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      From snoRNA to miRNA: Dual function regulatory non-coding RNAs

      review-article
      a , , b
      Biochimie
      Editions Scientifiques Elsevier
      Small nucleolar RNA, Micro RNA, Evolution, Dual function

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          Abstract

          Small nucleolar RNAs (snoRNAs) are an ancient class of small non-coding RNAs present in all eukaryotes and a subset of archaea that carry out a fundamental role in the modification and processing of ribosomal RNA. In recent years, however, a large proportion of snoRNAs have been found to be further processed into smaller molecules, some of which display different functionality. In parallel, several studies have uncovered extensive similarities between snoRNAs and other types of small non-coding RNAs, and in particular microRNAs. Here, we explore the extent of the relationship between these types of non-coding RNA and the possible underlying evolutionary forces that shaped this subset of the current non-coding RNA landscape.

          Highlights

          ► snoRNAs and miRNAs are extensively characterized small non-coding regulatory RNAs. ► snoRNAs and miRNAs have distinct and central regulatory roles in cells. ► recent studies reveal that snoRNAs and miRNAs display similarities at numerous levels. ► molecules showing both snoRNA and miRNA characteristics and functionality exist. ► subsets of snoRNAs and miRNAs likely share a functional and evolutionary relationship.

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          Most cited references66

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          Switching from repression to activation: microRNAs can up-regulate translation.

          AU-rich elements (AREs) and microRNA target sites are conserved sequences in messenger RNA (mRNA) 3' untranslated regions (3'UTRs) that control gene expression posttranscriptionally. Upon cell cycle arrest, the ARE in tumor necrosis factor-alpha (TNFalpha) mRNA is transformed into a translation activation signal, recruiting Argonaute (AGO) and fragile X mental retardation-related protein 1 (FXR1), factors associated with micro-ribonucleoproteins (microRNPs). We show that human microRNA miR369-3 directs association of these proteins with the AREs to activate translation. Furthermore, we document that two well-studied microRNAs-Let-7 and the synthetic microRNA miRcxcr4-likewise induce translation up-regulation of target mRNAs on cell cycle arrest, yet they repress translation in proliferating cells. Thus, activation is a common function of microRNPs on cell cycle arrest. We propose that translation regulation by microRNPs oscillates between repression and activation during the cell cycle.
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            Gene silencing by microRNAs: contributions of translational repression and mRNA decay.

            Despite their widespread roles as regulators of gene expression, important questions remain about target regulation by microRNAs. Animal microRNAs were originally thought to repress target translation, with little or no influence on mRNA abundance, whereas the reverse was thought to be true in plants. Now, however, it is clear that microRNAs can induce mRNA degradation in animals and, conversely, translational repression in plants. Recent studies have made important advances in elucidating the relative contributions of these two different modes of target regulation by microRNAs. They have also shed light on the specific mechanisms of target silencing, which, although it differs fundamentally between plants and animals, shares some common features between the two kingdoms.
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              Identification of mammalian microRNA host genes and transcription units.

              To derive a global perspective on the transcription of microRNAs (miRNAs) in mammals, we annotated the genomic position and context of this class of noncoding RNAs (ncRNAs) in the human and mouse genomes. Of the 232 known mammalian miRNAs, we found that 161 overlap with 123 defined transcription units (TUs). We identified miRNAs within introns of 90 protein-coding genes with a broad spectrum of molecular functions, and in both introns and exons of 66 mRNA-like noncoding RNAs (mlncRNAs). In addition, novel families of miRNAs based on host gene identity were identified. The transcription patterns of all miRNA host genes were curated from a variety of sources illustrating spatial, temporal, and physiological regulation of miRNA expression. These findings strongly suggest that miRNAs are transcribed in parallel with their host transcripts, and that the two different transcription classes of miRNAs ('exonic' and 'intronic') identified here may require slightly different mechanisms of biogenesis.
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                Author and article information

                Journal
                Biochimie
                Biochimie
                Biochimie
                Editions Scientifiques Elsevier
                0300-9084
                1638-6183
                November 2011
                November 2011
                : 93
                : 11
                : 1987-1992
                Affiliations
                [a ]Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
                [b ]Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
                Author notes
                []Corresponding author. Tel.: +44 1382 386097; fax: +44 1382 345893. michelle@ 123456compbio.dundee.ac.uk
                Article
                BIOCHI3594
                10.1016/j.biochi.2011.05.026
                3476530
                21664409
                9a23655d-471b-4344-9f72-e197eb4b8f4e
                © 2011 Elsevier Masson SAS.

                This document may be redistributed and reused, subject to certain conditions.

                History
                : 30 March 2011
                : 19 May 2011
                Categories
                Review

                Biochemistry
                micro rna,small nucleolar rna,evolution,dual function
                Biochemistry
                micro rna, small nucleolar rna, evolution, dual function

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