Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.

By Charles Addo-Quaye, Tifani W. Eshoo, David P. Bartel, Michael J. Axtell. Current Biology, 2008

760 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/fc53fe94176427c313b69a53cd31a32ab4873eea

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Citations in the corpus

MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship (2012, background): “Cleavage products can be cloned and identified to validate direct miRNA–target interaction”
The Functions of MicroRNAs: mRNA Decay and Translational Repression. (2015, methodology): “thaliana revealed that mRNAs with highly complementary target sites were cleaved by plant miRNAs at the position facing nucleotides 10 and 11 of miRNAs [110,138].”
Biological principles of microRNA-mediated regulation: shared themes amid diversity (2008, background): “High-throughput sequencing of RNAs with 5′ monophosphates (which excludes capped mRNAs) provides an opportunity to identify miRNA-cleaved transcripts genome-wid”
Abiotic Stress Responses in Plants: Unraveling the Complexity of Genes and Networks to Survive (2013, background): “These targets were further confirmed by deep sequencing of cleaved miRNA targets (Parallel Analysis of RNA Ends - PARE) [150-151] in M.”
Origin, biogenesis, and activity of plant microRNAs. (2009, positive): “This approach depends on the cloning and sequencing of 30-cleavage products of miRNA target transcripts (Addo-Quaye et al., 2008; German et al., 2008).”
Evolution and Functional Diversification of MIRNA Genes (2011, background): “…A. thaliana triggers the production of secondary siRNAs with the theoretical potential to target other PPR transcripts in trans, although compelling evidence for the activity of the secondary siRNAs is lacking (Axtell et al., 2006; Chen et al., 2007; Howell et al., 2007; Addo-Quaye et al., 2008).”
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics (2010, methodology): “To test and compare the TAPIR web server algorithms to existing web tools, we have compiled a reference set of 102 miRNA-target pairs that have been validated experimentally (the complete list is available as Supplementary Table S1; Addo-Quaye et al., 2008; Allen et al., 2005; German et al., 2008).”
Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica) (2010, methodology): “The PCR products were digested with an enzyme Mme I (NEB).”
XRN 5’→3’ exoribonucleases: Structure, mechanisms and functions (2013, methodology): “However, using a genomic approach called PARE (Parallel Analysis of RNA Ends) or RNAdegradome analysis [77–79], additional experimental evidence for these rare instances of target cleavage that generate XRN1 substrates inmammalian cells has been obtained [80–82].”