordingly, the text is divided into the following four sections: (I) Small RNA:target RNA base pairing, (II) Other key factors influencing target recognition and repression, (III) Off-targeting -causes and remedies, (III) Smal RNA target identification.

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Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana)

Usha

Jyothi

Suchithra³

et al. 2015

Interdiscip Sci Comput Life Sci

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MicroRNAs are endogenous small RNAs regulating intrinsic normal growth and development of plant. Discovering miRNAs, their targets and further inferring their functions had become routine process to comprehend the normal biological processes of miRNAs and their roles in plant development. In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development.

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Computational identification of miRNA genes and their targets in mulberry

Cited by 9 publications

References 28 publications

Introduction to RNAi and miRNA pathways

Introduction to RNAi and miRNA pathways

Specificity of targeting in RNAi and miRNA pathways

Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana)

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