Global Identification of Small RNA Targets in Plants by Sequencing Sliced Ends of Messenger RNAs

2012 ◽  
pp. 119-129 ◽  
Author(s):  
Yong-Fang Li ◽  
Ramanjulu Sunkar
Keyword(s):  
Small Rna ◽  
Messenger Rnas ◽  
Rna Targets ◽  
Global Identification

scholarly journals Sequencing of small RNAs of the fern Pleopeltis minima (Polypodiaceae) offers insight into the evolution of the microRNA repertoire in land plants

2016 ◽  
Author(s):  
Florencia Berruezo ◽  
Flavio S. J. de Souza ◽  
Pablo I. Picca ◽  
Sergio I. Nemirovsky ◽  
Leandro Martinez-Tosar ◽  
...  
Keyword(s):  
Small Rna ◽  
Land Plant ◽  
Land Plants ◽  
Phylogenetic Position ◽  
Seed Plants ◽  
Messenger Rnas ◽  
Rna Molecules ◽  
Functional Studies ◽  
Mirna Genes ◽  
Ecological Importance

AbstractMicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, and functional studies indicate that ancient miRNAs play key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plant miRNAs. Land plants are divided into bryophytes (liverworts, mosses), lycopods (clubmosses and spikemosses), monilophytes (ferns and horsetails), gymnosperms (cycads, conifers and allies) and angiosperms (flowering plants). Among these, the fern group occupies a key phylogenetic position, since it represents the closest extant cousin taxon of seed plants, i.e. gymno- and angiosperms. However, in spite of their evolutionary, economic and ecological importance, no fern genome has been sequenced yet and few genomic resources are available for this group. Here, we sequenced the small RNA fraction of an epiphytic South American fern, Pleopeltis minima (Polypodiaceae), and compared it to plant miRNA databases, allowing for the identification of miRNA families that are shared by all land plants, shared by all vascular plants (tracheophytes) or shared by euphyllophytes (ferns and seed plants) only. Using the recently described transcriptome of another fern, Lygodium japonicum, we also estimated the degree of conservation of fern miRNA targets in relation to other plant groups. Our results pinpoint the origin of several miRNA families in the land plant evolutionary tree with more precision and are a resource for future genomic and functional studies of fern miRNAs.

scholarly journals CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

2008 ◽  
Vol 25 (1) ◽  
pp. 130-131 ◽  
Author(s):  
C. Addo-Quaye ◽  
W. Miller ◽  
M. J. Axtell
Keyword(s):  
Small Rna ◽  
Rna Targets

scholarly journals PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules

2018 ◽  
Author(s):  
Joshua Thody ◽  
Leighton Folkes ◽  
Zahara Medina-Calzada ◽  
Ping Xu ◽  
Tamas Dalmay ◽  
...  
Keyword(s):  
High Throughput ◽  
Small Rna ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Rna Targets

scholarly journals StarScan: a web server for scanning small RNA targets from degradome sequencing data

2015 ◽  
Vol 43 (W1) ◽  
pp. W480-W486 ◽  
Author(s):  
Shun Liu ◽  
Jun-Hao Li ◽  
Jie Wu ◽  
Ke-Ren Zhou ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
Web Server ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Rna Targets

scholarly journals PAREameters: a tool for computational inference of plant miRNA–mRNA targeting rules using small RNA and degradome sequencing data

2020 ◽  
Vol 48 (5) ◽  
pp. 2258-2270 ◽  
Author(s):  
Joshua Thody ◽  
Vincent Moulton ◽  
Irina Mohorianu
Keyword(s):  
Small Rna ◽  
Mirna Target ◽  
Target Prediction ◽  
Model Organisms ◽  
Messenger Rnas ◽  
Mirna Target Prediction ◽  
Sequencing Data ◽  
Translation Rate ◽  
Degradome Sequencing ◽  
Using Data

Abstract MicroRNAs (miRNAs) are short, non-coding RNAs that modulate the translation-rate of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to sequence-specific targets. In plants, this typically results in cleavage and subsequent degradation of the mRNA. Degradome sequencing is a high-throughput technique developed to capture cleaved mRNA fragments and thus can be used to support miRNA target prediction. The current criteria used for miRNA target prediction were inferred on a limited number of experimentally validated A. thaliana interactions and were adapted to fit these specific interactions; thus, these fixed criteria may not be optimal across all datasets (organisms, tissues or treatments). We present a new tool, PAREameters, for inferring targeting criteria from small RNA and degradome sequencing datasets. We evaluate its performance using a more extensive set of experimentally validated interactions in multiple A. thaliana datasets. We also perform comprehensive analyses to highlight and quantify the differences between subsets of miRNA–mRNA interactions in model and non-model organisms. Our results show increased sensitivity in A. thaliana when using the PAREameters inferred criteria and that using data-driven criteria enables the identification of additional interactions that further our understanding of the RNA silencing pathway in both model and non-model organisms.

A small RNA targets pokeweed antiviral protein transcript

2015 ◽  
Vol 156 (3) ◽  
pp. 241-251 ◽  
Author(s):  
Alexander Klenov ◽  
Kira C. M. Neller ◽  
Lydia A. Burns ◽  
Gabriela Krivdova ◽  
Katalin A. Hudak
Keyword(s):  
Small Rna ◽  
Pokeweed Antiviral Protein ◽  
Antiviral Protein ◽  
Rna Targets

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

2010 ◽  
Vol 5 (1) ◽  
pp. 67-90 ◽  
Author(s):  
Ming Zhou ◽  
Lianfeng Gu ◽  
Pingchuan Li ◽  
Xianwei Song ◽  
Liya Wei ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Small Rna ◽  
Oryza Sativa L ◽  
Degradome Sequencing ◽  
Rna Targets

scholarly journals CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

2014 ◽  
Vol 42 (W1) ◽  
pp. W119-W123 ◽  
Author(s):  
Patrick R. Wright ◽  
Jens Georg ◽  
Martin Mann ◽  
Dragos A. Sorescu ◽  
Andreas S. Richter ◽  
...  
Keyword(s):  
Small Rna ◽  
Rna Targets ◽  
Interaction Domains

scholarly journals Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 15 ◽  
Author(s):  
Cheng-Yu Hou ◽  
Ming-Tsung Wu ◽  
Shin-Hua Lu ◽  
Yue-Ie Hsing ◽  
Ho-Ming Chen
Keyword(s):  
Small Rna ◽  
Rna Targets
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