301
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Katoh T, Sakaguchi Y, Miyauchi K, Suzuki T, Kashiwabara SI, Baba T, Suzuki T. Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev 2009; 23:433-8. [PMID: 19240131 DOI: 10.1101/gad.1761509] [Citation(s) in RCA: 349] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The steady-state levels of microRNAs (miRNAs) and their activities are regulated by the post-transcriptional processes. It is known that 3' ends of several miRNAs undergo post-dicing adenylation or uridylation. We isolated the liver-specific miR-122 from human hepatocytes and mouse livers. Direct analysis by mass spectrometry revealed that one variant of miR-122 has a 3'-terminal adenosine that is introduced after processing by Dicer. We identified GLD-2, which is a regulatory cytoplasmic poly(A) polymerase, as responsible for the 3'-terminal adenylation of miR-122 after unwinding of the miR-122/miR-122* duplex. In livers from GLD-2-null mice, the steady-state level of the mature form of miR-122 was specifically lower than in heterozygous mice, whereas no reduction of pre-miR-122 was observed, demonstrating that 3'-terminal adenylation by GLD-2 is required for the selective stabilization of miR-122 in the liver.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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302
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Abstract
From the earliest comparisons of RNA production with steady-state levels, it has been clear that cells transcribe more RNA than they accumulate, implying the existence of active RNA degradation systems. In general, RNA is degraded at the end of its useful life, which is long for a ribosomal RNA but very short for excised introns or spacer fragments, and is closely regulated for most mRNA species. RNA molecules with defects in processing, folding, or assembly with proteins are identified and rapidly degraded by the surveillance machinery. Because RNA degradation is ubiquitous in all cells, it is clear that it must be carefully controlled to accurately recognize target RNAs. How this is achieved is perhaps the most pressing question in the field.
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Affiliation(s)
- Jonathan Houseley
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3JR, UK
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303
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Abstract
MicroRNAs (miRNAs) are key posttranscriptional regulators of eukaryotic gene expression. Plants use highly conserved as well as more recently evolved, species-specific miRNAs to control a vast array of biological processes. This Review discusses current advances in our understanding of the origin, biogenesis, and mode of action of plant miRNAs and draws comparisons with their metazoan counterparts.
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Affiliation(s)
- Olivier Voinnet
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357-Université de Strasbourg, 67084 Strasbourg, France.
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304
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Winter J, Jung S, Keller S, Gregory RI, Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 2009. [PMID: 19255566 DOI: 10.1038/ncb0309‐228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
MicroRNAs are important regulators of gene expression that control both physiological and pathological processes such as development and cancer. Although their mode of action has attracted great attention, the principles governing their expression and activity are only beginning to emerge. Recent studies have introduced a paradigm shift in our understanding of the microRNA biogenesis pathway, which was previously believed to be universal to all microRNAs. Maturation steps specific to individual microRNAs have been uncovered, and these offer a plethora of regulatory options after transcription with multiple proteins affecting microRNA processing efficiency. Here we review the recent advances in knowledge of the microRNA biosynthesis pathways and discuss their impact on post-transcriptional microRNA regulation during tumour development.
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Affiliation(s)
- Julia Winter
- Helmholtz-University-Group Molecular RNA Biology & Cancer, German Cancer Research Center (DKFZ) and Institute of Pathology, University of Heidelberg, B150 INF 581, D-69120 Heidelberg, Germany
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305
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Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 2009; 37:2461-70. [PMID: 19255090 PMCID: PMC2677864 DOI: 10.1093/nar/gkp093] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3′ micro RNA uridine extensions and 5′ micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5′ deletions and 3′ uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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306
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Abstract
Small RNAs of 20-30 nucleotides can target both chromatin and transcripts, and thereby keep both the genome and the transcriptome under extensive surveillance. Recent progress in high-throughput sequencing has uncovered an astounding landscape of small RNAs in eukaryotic cells. Various small RNAs of distinctive characteristics have been found and can be classified into three classes based on their biogenesis mechanism and the type of Argonaute protein that they are associated with: microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs) and Piwi-interacting RNAs (piRNAs). This Review summarizes our current knowledge of how these intriguing molecules are generated in animal cells.
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Affiliation(s)
- V Narry Kim
- School of Biological Sciences and Center for National Creative Research, Seoul National University, Seoul, 151-742, Korea.
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307
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Abstract
The modification or degradation of RNAs including miRNAs may play vital roles in regulating RNA functions. The polyadenylation- and exosome-mediated RNA decay is involved in the degradation of plant RNAs including the primary miRNA processing intermediates. However, plant miRNA levels are not affected by exosome depletion. Here, we report the cloning of a large number of 5' and/or 3' truncated versions of the known miRNAs from various tissues of Populus trichocarpa (black cottonwood). It suggests that plant miRNAs may be degraded through either 5' to 3' or 3' to 5' exonucleolytic digestion. We also show that a significant portion of the isolated miRNAs contains, at the 3'-end, one or a few post-transcriptionally added adenylic acid residues, which are distinct in length from the polyadenylate tail added to other plant RNAs for exosome-mediated degradation. Using an in vitro miRNA degradation system, where synthesized miRNA oligos were degraded in extracts of P. trichocarpa cells, we revealed that the adenylated miRNAs were degraded slower than others without adenylation. It indicates that addition of adenylic acid residues on the 3'-end plays a negative role in miRNA degradation. Our results provide new information for understanding the mechanism of miRNA degradation.
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Affiliation(s)
- Shanfa Lu
- Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA.
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308
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Abstract
MicroRNA (miRNA) control has emerged as a critical regulatory principle in the mammalian immune system. Genetic ablation of the miRNA machinery, as well as loss or deregulation of certain individual miRNAs, severely compromises immune development and response and can lead to immune disorders like autoimmunity and cancer. Although individual miRNAs modulate protein output from hundreds of target genes, they may impact physiological processes by regulating the concentrations of just a few key cellular proteins that may be components of a single or of functionally interrelated pathways in a given cellular context.
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Affiliation(s)
- Changchun Xiao
- Immune Disease Institute, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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309
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Abstract
Small RNAs of 20-30 nucleotides guide regulatory processes at the DNA or RNA level in a wide range of eukaryotic organisms. Many, although not all, small RNAs are processed from double-stranded RNAs or single-stranded RNAs with local hairpin structures by RNase III enzymes and are loaded into argonaute-protein-containing effector complexes. Many eukaryotic organisms have evolved multiple members of RNase III and the argonaute family of proteins to accommodate different classes of small RNAs with specialized molecular functions. Some small RNAs cause transcriptional gene silencing by guiding heterochromatin formation at homologous loci, whereas others lead to posttranscriptional gene silencing through mRNA degradation or translational inhibition. Small RNAs are not only made from and target foreign nucleic acids such as viruses and transgenes, but are also derived from endogenous loci and regulate a multitude of developmental and physiological processes. Here I review the biogenesis and function of three major classes of endogenous small RNAs in plants: microRNAs, trans-acting siRNAs, and heterochromatic siRNAs, with an emphasis on the roles of these small RNAs in developmental regulation.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA.
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310
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311
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Abstract
MicroRNAs (miRNA) are small RNAs that regulate the translation of thousands of message RNAs and play a profound role in mammalian biology. Over the past 5 years, significant advances have been made towards understanding the pathways that generate miRNAs and the mechanisms by which miRNAs exert their regulatory functions. An emerging theme is that miRNAs are both generated by and utilized by large and complex macromolecular assemblies. Here, we review the biology of mammalian miRNAs with a focus on the macromolecular complexes that generate and control the biogenesis of miRNAs.
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Affiliation(s)
- Pick-Wei Lau
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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312
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Ding XC, Weiler J, Grosshans H. Regulating the regulators: mechanisms controlling the maturation of microRNAs. Trends Biotechnol 2008; 27:27-36. [PMID: 19012978 DOI: 10.1016/j.tibtech.2008.09.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 09/22/2008] [Accepted: 09/25/2008] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that control diverse cellular and developmental events through repression of large sets of target mRNAs. Regulated transcription of the genes encoding miRNAs by RNA polymerase II promotes specific expression patterns of individual miRNAs. However, recent studies have established that substantial regulation of mature miRNA accumulation also occurs after transcription. Here, we review the mechanisms of such post-transcriptional regulation, with a particular focus on examples where molecular mechanisms or physiological principles are beginning to emerge. Elucidating these mechanisms will increase our understanding of gene regulation and provide new insights into causes of miRNA misexpression in diseases such as cancer.
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Affiliation(s)
- Xavier C Ding
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, WRO-1066.1.38, CH-4002 Basel, Switzerland
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313
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In Brief. Nat Rev Genet 2008. [DOI: 10.1038/nrg2464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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