Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

By M. German, Manoj Pillay, D. Jeong, Amit Hetawal, Shujun J Luo, P. Janardhanan, V. Kannan, Linda Rymarquis, K. Nobuta, Rana German and 5 more. Nature Biotechnology, 2008

834 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/873e5e81f100e3cf11fa5a3a924c97dfee8a9fed

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Citations in the corpus

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing (2010, background): “…are predominantly 5’ → 3’ exonuclease degradation intermediates, they also include 3’ fragments of Argonaute-catalyzed mRNA cleavage in sufficient numbers to enable empirical detection of endogenous cleavage targets of plant miRNAs and siRNAs (Addo-Quaye et al., 2008; German et al., 2008).”
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions (2013, background): “(33) also developed an NGS approach to detect MTIs by identifying mRNA cleavage products through parallel analysis of Nucleic Acids Research, 2014, Vol.”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “napus, the present study performed a genome-wide analysis of miRNAcleaved mRNAs using a recently developed high-throughput degradome sequencing technology (Addo-Quaye et al., 2008; German et al., 2008).”
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”
The human mitochondrial transcriptome (2011, positive): “PARE Sequencing and Alignment PARE sequencing was performed as previously described (German et al., 2008) and further detailed in the Extended Experimental Procedures.”
The database of experimentally supported targets: a functional update of TarBase (2008, methodology): “Other high-throughput methods like degradome sequencing (17, 18 ) are also immensely useful but only in the scenarios where a miRNA induces RISCmediated mRNA cleavage.”
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”
MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. (2011, methodology): “Predicted matches with penalty scores #5 (>50,000 predicted miRNA–target pairs in the genome, and >15,000 pairs from cDNAs) were combined with a PARE (parallel analysis of RNA ends) library (German et al. 2008) made from M. truncatula flower tissue (Supplemental Table S1).”
High-Throughput Sequencing Technologies (2015, methodology): “For instance, microRNA-target discovery has been facilitated by sequencing signatures of miRNA-mediated mRNA decay, using parallel analysis of RNA ends (PAREs) (German et al., 2008).”
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].”
starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data (2010, methodology): “…[CLIP-Seq, also referred to as high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP)] (20–22) and high-throughput degradome sequencing [Degradome-Seq, also referred to as ‘parallel analysis of RNA ends’ (PARE)] (23–27) to isolate targets in animals and plants.”