Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
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In this article, the authors used the TargetScan tool for quantitatively predicting miRNA regulation (and siRNA off-targeting) to model differential miRNA proficiencies, thereby improving prediction performance.Abstract:
Most metazoan microRNAs (miRNAs) target many genes for repression, but the nematode lsy-6 miRNA is much less proficient. Here we show that the low proficiency of lsy-6 can be recapitulated in HeLa cells and that miR-23, a mammalian miRNA, also has low proficiency in these cells. Reporter results and array data indicate two properties of these miRNAs that impart low proficiency: their weak predicted seed-pairing stability (SPS) and their high target-site abundance (TA). These two properties also explain differential propensities of small interfering RNAs (siRNAs) to repress unintended targets. Using these insights, we expand the TargetScan tool for quantitatively predicting miRNA regulation (and siRNA off-targeting) to model differential miRNA (and siRNA) proficiencies, thereby improving prediction performance. We propose that siRNAs designed to have both weaker SPS and higher TA will have fewer off-targets without compromised on-target activity.read more
Citations
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Identification and validation of mRNA 3'untranslated regions of DNMT3B and TET3 as novel competing endogenous RNAs of the tumor suppressor PTEN.
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Statistical Principle-Based Approach for Detecting miRNA-Target Gene Interaction Articles
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Genome-Wide Analysis of MicroRNA-Regulated Transcripts.
TL;DR: This chapter discusses the advantages and limitations of both classic and comprehensive strategies for miRNA target prediction, as well as their potential uses as therapeutic tools, from several laboratory-based, comprehensive strategies developed recently.
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Principles and pitfalls of high-throughput analysis of microRNA-binding thermodynamics and kinetics by RNA Bind-n-Seq
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miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data.
Luiz A. Bovolenta,Danillo Pinhal,Marcio Luis Acencio,Arthur C. Oliveira,Simon Moxon,Cesar Martins,Ney Lemke +6 more
TL;DR: An open repository dedicated to Nile Tilapia miRNAs, the “miRTil database” is presented, which stores data on 734 mature mi RNAs identified in 11 distinct tissues and five key developmental stages and includes a comprehensive pre-computed miRNA-target interaction network containing 4936 targets and 19,580 interactions.
References
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
MicroRNAs: Target Recognition and Regulatory Functions
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Journal ArticleDOI
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Journal ArticleDOI
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