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      Assessment of isomiR Discrimination Using Commercial qPCR Methods

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          Abstract

          We sought to determine whether commercial quantitative polymerase chain reaction (qPCR) methods are capable of distinguishing isomiRs: variants of mature microRNAs (miRNAs) with sequence endpoint differences. We used two commercially available miRNA qPCR methods to quantify miR-21-5p in both synthetic and real cell contexts. We find that although these miRNA qPCR methods possess high sensitivity for specific sequences, they also pick up background signals from closely related isomiRs, which influences the reliable quantification of individual isomiRs. We conclude that these methods do not possess the requisite specificity for reliable isomiR quantification.

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          miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

          Chih-Hung Chou, Nai-Wen Chang, Sirjana Devi Shrestha … (2015)
          MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.
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            miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay.

            S. Djuranovic, A. Nahvi, R. Green (2012)
            microRNAs (miRNAs) regulate gene expression through translational repression and/or messenger RNA (mRNA) deadenylation and decay. Because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. We have investigated the kinetics of these events in miRNA-mediated gene silencing by using a Drosophila S2 cell-based controllable expression system and show that mRNAs with both natural and engineered 3' untranslated regions with miRNA target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. We next used a natural translational elongation stall to show that miRNA-mediated silencing inhibits translation at an early step, potentially translation initiation.
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              Principles of microRNA regulation of a human cellular signaling network

              Qinghua Cui, Zhenbao Yu, Enrico Purisima … (2006)
              MicroRNAs (miRNAs) are endogenous ∼22-nucleotide RNAs, which suppress gene expression by selectively binding to the 3′-noncoding region of specific messenger RNAs through base-pairing. Given the diversity and abundance of miRNA targets, miRNAs appear to functionally interact with various components of many cellular networks. By analyzing the interactions between miRNAs and a human cellular signaling network, we found that miRNAs predominantly target positive regulatory motifs, highly connected scaffolds and most downstream network components such as signaling transcription factors, but less frequently target negative regulatory motifs, common components of basic cellular machines and most upstream network components such as ligands. In addition, when an adaptor has potential to recruit more downstream components, these components are more frequently targeted by miRNAs. This work uncovers the principles of miRNA regulation of signal transduction networks and implies a potential function of miRNAs for facilitating robust transitions of cellular response to extracellular signals and maintaining cellular homeostasis.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101652294
                Journal ID (pubmed-jr-id): 43597
                Journal ID (nlm-ta): Noncoding RNA
                Journal ID (iso-abbrev): Noncoding RNA
                Title: Non-coding RNA
                ISSN (Electronic): 2311-553X
                Publication date Nihms-submitted: 17 May 2017
                Publication date (Electronic): 24 March 2017
                Publication date (Print): June 2017
                Publication date PMC-release: 18 July 2017
                Volume: 3
                Issue: 2
                Electronic Location Identifier: 18
                Affiliations
                Computational Medicine Center, http://cm.jefferson.edu/, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
                Author notes
                [* ]Correspondence: eric.londin@ 123456jefferson.edu ; Tel.: +1-215-503-0454
                Article
                Manuscript ID: NIHMS875844
                DOI: 10.3390/ncrna3020018
                PMC ID: 5514785
                PubMed ID: 28730153
                SO-VID: 86dca967-c71c-4c94-9182-aa8b89bbe70c
                License:

                Submitted for possible open access publication under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Categories
                Subject: Article

                Keywords: isomir,mirna,qpcr,short non-coding rna
                Data availability:
                Keywords: isomir, mirna, qpcr, short non-coding rna

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