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      Reexamining assumptions about miRNA-guided gene silencing

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      , ,
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          MicroRNAs (miRNAs) are short endogenously expressed RNAs that have the potential to regulate the expression of any RNA. This potential has led to the publication of several thousand papers each year connecting miRNAs to many different genes and human diseases. By contrast, relatively few papers appear that investigate the molecular mechanism used by miRNAs. There is a disconnect between rigorous understanding of mechanism and the extraordinary diversity of reported roles for miRNAs. Consequences of this disconnect include confusion about the assumptions underlying the basic science of human miRNAs and slow development of therapeutics that target miRNAs. Here, we present an overview of investigations into miRNAs and their impact on gene expression. Progress in our understanding of miRNAs would be aided by a greater focus on the mechanism of miRNAs and a higher burden of evidence on researchers who seek to link expression of a particular miRNA to a biological phenotype.

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          Most cited references117

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          MicroRNAs: genomics, biogenesis, mechanism, and function.

          MicroRNAs (miRNAs) are endogenous approximately 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
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            MicroRNAs: target recognition and regulatory functions.

            MicroRNAs (miRNAs) are endogenous approximately 23 nt RNAs that play important gene-regulatory roles in animals and plants by pairing to the mRNAs of protein-coding genes to direct their posttranscriptional repression. This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.
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              Predicting effective microRNA target sites in mammalian mRNAs

              MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks. DOI: http://dx.doi.org/10.7554/eLife.05005.001
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                Author and article information

                Contributors
                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                25 January 2022
                30 December 2021
                30 December 2021
                : 50
                : 2
                : 617-634
                Affiliations
                Department of Pharmacology and Biochemistry, UT Southwestern Medical Center , 6001 Forest Park Road, Dallas, TX, USA
                Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg , Regensburg, Germany
                Department of Pharmacology and Biochemistry, UT Southwestern Medical Center , 6001 Forest Park Road, Dallas, TX, USA
                Author notes
                To whom correspondence should be addressed. Email: david.corey@ 123456utsouthwestern.edu
                Author information
                https://orcid.org/0000-0001-8973-493X
                Article
                gkab1256
                10.1093/nar/gkab1256
                8789053
                34967419
                84730b4b-0cad-4672-b166-8295232d7b1b
                © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 06 December 2021
                : 01 December 2021
                : 12 October 2021
                Page count
                Pages: 18
                Funding
                Funded by: National Institutes of Health, DOI 10.13039/100000002;
                Award ID: GM118103
                Categories
                AcademicSubjects/SCI00010
                Critical Reviews and Perspectives

                Genetics
                Genetics

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