microRNA target predictions in animals

By Nikolaus Rajewsky. Nature Genetics, 2006

1,149 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e0f214e7ec8d76efb4e2cfb14fed0c67ab1da543

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Citations in the corpus

The database of experimentally supported targets: a functional update of TarBase (2008, background): “A number of computational algorithms have been developed for the prediction of such targets ( 6 ).”
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. (2006, background): “The inherent difficulty of the microRNA target prediction problem is underscored by the fact that the number of confirmed heteroduplexes remains small by comparison to the expended effort and by the observation that predictions made by the various algorithms generally have little overlap ( Rajewsky,”
MiRNA-Directed Regulation of VEGF and Other Angiogenic Factors under Hypoxia (2006, methodology): “In the design of the FindTar algorithm, we started with experimental results from other groups [14,18], and used a slightly relaxed seed criterion to search the mRNA sequences for a binding site, so that more potential miRNA targets could be included in the primary screening.”
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes (2007, background): “The expanse of genetic information regulated posttranscriptionally by small RNAs is potentially large in animals and plants [11– 13].”
MicroRNA-125b is a novel negative regulator of p53. (2009, background): “They believe that a morphant phenotype can be considered as on-target only if it can be rescued by overexpression of the targeted gene (Robu et al. 2007).”
Hypoxia inducible mir-210 regulates normoxic gene expression involved in tumor initiation (2009, positive): “It has been reported that closely located multiple miRNA target sites in a gene's 3 0 UTR region may function synergistically in mediating miRNA translation repression (Grimson et al., 2007; Rajewsky, 2006).”
Identifying miRNAs, targets and functions (2012, background): “It has been generally believed that miRNAs bind to the 30-UTRs of the target transcripts in at least one of two classes of binding patterns [17].”
Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage. (2008, positive): “Since thousands of human protein-encoding genes are predicted to be regulated by miRNAs (Rajewsky, 2006), and miRNA control is in part exerted at the level of mRNA stability, we assessed to what extent Dicer ablation affects gene expression in pro-B cells.”
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions (2008, background): “While most of the aforementioned approaches use the free energy of the hybridized duplex to predict the potential targe t site, in general, the free energy of the entire duplex is a poor predictor for that aim ( Rajewsky, 2006 ).”
Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. (2007, background): “While a few targets have been validated at the protein level for miR-1 and several other miRNAs, each miRNA likely targets tens of different mRNAs (Brennecke et al., 2005; Lewis et al., 2005; Rajewsky, 2006).”
A mammalian microRNA expression atlas based on small RNA library sequencing. (2007, background): “Many computational studies have been conducted to define miRNA regulatory networks (reviewed in Rajewsky, 2006), yet most molecular targets of miRNAs remain experimentally undefined.”
Biological principles of microRNA-mediated regulation: shared themes amid diversity (2008, background): “Instead, most miRNA target sites contain seven nucleotides of Watson–Crick base-pairing to positions 2–8 of the miRNA (numbering from the 5′ end), also known as the miRNA 'seed”
MicroRNA signatures in human cancers (2006, background): “, through imperfect pairing with target messenger RNAs (mRNAs) of protein-coding genes and the transcriptional or post-transcriptional regulation of their expressio”
The evolution of gene regulation by transcription factors and microRNAs (2007, background): “Do animals need so many miRNAs, and if so, why? Also, given that an animal miRNA can apparently target easily hundreds of genes ( Box 3 ) (reviewed in Ref”
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP (2010, background): “Target sites were thought to be predominantly located in the 30UTRs of mRNAs, and computational miRNA target prediction methods frequently resort to identification of evolutionarily conserved sites that are located in 30UTRs and are complementary to miRNA seed regions (Bartel, 2009; Rajewsky, 2006).”