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Dozier C, Montigny A, Viladrich M, Culerrier R, Combier JP, Besson A, Plaza S. Small ORFs as New Regulators of Pri-miRNAs and miRNAs Expression in Human and Drosophila. Int J Mol Sci 2022; 23:5764. [PMID: 35628573 PMCID: PMC9144653 DOI: 10.3390/ijms23105764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). However, several lnc pri-miRNAs contain translatable small open reading frames (smORFs). If smORFs present within lncRNAs can encode functional small peptides, they can also constitute cis-regulatory elements involved in lncRNA decay. Here, we investigated the possible involvement of smORFs in the regulation of lnc pri-miRNAs in Human and Drosophila, focusing on pri-miRNAs previously shown to contain translatable smORFs. We show that smORFs regulate the expression levels of human pri-miR-155 and pri-miR-497, and Drosophila pri-miR-8 and pri-miR-14, and also affect the expression and activity of their associated miRNAs. This smORF-dependent regulation is independent of the nucleotidic and amino acidic sequences of the smORFs and is sensitive to the ribosome-stalling drug cycloheximide, suggesting the involvement of translational events. This study identifies smORFs as new cis-acting elements involved in the regulation of pri-miRNAs and miRNAs expression, in both Human and Drosophila melanogaster.
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Affiliation(s)
- Christine Dozier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Mireia Viladrich
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Raphael Culerrier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
| | - Arnaud Besson
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; (R.C.); (A.B.)
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546 CNRS, UPS Université de Toulouse, INP, 31320 Auzeville-Tolosan, France; (A.M.); (M.V.); (J.-P.C.)
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2
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Martins RP, Fåhraeus R. A matter of maturity: The impact of pre-mRNA processing in gene expression and antigen presentation. Int J Biochem Cell Biol 2017; 91:203-211. [PMID: 28549625 DOI: 10.1016/j.biocel.2017.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 12/28/2022]
Abstract
RNA processing plays a pivotal role in the diversification of high eukaryotes transcriptome and proteome. The expression of gene products controlling a variety of cellular and physiological processes depends largely on a complex maturation process undergone by pre-mRNAs to become translation-competent mRNAs. Here we review the different mechanisms involved in the pre-mRNA processing and disclose their impact in the gene regulation process in eukaryotic cells. We describe some viral strategies targeting pre-mRNA processing to control gene expression and host immune response and discuss their relevance as tools for a better understanding of cell biology. Finally, we highlight accumulating evidences toward the occurrence of a translation event coupled to mRNA biogenesis in the nuclear compartment and argue how this is relevant for the production of antigenic peptide substrates for the major histocompatibility complex class I pathway.
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Affiliation(s)
- Rodrigo Prado Martins
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 rue Juliette Dodu, 75010 Paris, France.
| | - Robin Fåhraeus
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 rue Juliette Dodu, 75010 Paris, France; Department of Medical Biosciences, Umeå University, Umeå, Sweden; RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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3
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Nickless A, Bailis JM, You Z. Control of gene expression through the nonsense-mediated RNA decay pathway. Cell Biosci 2017; 7:26. [PMID: 28533900 PMCID: PMC5437625 DOI: 10.1186/s13578-017-0153-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/12/2017] [Indexed: 11/25/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) was originally discovered as a cellular surveillance pathway that safeguards the quality of mRNA transcripts in eukaryotic cells. In its canonical function, NMD prevents translation of mutant mRNAs harboring premature termination codons (PTCs) by targeting them for degradation. However, recent studies have shown that NMD has a much broader role in gene expression by regulating the stability of many normal transcripts. In this review, we discuss the function of NMD in normal physiological processes, its dynamic regulation by developmental and environmental cues, and its association with human disease.
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Affiliation(s)
- Andrew Nickless
- Department of Cell Biology & Physiology, Washington University School of Medicine, Campus Box 8228, 660 S. Euclid Ave., St. Louis, MO 63110 USA
| | - Julie M Bailis
- Department of Oncology Research, Amgen, South San Francisco, CA 94080 USA
| | - Zhongsheng You
- Department of Cell Biology & Physiology, Washington University School of Medicine, Campus Box 8228, 660 S. Euclid Ave., St. Louis, MO 63110 USA
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4
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Hsu MK, Lin HY, Chen FC. NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events. PLoS One 2017; 12:e0174798. [PMID: 28369084 PMCID: PMC5378362 DOI: 10.1371/journal.pone.0174798] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/15/2017] [Indexed: 01/23/2023] Open
Abstract
Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation–an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.
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Affiliation(s)
- Min-Kung Hsu
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan
| | - Hsuan-Yu Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan
| | - Feng-Chi Chen
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan
- School of Dentistry, China Medical University, Taichung City, Taiwan
- * E-mail:
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5
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Attig J, Ruiz de Los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J, Ule J. Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. eLife 2016; 5. [PMID: 27861119 PMCID: PMC5115870 DOI: 10.7554/elife.19545] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023] Open
Abstract
Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of concerted repression by splicing and NMD. We show that evolutionary progression of 3' splice sites is coupled with longer repressive uridine tracts. Once the 3' splice site at ancient Alu-exons reaches a stable phase, splicing repression by hnRNPC decreases, but the exons generally remain sensitive to NMD. We conclude that repressive motifs are strongest next to cryptic exons and that gradual weakening of these motifs contributes to the evolutionary emergence of new alternative exons.
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Affiliation(s)
- Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom.,MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Igor Ruiz de Los Mozos
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Nejc Haberman
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Zhen Wang
- Institute de Biologie de l'ENS (IBENS), CNRS UMR 8197, Paris, France
| | - Warren Emmett
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom.,University College London Genetics Institute, London, United Kingdom
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom.,MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
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6
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Das S, Das B. eIF4G—an integrator of mRNA metabolism? FEMS Yeast Res 2016; 16:fow087. [DOI: 10.1093/femsyr/fow087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 11/14/2022] Open
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7
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Tatsuno T, Nakamura Y, Ma S, Tomosugi N, Ishigaki Y. Nonsense-mediated mRNA decay factor Upf2 exists in both the nucleoplasm and the cytoplasm. Mol Med Rep 2016; 14:655-60. [PMID: 27221324 PMCID: PMC4918542 DOI: 10.3892/mmr.2016.5331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 04/20/2016] [Indexed: 11/24/2022] Open
Abstract
Upf2 protein predominantly localizes to the cytoplasmic fraction, and binds to the exon junction complex (EJC) on spliced mRNA. The present study aimed to determine the cellular site where the interaction between Upf2 and EJC occurs. First, the cell lysate was fractionated into the cytoplasm and nucleoplasm, and western blotting to detect levels of Upf2 protein was performed. Upf2 was clearly detected in the cytoplasm and in the nucleoplasm. Secondly, immunostaining was performed, and the majority of Upf2 was detected in the cytoplasmic perinuclear region; a small quantity of Upf2 was detected in the intranuclear region. RNase treatment of the cells reduced the Upf2 immunostained signal. The immune-purified fractions containing nuclear and cytoplasmic Upf2 also contained one of the EJC core factors, RBM8A. These results implied the existence of Upf2 in the nucleoplasm and the cytoplasm, and it appeared to be involved in the construction of the mRNA complex. In order to verify the construction of Upf2-binding EJC in the nucleoplasm, an in situ proximity ligation assay was performed with anti-Upf2 and anti-RBM8A antibodies. These results demonstrated that their interaction occurred not only in the cytoplasmic region, but also in the intranuclear region. Taken together, these results suggested that Upf2 combines with EJC in both the cytoplasmic and the intranuclear fractions, and that it is involved in mRNA metabolism in human cells.
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Affiliation(s)
- Takanori Tatsuno
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Yuka Nakamura
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Shaofu Ma
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Naohisa Tomosugi
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Yasuhito Ishigaki
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
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8
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Zhang LN, Yan YB. Depletion of poly(A)-specific ribonuclease (PARN) inhibits proliferation of human gastric cancer cells by blocking cell cycle progression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:522-34. [PMID: 25499764 DOI: 10.1016/j.bbamcr.2014.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/20/2022]
Abstract
Regulation of mRNA decay plays a crucial role in the post-transcriptional control of cell growth, survival, differentiation, death and senescence. Deadenylation is a rate-limiting step in the silence and degradation of the bulk of highly regulated mRNAs. However, the physiological functions of various deadenylases have not been fully deciphered. In this research, we found that poly(A)-specific ribonuclease (PARN) was upregulated in gastric tumor tissues and gastric cancer cell lines MKN28 and AGS. The cellular function of PARN was investigated by stably knocking down the endogenous PARN in the MKN28 and AGS cells. Our results showed that PARN-depletion significantly inhibited the proliferation of the two types of gastric cancer cells and promoted cell death, but did not significantly affect cell motility and invasion. The depletion of PARN arrested the gastric cancer cells at the G0/G1 phase by upregulating the expression levels of p53 and p21 but not p27. The mRNA stability of p53 was unaffected by PARN-knockdown in both types of cells. A significant stabilizing effect of PARN-depletion on p21 mRNA was observed in the AGS cells but not in the MKN28 cells. We further showed that the p21 3'-UTR triggered the action of PARN in the AGS cells. The dissimilar observations between the MKN28 and AGS cells as well as various stress conditions suggested that the action of PARN strongly relied on protein expression profiles of the cells, which led to heterogeneity in the stability of PARN-targeted mRNAs.
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Affiliation(s)
- Li-Na Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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9
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Cougot N, Daguenet E, Baguet A, Cavalier A, Thomas D, Bellaud P, Fautrel A, Godey F, Bertrand E, Tomasetto C, Gillet R. Overexpression of MLN51 triggers P-body disassembly and formation of a new type of RNA granules. J Cell Sci 2014; 127:4692-701. [PMID: 25205763 DOI: 10.1242/jcs.154500] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Metastatic lymph node 51 (MLN51, also known as CASC3) is a core component of the exon junction complex (EJC), which is loaded onto spliced mRNAs and plays an essential role in determining their fate. Unlike the three other EJC core components [eIF4AIII, Magoh and Y14 (also known as RBM8A)], MLN51 is mainly located in the cytoplasm, where it plays a key role in the assembly of stress granules. In this study, we further investigated the cytoplasmic role of MLN51. We show that MLN51 is a new component of processing bodies (P-bodies). When overexpressed, MLN51 localizes in novel small cytoplasmic foci. These contain RNA, show directed movements and are distinct from stress granules and P-bodies. The appearance of these foci correlates with the process of P-body disassembly. A similar reduction in P-body count is also observed in human HER2-positive (HER2(+)) breast cancer cells overexpressing MLN51. This suggests that P-body disassembly and subsequent mRNA deregulation might correlate with cancer progression.
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Affiliation(s)
- Nicolas Cougot
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
| | - Elisabeth Daguenet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, CNRS/U964 INSERM/Université de Strasbourg, 67404 Illkirch, France
| | - Aurélie Baguet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, CNRS/U964 INSERM/Université de Strasbourg, 67404 Illkirch, France
| | - Annie Cavalier
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
| | - Daniel Thomas
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
| | - Pascale Bellaud
- Unité INSERM 991, Plateforme histopathologique, IFR 140 GFAS, Université de Rennes 1, 35043 Rennes, France
| | - Alain Fautrel
- Unité INSERM 991, Plateforme histopathologique, IFR 140 GFAS, Université de Rennes 1, 35043 Rennes, France
| | - Florence Godey
- Centre de Ressources Biologiques Santé de Rennes, Centre Eugène Marquis, Rue de la Bataille Flandres Dunkerque - 35042 Rennes cedex, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS, UMR 5535, 34293 Montpellier cedex 5, France
| | - Catherine Tomasetto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, CNRS/U964 INSERM/Université de Strasbourg, 67404 Illkirch, France
| | - Reynald Gillet
- Université de Rennes 1, UMR CNRS 6290 IGDR, «Translation and Folding Team», Campus de Beaulieu, 35042 Rennes cedex, France
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10
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Abstract
Cells use messenger RNAs (mRNAs) to ensure the accurate dissemination of genetic information encoded by DNA. Given that mRNAs largely direct the synthesis of a critical effector of cellular phenotype, i.e., proteins, tight regulation of both the quality and quantity of mRNA is a prerequisite for effective cellular homeostasis. Here, we review nonsense-mediated mRNA decay (NMD), which is the best-characterized posttranscriptional quality control mechanism that cells have evolved in their cytoplasm to ensure transcriptome fidelity. We use protein quality control as a conceptual framework to organize what is known about NMD, highlighting overarching similarities between these two polymer quality control pathways, where the protein quality control and NMD pathways intersect, and how protein quality control can suggest new avenues for research into mRNA quality control.
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Affiliation(s)
- Maximilian Wei-Lin Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642;
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11
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Abstract
In mammalian cells, aberrant transcripts harboring a premature termination codon (PTC) can be generated by abnormal or inefficient biogenesis of mRNAs or by somatic mutation. Truncated polypeptides synthesized from these aberrant transcripts could be toxic to normal cellular functions. However, mammalian cells have evolved sophisticated mechanisms for monitoring the quality of mRNAs. The faulty transcripts harboring PTC are subject to nonsense-mediated mRNA decay (NMD), nonsense-mediated translational repression (NMTR), nonsense-associated alternative splicing (NAS), or nonsense-mediated transcriptional gene silencing (NMTGS). In this review, we briefly outline the molecular characteristics of each pathway and suggest mRNA quality control mechanisms as a means to regulate normal gene expression. [BMB Reports 2013; 46(1): 9-16]
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Affiliation(s)
- Jungwook Hwang
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
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12
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Trcek T, Sato H, Singer RH, Maquat LE. Temporal and spatial characterization of nonsense-mediated mRNA decay. Genes Dev 2013; 27:541-51. [PMID: 23431032 PMCID: PMC3605467 DOI: 10.1101/gad.209635.112] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/29/2013] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism responsible for "surveying" mRNAs during translation and degrading those that harbor a premature termination codon (PTC). Currently the intracellular spatial location of NMD and the kinetics of its decay step in mammalian cells are under debate. To address these issues, we used single-RNA fluorescent in situ hybridization (FISH) and measured the NMD of PTC-containing β-globin mRNA in intact single cells after the induction of β-globin gene transcription. This approach preserves temporal and spatial information of the NMD process, both of which would be lost in an ensemble study. We determined that decay of the majority of PTC-containing β-globin mRNA occurs soon after its export into the cytoplasm, with a half-life of <1 min; the remainder is degraded with a half-life of >12 h, similar to the half-life of normal PTC-free β-globin mRNA, indicating that it had evaded NMD. Importantly, NMD does not occur within the nucleoplasm, thus countering the long-debated idea of nuclear degradation of PTC-containing transcripts. We provide a spatial and temporal model for the biphasic decay of NMD targets.
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Affiliation(s)
- Tatjana Trcek
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Hanae Sato
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Robert H. Singer
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Lynne E. Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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13
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Identification of a novel CCM2 gene mutation in an Italian family with multiple cerebral cavernous malformations and epilepsy: a causative mutation? Gene 2012; 519:202-7. [PMID: 23000020 DOI: 10.1016/j.gene.2012.09.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 09/06/2012] [Accepted: 09/12/2012] [Indexed: 02/01/2023]
Abstract
Cerebral cavernous malformations (CCMs; OMIM 116860) are vascular anomalies mostly located in the central nervous system (CNS) and occasionally within the skin and retina. Main clinical manifestations are seizure, hemorrhage, recurrent headaches, focal neurological deficits and epileptic attacks. The CCMs can occur as sporadic or autosomal dominant conditions, although with incomplete penetrance and variable clinical expression. Familial CCMs were associated with causative mutations in the CCM1 [K-Rev interaction trapped 1 (KRIT1)], CCM2 (MGC4607) and CCM3 (PDCD10) genes. This study reports the identification of a previously undescribed deletion mutation in CCM2 gene exon 5, in an Italian family with multiple cerebral cavernous malformations and epilepsy. Mutation c.502_503delAG results in a frame shift causing a TGA stop codon. This truncates the mutant CCM2 gene protein, the malcavernin, to 233 amino acids, respect to 444 amino acids of the wild-type malcavernin. By using real-time RT-PCR, we have found that the mRNA resulting from two nucleotides deletion showed a 70% reduction relative to the wild-type transcript, indicating that it may be subject to a degradation mechanism such as nonsense-mediated decay (NMD).
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14
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de Turris V, Nicholson P, Orozco RZ, Singer RH, Mühlemann O. Cotranscriptional effect of a premature termination codon revealed by live-cell imaging. RNA (NEW YORK, N.Y.) 2011; 17:2094-107. [PMID: 22028363 PMCID: PMC3222123 DOI: 10.1261/rna.02918111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 08/30/2011] [Indexed: 05/29/2023]
Abstract
Aberrant mRNAs with premature translation termination codons (PTCs) are recognized and eliminated by the nonsense-mediated mRNA decay (NMD) pathway in eukaryotes. We employed a novel live-cell imaging approach to investigate the kinetics of mRNA synthesis and release at the transcription site of PTC-containing (PTC+) and PTC-free (PTC-) immunoglobulin-μ reporter genes. Fluorescence recovery after photobleaching (FRAP) and photoconversion analyses revealed that PTC+ transcripts are specifically retained at the transcription site. Remarkably, the retained PTC+ transcripts are mainly unspliced, and this RNA retention is dependent upon two important NMD factors, UPF1 and SMG6, since their depletion led to the release of the PTC+ transcripts. Finally, ChIP analysis showed a physical association of UPF1 and SMG6 with both the PTC+ and the PTC- reporter genes in vivo. Collectively, our data support a mechanism for regulation of PTC+ transcripts at the transcription site.
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Affiliation(s)
| | - Pamela Nicholson
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | | | | | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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15
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Sha Z, Brill LM, Cabrera R, Kleifeld O, Scheliga JS, Glickman MH, Chang EC, Wolf DA. The eIF3 interactome reveals the translasome, a supercomplex linking protein synthesis and degradation machineries. Mol Cell 2009; 36:141-52. [PMID: 19818717 PMCID: PMC2789680 DOI: 10.1016/j.molcel.2009.09.026] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 06/23/2009] [Accepted: 09/11/2009] [Indexed: 01/18/2023]
Abstract
eIF3 promotes translation initiation, but relatively little is known about its full range of activities in the cell. Here, we employed affinity purification and highly sensitive LC-MS/MS to decipher the fission yeast eIF3 interactome, which was found to contain 230 proteins. eIF3 assembles into a large supercomplex, the translasome, which contains elongation factors, tRNA synthetases, 40S and 60S ribosomal proteins, chaperones, and the proteasome. eIF3 also associates with ribosome biogenesis factors and the importins-beta Kap123p and Sal3p. Our genetic data indicated that the binding to both importins-beta is essential for cell growth, and photobleaching experiments revealed a critical role for Sal3p in the nuclear import of one of the translasome constituents, the proteasome. Our data reveal the breadth of the eIF3 interactome and suggest that factors involved in translation initiation, ribosome biogenesis, translation elongation, quality control, and transport are physically linked to facilitate efficient protein synthesis.
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Affiliation(s)
- Zhe Sha
- 1 Baylor Plaza, Molecular and Cellular Biology Department, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
| | - Laurence M. Brill
- Burnham Institute for Medical Research, Signal Transduction Program, NCI Cancer Center Proteomics Facility, 10901 North Torrey Pines Road, La Jolla, CA 92037
| | - Rodrigo Cabrera
- 1 Baylor Plaza, Molecular and Cellular Biology Department, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
| | - Oded Kleifeld
- Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa Israel
| | - Judith S. Scheliga
- Burnham Institute for Medical Research, Signal Transduction Program, NCI Cancer Center Proteomics Facility, 10901 North Torrey Pines Road, La Jolla, CA 92037
| | - Michael H. Glickman
- Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa Israel
| | - Eric C. Chang
- 1 Baylor Plaza, Molecular and Cellular Biology Department, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
| | - Dieter A. Wolf
- Burnham Institute for Medical Research, Signal Transduction Program, NCI Cancer Center Proteomics Facility, 10901 North Torrey Pines Road, La Jolla, CA 92037
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16
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Kim SH, Koroleva OA, Lewandowska D, Pendle AF, Clark GP, Simpson CG, Shaw PJ, Brown JWS. Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. THE PLANT CELL 2009; 21:2045-57. [PMID: 19602621 PMCID: PMC2729600 DOI: 10.1105/tpc.109.067736] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/10/2009] [Accepted: 06/24/2009] [Indexed: 05/19/2023]
Abstract
The eukaryotic nucleolus is multifunctional and involved in the metabolism and assembly of many different RNAs and ribonucleoprotein particles as well as in cellular functions, such as cell division and transcriptional silencing in plants. We previously showed that Arabidopsis thaliana exon junction complex proteins associate with the nucleolus, suggesting a role for the nucleolus in mRNA production. Here, we report that the plant nucleolus contains mRNAs, including fully spliced, aberrantly spliced, and single exon gene transcripts. Aberrant mRNAs are much more abundant in nucleolar fractions, while fully spliced products are more abundant in nucleoplasmic fractions. The majority of the aberrant transcripts contain premature termination codons and have characteristics of nonsense-mediated decay (NMD) substrates. A direct link between NMD and the nucleolus is shown by increased levels of the same aberrant transcripts in both the nucleolus and in Up-frameshift (upf) mutants impaired in NMD. In addition, the NMD factors UPF3 and UPF2 localize to the nucleolus, suggesting that the Arabidopsis nucleolus is therefore involved in identifying aberrant mRNAs and NMD.
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Affiliation(s)
- Sang Hyon Kim
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
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17
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Bhalla AD, Gudikote JP, Wang J, Chan WK, Chang YF, Olivas OR, Wilkinson MF. Nonsense codons trigger an RNA partitioning shift. J Biol Chem 2009; 284:4062-72. [PMID: 19091751 PMCID: PMC2640978 DOI: 10.1074/jbc.m805193200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 11/24/2008] [Indexed: 11/06/2022] Open
Abstract
T-cell receptor-beta (TCRbeta) genes naturally acquire premature termination codons (PTCs) as a result of programmed gene rearrangements. PTC-bearing TCRbeta transcripts are dramatically down-regulated to protect T-cells from the deleterious effects of the truncated proteins that would otherwise be produced. Here we provide evidence that two responses collaborate to elicit this dramatic down-regulation. One is rapid mRNA decay triggered by the nonsense-mediated decay (NMD) RNA surveillance pathway. We demonstrate that this occurs in highly purified nuclei lacking detectable levels of three different cytoplasmic markers, but containing an outer nuclear membrane marker, suggesting that decay occurs either in the nucleoplasm or at the outer nuclear membrane. The second response is a dramatic partitioning shift in the nuclear fraction-to-cytoplasmic fraction mRNA ratio that results in few TCRbeta transcripts escaping to the cytoplasmic fraction of cells. Analysis of TCRbeta mRNA kinetics after either transcriptional repression or induction suggested that this nonsense codon-induced partitioning shift (NIPS) response is not the result of cytoplasmic NMD but instead reflects retention of PTC(+) TCRbeta mRNA in the nuclear fraction of cells. We identified TCRbeta sequences crucial for NIPS but found that NIPS is not exclusively a property of TCRbeta transcripts, and we identified non-TCRbeta sequences that elicit NIPS. RNA interference experiments indicated that NIPS depends on the NMD factors UPF1 and eIF4AIII but not the NMD factor UPF3B. We propose that NIPS collaborates with NMD to retain and degrade a subset of PTC(+) transcripts at the outer nuclear membrane and/or within the nucleoplasm.
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MESH Headings
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Codon, Nonsense/genetics
- Codon, Nonsense/metabolism
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Down-Regulation/physiology
- Eukaryotic Initiation Factor-4A
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor/physiology
- HeLa Cells
- Humans
- Kinetics
- Pol1 Transcription Initiation Complex Proteins/genetics
- Pol1 Transcription Initiation Complex Proteins/metabolism
- RNA Interference
- RNA Stability/physiology
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
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Affiliation(s)
- Angela D Bhalla
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030-4009, USA
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18
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Abstract
Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs. In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy.
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19
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Singh G, Jakob S, Kleedehn MG, Lykke-Andersen J. Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm. Mol Cell 2007; 27:780-92. [PMID: 17803942 DOI: 10.1016/j.molcel.2007.06.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 05/16/2007] [Accepted: 06/21/2007] [Indexed: 10/22/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway rids eukaryotic cells of mRNAs with premature termination codons. There is contradictory evidence as to whether mammalian NMD is a nuclear or a cytoplasmic process. Here, we show evidence that NMD in human cells occurs primarily, if not entirely, in the cytoplasm. Polypeptides designed to inhibit interactions between NMD factors specifically impede NMD when exogenously expressed in the cytoplasm. However, restricting the polypeptides to the nucleus strongly impairs their NMD-inhibitory function, even for those intended to inhibit interactions between the exon-junction complex (EJC) and hUpf3 proteins, which localize primarily in the nucleus. NMD substrates classified based on cell fractionation assays as "nucleus associated" or "cytoplasmic" are all inhibited in the same manner. Furthermore, retention of the NMD factor hUpf1 in the nucleus strongly impairs NMD. These observations suggest that the hUpf complex communicates with the EJC and triggers NMD in the cytoplasm.
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Affiliation(s)
- Guramrit Singh
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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20
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McAlinden A, Johnstone B, Kollar J, Kazmi N, Hering TM. Expression of two novel alternatively spliced COL2A1 isoforms during chondrocyte differentiation. Matrix Biol 2007; 27:254-66. [PMID: 18023161 DOI: 10.1016/j.matbio.2007.10.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 10/06/2007] [Accepted: 10/11/2007] [Indexed: 01/06/2023]
Abstract
Alternative splicing of the type II procollagen gene (COL2A1) is developmentally regulated during chondrogenesis. Type IIA procollagen (+ exon 2) is synthesized by chondroprogenitor cells while type IIB procollagen (- exon 2) is synthesized by differentiated chondrocytes. Here, we report expression of two additional alternatively spliced COL2A1 isoforms during chondrocyte differentiation of bone marrow-derived mesenchymal stem cells (MSCs). One isoform, named IIC, contains only the first 34 nucleotides of exon 2 by the use of an alternative 5' splice site, resulting in a premature termination codon and possible nonsense-mediated decay of IIC mRNA. Low levels of the IIC isoform were detected by RT-PCR and Southern analysis of COL2A1 cDNA amplified from differentiating rabbit and human MSCs. A second novel transcript, named IID, arises by the use of another 5' alternative splice site in intron 2. The IID isoform contains exon 2 plus 3 nucleotides, resulting in the insertion of an additional amino acid. The IID isoform was co-expressed with the IIA isoform during chondrogenesis, and was approximately one-third as abundant. Deletion of the IIC alternative 5' splice site from a COL2A1 mini-gene construct resulted in a significant increase in the IIA:IIB ratio. A mutant mini-gene that inhibited production of the IID isoform, however, had differential effects on the production of the IIA and IIB isoforms: this was apparently related to the differentiation status of the cell type used. These data suggest that COL2A1 mRNA abundance and other aspects of chondrocyte differentiation may be regulated by the use of these previously undetermined alternative splice sites.
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Affiliation(s)
- Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine 4940 Parkview Place, St Louis, MO 63110, United States
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21
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Chang YF, Chan WK, Imam JS, Wilkinson MF. Alternatively Spliced T-cell Receptor Transcripts Are Up-regulated in Response to Disruption of Either Splicing Elements or Reading Frame. J Biol Chem 2007; 282:29738-47. [PMID: 17693403 DOI: 10.1074/jbc.m704372200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nonsense mutations create premature termination codons (PTCs), leading to the generation of truncated proteins, some of which have deleterious gain-of-function or dominant-negative activity. Protecting cells from such aberrant proteins is non-sense-mediated decay (NMD), an RNA surveillance pathway that degrades transcripts harboring PTCs. A second response to nonsense mutations is the up-regulation of alternatively spliced transcripts that skip the PTC. This nonsense-associated altered splicing (NAS) response has the potential to rescue protein function, but the mechanism by which it is triggered has been controversial. Some studies suggest that, like NMD, NAS is triggered as a result of nonsense mutations disrupting reading frame, whereas other studies suggest that NAS is triggered when nonsense mutations disrupt exonic splicing enhancers (ESEs). Using T-cell receptor-beta (TCRbeta), which naturally acquires PTCs at high frequency, we provide evidence that both mechanisms act on a single type of mRNA. Mutations that disrupt consensus ESE sites up-regulated an alternatively spliced TCRbeta transcript that skipped the mutations independently of reading frame disruption and the NMD factor UPF1. In contrast, reading frame-disrupting mutations that did not disrupt consensus ESE sites elicited UPF1-dependent up-regulation of the alternatively spliced TCRbeta transcript. Restoration of reading frame prevented this up-regulation. Our results suggest that the response of an mRNA to a nonsense mutation depends on its context.
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Affiliation(s)
- Yao-Fu Chang
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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22
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Isken O, Maquat LE. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev 2007; 21:1833-56. [PMID: 17671086 DOI: 10.1101/gad.1566807] [Citation(s) in RCA: 433] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cells routinely make mistakes. Some mistakes are encoded by the genome and may manifest as inherited or acquired diseases. Other mistakes occur because metabolic processes can be intrinsically inefficient or inaccurate. Consequently, cells have developed mechanisms to minimize the damage that would result if mistakes went unchecked. Here, we provide an overview of three quality control mechanisms--nonsense-mediated mRNA decay, nonstop mRNA decay, and no-go mRNA decay. Each surveys mRNAs during translation and degrades those mRNAs that direct aberrant protein synthesis. Along with other types of quality control that occur during the complex processes of mRNA biogenesis, these mRNA surveillance mechanisms help to ensure the integrity of protein-encoding gene expression.
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Affiliation(s)
- Olaf Isken
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
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23
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Fish JE, Matouk CC, Yeboah E, Bevan SC, Khan M, Patil K, Ohh M, Marsden PA. Hypoxia-inducible expression of a natural cis-antisense transcript inhibits endothelial nitric-oxide synthase. J Biol Chem 2007; 282:15652-66. [PMID: 17403686 DOI: 10.1074/jbc.m608318200] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The destabilization of endothelial nitric-oxide synthase (eNOS) mRNA in hypoxic endothelial cells may be important in the etiology of vascular diseases, such as pulmonary hypertension. Recently, an overlapping antisense transcript to eNOS/NOS3 was implicated in the post-transcriptional regulation of eNOS. We demonstrate here that expression of sONE, also known as eNOS antisense (NOS3AS) or autophagy 9-like 2 (APG9L2), is robustly induced by hypoxia or functional deficiency of von Hippel-Lindau protein. sONE is also up-regulated in the aortas of hypoxic rats. In hypoxic endothelial cells, sONE expression negatively correlates with eNOS expression. Blocking the hypoxic induction of sONE by RNA interference attenuates the fall in both eNOS RNA and protein. We provide evidence that the induction of sONE primarily involves transcript stabilization rather than increased transcriptional activity and is von Hippel-Lindaubut not hypoxia-inducible factor 2alpha-dependent. We also demonstrate that sONE transcripts are enriched in the nucleus of normoxic cells and that hypoxia promotes an increase in the level of cytoplasmic and polyribosome-associated, sONE mRNA. The finding that eNOS expression can be regulated by an overlapping cis-antisense transcript in a stimulus-dependent fashion provides evidence that sense/antisense interactions may play a previously unappreciated role in vascular disease pathogenesis.
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Affiliation(s)
- Jason E Fish
- Department of Medical Biophysics, St. Michael's Hospital, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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24
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Ghiorzo P, Gargiulo S, Pastorino L, Nasti S, Cusano R, Bruno W, Gliori S, Sertoli MR, Burroni A, Savarino V, Gensini F, Sestini R, Queirolo P, Goldstein AM, Scarrà GB. Impact of E27X, a novel CDKN2A germ line mutation, on p16 and p14ARF expression in Italian melanoma families displaying pancreatic cancer and neuroblastoma. Hum Mol Genet 2006; 15:2682-9. [PMID: 16893909 DOI: 10.1093/hmg/ddl199] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in the CDKN2A gene underlie melanoma susceptibility in as many as 50% of melanoma kindreds in selected populations, and several CDKN2A founder mutations have been described. Inherited mutations in CDKN2A have been found to be associated with other, non-melanoma cancers including pancreatic cancer (PC) and neural system tumors (NST). Here we report a novel germline mutation in exon 1 of the CDKN2A gene, E27X, which we first detected in melanoma patients living in or originally from a small geographic area bordering Liguria in north-western Italy. A subset of melanoma kindreds positive for this mutation displayed PC and neuroblastoma. E27X generates a premature stop codon, leading to dramatically reduced protein levels of p16 and leaving p14ARF unaltered. As PC and NSTs have been postulated to be preferentially associated with CDKN2A mutations located in exon 2 and/or affecting p14ARF alone, the position of E27X in exon 1alpha provides interesting insights towards clarifying the mechanisms by which the CDKN2A/ARF locus is involved in cancer predisposition.
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Affiliation(s)
- Paola Ghiorzo
- Department of Oncology, Biology and Genetics/Medical Genetics Service, University of Genoa, and Dermatology Unit, San Martino Hospital, Italy.
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25
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Abstract
Although it is universally accepted that protein synthesis occurs in the cytoplasm, the possibility that translation can also take place in the nucleus has been hotly debated. Reports have been published claiming to demonstrate nuclear translation, but alternative explanations for these results have not been excluded, and other experiments argue against it. Much of the appeal of nuclear translation is that functional proofreading of newly made mRNAs in the nucleus would provide an efficient way to monitor mRNAs for the presence of premature termination codons, thereby avoiding the synthesis of deleterious proteins. mRNAs that are still in the nucleus-associated fraction of cells are subject to translational proofreading resulting in nonsense-mediated mRNA decay and perhaps nonsense-associated alternate splicing. However, these mRNAs are likely to be in the perinuclear cytoplasm rather than within the nucleus. Therefore, in the absence of additional evidence, we conclude that nuclear translation is unlikely to occur.
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Affiliation(s)
- James E Dahlberg
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 53706, USA.
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26
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Schroder PA, Moore MJ. Association of ribosomal proteins with nascent transcripts in S. cerevisiae. RNA (NEW YORK, N.Y.) 2005; 11:1521-9. [PMID: 16199762 PMCID: PMC1370836 DOI: 10.1261/rna.2134305] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Accepted: 07/15/2005] [Indexed: 05/04/2023]
Abstract
Although it is generally accepted that transcription and translation are spatially separated in eukaryotes, a number of recent observations have called this belief into question. In particular, several studies have shown that parts of the translation machinery, including ribosomal proteins, can be found associated with sites of active transcription in metazoans. Here we describe results of chromatin immunoprecipitation (ChIP) experiments designed to determine whether ribosomal proteins associate with nascent transcripts in Saccharomyces cerevisiae and whether this association reflects a functional engagement of the translation machinery. We find that HAT-tagged ribosomal proteins can be detected in association with nascent RNAs in budding yeast. However, our data clearly indicate that this binding is independent of transcript translatability, so is therefore not indicative of nuclear translation.
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Affiliation(s)
- Patricia A Schroder
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454-9110, USA
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27
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Abstract
From the very beginning, mRNAs have a complex existence. They are transcribed, capped, spliced, modified at the 3'end, exported from the nucleus, translated, and eventually degraded. These many events not only affect the overall survival and properties of an mRNA, but are also carefully co-ordinated and integrated with quality control mechanisms that function to ensure that only 'proper' mRNAs are translated at the correct developmental time and place. This does not mean that all mRNAs follow a single or uniform path from synthesis to death. Instead, there are diverse means by which the activities of specific mRNAs are regulated, and these controls often depend upon multiple events in the mRNA's life. mRNAs are not found naked in the cell, instead they are part of complex RNPs (ribonucleoproteins) that consist of many factors. These RNPs are highly dynamic structures that change during the lifetime of a given RNA; linking events such as synthesis and processing to the final fate of the mRNA. Here, we will discuss what is known of the assembly of RNPs in general, with specific reference to the myriad of connections between different nuclear events and the cytoplasmic activity of an mRNA. Due to space limitations this review is not comprehensive, instead we focus on specific examples to illustrate these emerging themes in gene expression.
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Affiliation(s)
- Scott Kuersten
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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28
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Bühler M, Mohn F, Stalder L, Mühlemann O. Transcriptional silencing of nonsense codon-containing immunoglobulin minigenes. Mol Cell 2005; 18:307-17. [PMID: 15866173 DOI: 10.1016/j.molcel.2005.03.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 03/17/2005] [Accepted: 03/31/2005] [Indexed: 01/28/2023]
Abstract
Cells possess mechanisms to prevent synthesis of potentially deleterious truncated proteins caused by premature translation-termination codons (PTCs). Here, we show that PTCs can induce silencing of transcription of its cognate gene. We demonstrate for immunoglobulin (Ig)-mu minigenes expressed in HeLa cells that this transcriptional silencing is PTC specific and reversible by treatment of the cells with histone deacetylase inhibitors. Furthermore, PTC-containing Ig-mu minigenes are significantly more associated with K9-methylated histone H3 and less associated with acetylated H3 than the PTC-free Ig-mu minigene. This nonsense-mediated transcriptional gene silencing (NMTGS) is also observed with an Ig-gamma minigene, but not with several classic NMD reporter genes, suggesting that NMTGS might be specific for Ig genes. NMTGS represents a nonsense surveillance mechanism by which truncation of a gene's open reading frame (ORF) induces transcriptional silencing through chromatin remodeling. Remarkably, NMTGS is inhibited by overexpression of the putative siRNase 3'hExo, suggesting that siRNA-like molecules are involved in NMTGS.
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Affiliation(s)
- Marc Bühler
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
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29
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Abstract
Although it is frequently assumed that translation does not occur in eukaryotic nuclei, recent evidence suggests that some translation can take place and that it is closely coupled to transcription. The first evidence concerns the destruction of nuclear mRNAs containing premature termination codons by nonsense-mediated decay (NMD). Only ribosomes can detect termination codons, and as some NMD occurs within the nuclear fraction, active nuclear ribosomes could perform the required detection. The second evidence is the demonstration that tagged amino acids are incorporated into nascent polypeptides in a nuclear process coupled to transcription. The third evidence is that components involved in translation, NMD and transcription colocalize, coimmunoprecipitate and co-purify. All these results are simply explained if nuclear ribosomes scan nascent transcripts for premature termination codons at the site of transcription. Alternatively, the scanning needed for NMD might take place at the nuclear membrane, and contaminating cytoplasmic ribosomes might give the appearance of some nuclear translation. We argue, however, that the balance of evidence favours bona fide nuclear translation.
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Affiliation(s)
- Francisco J Iborra
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
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30
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Mohn F, Bühler M, Mühlemann O. Nonsense-associated alternative splicing of T-cell receptor beta genes: no evidence for frame dependence. RNA (NEW YORK, N.Y.) 2005; 11:147-56. [PMID: 15613535 PMCID: PMC1370704 DOI: 10.1261/rna.7182905] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Mutations that generate premature translation-termination codons (PTCs) often result in production of alternatively spliced mRNAs. While in many cases, the PTC-causing mutation was found to affect splicing directly by disrupting an exonic splicing enhancer, induction of alternative splicing of TCR-beta pre-mRNA has been reported to be specific for mutations that prematurely terminate the open reading frame. During testing of a cyto-nuclear feedback model that would have explained how cytoplasmic translation could influence nuclear splicing of TCR-beta transcripts, control experiments questioned the frame dependence of the nonsense-associated altered splicing (NAS) of TCR-beta pre-mRNA. A subsequent detailed analysis of alternatively spliced TCR-beta mRNA expressed from different minigene constructs with nonsense, silent, or frame-shift mutations at various positions revealed no correlation between truncation of the reading frame and production of alternatively spliced mRNA. Our study thus contradicts the previously reported PTC specificity of TCR-beta NAS and points out the need for systematically testing the PTC specificity in other cases where NAS has been observed.
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Affiliation(s)
- Fabio Mohn
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
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31
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Koroleva OA, Tomlinson ML, Leader D, Shaw P, Doonan JH. High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 41:162-74. [PMID: 15610358 DOI: 10.1111/j.1365-313x.2004.02281.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe a streamlined and systematic method for cloning green fluorescent protein (GFP)-open reading frame (ORF) fusions and assessing their subcellular localization in Arabidopsis thaliana cells. The sequencing of the Arabidopsis genome has made it feasible to undertake genome-based approaches to determine the function of each protein and define its subcellular localization. This is an essential step towards full functional analysis. The approach described here allows the economical handling of hundreds of expressed plant proteins in a timely fashion. We have integrated recombinational cloning of full-length trimmed ORF clones (available from the SSP consortium) with high-efficiency transient transformation of Arabidopsis cell cultures by a hypervirulent strain of Agrobacterium. To demonstrate its utility, we have used a selection of trimmed ORFs, representing a variety of key cellular processes and have defined the localization patterns of 155 fusion proteins. These patterns have been classified into five main categories, including cytoplasmic, nuclear, nucleolar, organellar and endomembrane compartments. Several genes annotated in GenBank as unknown have been ascribed a protein localization pattern. We also demonstrate the application of flow cytometry to estimate the transformation efficiency and cell cycle phase of the GFP-positive cells. This approach can be extended to functional studies, including the precise cellular localization and the prediction of the role of unknown proteins, the confirmation of bioinformatic predictions and proteomic experiments, such as the determination of protein interactions in vivo, and therefore has numerous applications in the post-genomic analysis of protein function.
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32
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Abstract
Gene regulation by short RNAs is a ubiquitous and important mode of control. MicroRNAs are short, single-strand RNAs that bind with partial complementarity to the 3' untranslated region of several genes to silence their expression. This expanding class of endogenous short RNAs are evolutionarily conserved and participate in control of development and cell-specific gene function. Several of these microRNAs have been cloned uniquely from mammalian lymphocytes suggesting specialized roles in lymphocyte development and function. In addition, several genes linked to RNAi in lower eukaryotes have mammalian homologs with specialized roles in adaptive immunity. For example, in worms, the nonsense-mediated decay (NMD) and RNAi pathways appear to be intricately linked. NMD plays a key role in regulating antigen-receptor expression in lymphocytes and there are mammalian homologs for factors identified in worms that appear to be common in both RNAi and NMD pathways. On the other hand, RNA editing and RNAi have an inverse relationship and RNA editing has an important role in viral immunity. These observations indicate unique roles for dsRNAs in the mammalian immune system.
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Affiliation(s)
- Dipanjan Chowdhury
- Center for Blood Research and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
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33
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Abstract
Studies of nonsense-mediated mRNA decay in mammalian cells have proffered unforeseen insights into changes in mRNA-protein interactions throughout the lifetime of an mRNA. Remarkably, mRNA acquires a complex of proteins at each exon-exon junction during pre-mRNA splicing that influences the subsequent steps of mRNA translation and nonsense-mediated mRNA decay. Complex-loaded mRNA is thought to undergo a pioneer round of translation when still bound by cap-binding proteins CBP80 and CBP20 and poly(A)-binding protein 2. The acquisition and loss of mRNA-associated proteins accompanies the transition from the pioneer round to subsequent rounds of translation, and from translational competence to substrate for nonsense-mediated mRNA decay.
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Affiliation(s)
- Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 712, University of Rochester, Rochester, New York 14642, USA.
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34
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Abstract
Understanding gene expression control requires defining the molecular and cellular basis of mRNA turnover. We have previously shown that the human decapping factors hDcp2 and hDcp1a are concentrated in specific cytoplasmic structures. Here, we show that hCcr4, hDcp1b, hLsm, and rck/p54 proteins related to 5'-3' mRNA decay also localize to these structures, whereas DcpS, which is involved in cap nucleotide catabolism, is nuclear. Functional analysis using fluorescence resonance energy transfer revealed that hDcp1a and hDcp2 interact in vivo in these structures that were shown to differ from the previously described stress granules. Our data indicate that these new structures are dynamic, as they disappear when mRNA breakdown is abolished by treatment with inhibitors. Accumulation of poly(A)(+) RNA in these structures, after RNAi-mediated inactivation of the Xrn1 exonuclease, demonstrates that they represent active mRNA decay sites. The occurrence of 5'-3' mRNA decay in specific subcellular locations in human cells suggests that the cytoplasm of eukaryotic cells may be more organized than previously anticipated.
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Affiliation(s)
- Nicolas Cougot
- Equipe labellisée La Ligue, Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Avenue de la Terrasse, 91198 Gif sur Yvette, France
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35
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Lytle JR, Steitz JA. Premature termination codons do not affect the rate of splicing of neighboring introns. RNA (NEW YORK, N.Y.) 2004; 10:657-68. [PMID: 15037775 PMCID: PMC1370556 DOI: 10.1261/rna.5241404] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Accepted: 12/29/2003] [Indexed: 05/21/2023]
Abstract
Introduction of a premature termination codon (PTC) into an exon of a gene can lead to nonsense-mediated decay of the mRNA, which is best characterized as a cytoplasmic event. However, increasing evidence has suggested that PTCs may also influence the nuclear processing of an RNA transcript, leading to models of nuclear surveillance perhaps involving translating nuclear ribosomes. We used quantitative RT-PCR to measure the in vivo steady-state levels of every exon-intron junction in wild-type, PTC-containing, and missense-containing precursor mRNAs of both the nonrearranging dihydrofolate reductase (DHFR) and the somatically rearranging Ig- micro genes. We find that each exon-intron junction's abundance and, therefore, the rate of intron removal, is not significantly affected by the presence of a PTC in a neighboring exon in either the DHFR or Ig- micro pre-mRNA. Similarly, the abundance of the uncleaved Ig- micro polyadenylation sites does not differ between wild-type and PTC-containing Ig- micro pre-mRNAs. Our Ig- micro data were confirmed by RNase protection analyses, and multiple cell isolates were examined to resolve differences with previously published data on steady-state pre-mRNA levels. We conclude that the presence of a PTC affects the rate of neither splicing nor the cleavage step of 3' end formation during pre-mRNA processing in the nucleus. Our results are discussed with respect to existing evidence for nuclear surveillance mechanisms.
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Affiliation(s)
- J Robin Lytle
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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36
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Nongthomba U, Clark S, Cummins M, Ansari M, Stark M, Sparrow JC. Troponin I is required for myofibrillogenesis and sarcomere formation inDrosophilaflight muscle. J Cell Sci 2004; 117:1795-805. [PMID: 15075240 DOI: 10.1242/jcs.01024] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Myofibrillar proteins assemble to form the highly ordered repetitive contractile structural unit known as a sarcomere. Studies of myogenesis in vertebrate cell culture and embryonic developmental systems have identified some of the processes involved during sarcomere formation. However, isoform changes during vertebrate muscle development and a lack of mutants have made it difficult to determine how these proteins assemble to form sarcomeres. The indirect flight muscles (IFMs) of Drosophila provide a unique genetic system with which to study myofibrillogenesis in vivo. We show in this paper that neither sarcomeric myosin nor actin are required for myoblast fusion or the subsequent morphogenesis of muscle fibres, i.e. fibre morphogenesis does not depend on myofibrillogenesis. However, fibre formation and myofibrillogenesis are very sensitive to the interactions between the sarcomeric proteins. A troponin I (TnI) mutation, hdp3, leads to an absence of TnI in the IFMs and tergal depressor of trochanter (TDT) muscles due to a transcript-splicing defect. Sarcomeres do not form and the muscles degenerate. TnI is part of the thin filament troponin complex which regulates muscle contraction. The effects of the hdp3 mutation are probably caused by unregulated acto-myosin interactions between the thin and thick filaments as they assemble. We have tested this proposal by using a transgenic myosin construct to remove the force-producing myosin heads. The defects in sarcomeric organisation and fibre degeneration in hdp3 IFMs are suppressed, although not completely, indicating the need for inhibition of muscle contraction during muscle development. We show that mRNA and translated protein products of all the major thin filament proteins are reduced in hdp3 muscles and discuss how this and previous studies of thin filament protein mutants indicate a common co-ordinated control mechanism that may be the primary cause of the muscle defects.
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Iborra FJ, Escargueil AE, Kwek KY, Akoulitchev A, Cook PR. Molecular cross-talk between the transcription, translation, and nonsense-mediated decay machineries. J Cell Sci 2004; 117:899-906. [PMID: 14762111 DOI: 10.1242/jcs.00933] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is widely believed that translation occurs only in the cytoplasm of eukaryotes, but recent results suggest some takes place in nuclei, coupled to transcription. Support for this heterodoxy comes from studies of the nonsense-mediated decay (NMD) pathway; this pathway probably uses ribosomes to proofread messenger RNAs. We find components of the machineries involved in transcription, translation and NMD colocalise, interact and copurify, and that interactions between them are probably mediated by the C-terminal domain of the catalytic subunit of RNA polymerase II. These results are simply explained if the NMD machinery uses nuclear ribosomes to translate - and so proofread - newly made transcripts; then, faulty transcripts and any truncated peptides produced by nuclear translation would be degraded.
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Affiliation(s)
- Francisco J Iborra
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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38
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Hillman RT, Green RE, Brenner SE. An unappreciated role for RNA surveillance. Genome Biol 2004; 5:R8. [PMID: 14759258 PMCID: PMC395752 DOI: 10.1186/gb-2004-5-2-r8] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 12/05/2003] [Accepted: 01/02/2004] [Indexed: 12/27/2022] Open
Abstract
Following the hypothesis that the public databases contain cloned mRNAs that would be degraded in vivo by the nonsense-mediated mRNA decay mechanism, 144 isoform sequences deposited in SWISS-PROT have been identified that derive from mRNAs with premature termination codons
Background Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA surveillance mechanism that detects and degrades mRNAs with premature termination codons (PTC+ mRNAs). In mammals, a termination codon is recognized as premature if it lies more than about 50 nucleotides upstream of the final intron position. More than a third of reliably inferred alternative splicing events in humans have been shown to result in PTC+ mRNA isoforms. As the mechanistic details of NMD have only recently been elucidated, we hypothesized that many PTC+ isoforms may have been cloned, characterized and deposited in the public databases, even though they would be targeted for degradation in vivo. Results We analyzed the human alternative protein isoforms described in the SWISS-PROT database and found that 144 (5.8% of 2,483) isoform sequences amenable to analysis, from 107 (7.9% of 1,363) SWISS-PROT entries, derive from PTC+ mRNA. Conclusions For several of the PTC+ isoforms we identified, existing experimental evidence can be reinterpreted and is consistent with the action of NMD to degrade the transcripts. Several genes with mRNA isoforms that we identified as PTC+ - calpain-10, the CDC-like kinases (CLKs) and LARD - show how previous experimental results may be understood in light of NMD.
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Affiliation(s)
- R Tyler Hillman
- Department of Bioengineering, University of California, Berkeley, CA 94720-3102, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Richard E Green
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Steven E Brenner
- Department of Bioengineering, University of California, Berkeley, CA 94720-3102, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3102, USA
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39
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Kataoka N, Dreyfuss G. A Simple Whole Cell Lysate System for in Vitro Splicing Reveals a Stepwise Assembly of the Exon-Exon Junction Complex. J Biol Chem 2004; 279:7009-13. [PMID: 14625303 DOI: 10.1074/jbc.m307692200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pre-mRNA splicing removes introns and leaves in its wake a multiprotein complex near the exon-exon junctions of mRNAs. This complex, termed the exon-exon junction complex (EJC), contains at least seven proteins and provides a link between pre-mRNA splicing and downstream events, including transport, localization, and nonsense-mediated mRNA decay. Using a simple whole cell lysate system we developed for in vitro splicing, we prepared lysates from cells transfected with tagged EJC proteins and studied the association of these proteins with pre-mRNA, splicing intermediates, and mRNA, as well as formation of the EJC during splicing. Three of the EJC components, Aly/REF, RNPS1, and SRm160, are found on pre-mRNA by the time the spliceosome is formed, whereas Upf3b associates with splicing intermediates during or immediately after the first catalytic step of the splicing reaction (cleavage of exon 1 and intron-lariat formation). In contrast, Y14 and magoh, which remain stably associated with mRNA after export to the cytoplasm, join the EJC during or after completion of exon-exon ligation. These findings indicate that EJC formation is an ordered pathway that involves stepwise association of components and is coupled to specific intermediates of the splicing reaction.
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Affiliation(s)
- Naoyuki Kataoka
- Institute for Virus Research, Kyoto University, Kyoto 606, Japan
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40
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Pienaar S, Eley BS, Hughes J, Henderson HE. X-linked hyper IgM (HIGM1) in an African kindred: the first report from South Africa. BMC Pediatr 2003; 3:12. [PMID: 14641931 PMCID: PMC317313 DOI: 10.1186/1471-2431-3-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Accepted: 11/28/2003] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The objective of this study was to describe the clinical and molecular features of the first South African family with X-linked hyper-IgM syndrome (HIGM1). METHODS Diagnoses were based on immunoglobulin results and the absence of CD40 ligand (CD40L) expression on activated T-cells. Complete molecular characterisation involved CD40L cDNA sequencing, and genomic DNA analysis by polymerase chain reaction amplification, restriction enzyme digestion and sequencing. A PCR-based diagnostic assay was established for carrier detection and prenatal diagnosis in this family. RESULTS There were originally six children, three males and three females. The eldest boy died after being diagnosed with hypogammaglobulinaemia, before HIGM1 was considered. This disorder was diagnosed in the second eldest boy at the age of 5 years, after failing to detect CD40L expression on his activated T-cells. A deficiency of CD40L was also confirmed in the youngest male at the age of 5 years. Both younger brothers have since died of infections relating to HIGM1. Molecular investigation showed that exon 3 was deleted from the CD40L mRNA of the affected males. Genomic DNA analysis identified a 1.5 kilobase deletion, spanning exon 3 and including extended flanking intronic sequence. Carrier status in the mother was confirmed by RT-PCR of her CD40L mRNA. Genetic analysis of the three female children was deferred because they were below the legal consenting age of 18 years. A PCR-based assay for genomic DNA was established for easy identification of female carriers and affected males in the future. CONCLUSIONS This study confirmed the diagnosis of HIGM1 in the first South African family to be investigated and identified a novel mutation in the CD40L gene.
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Affiliation(s)
- Sandra Pienaar
- Department of Paediatrics and Child Health and the School of Adolescent Health, Red Cross Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Brian S Eley
- Department of Paediatrics and Child Health and the School of Adolescent Health, Red Cross Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Jane Hughes
- Department of Paediatrics and Child Health and the School of Adolescent Health, Red Cross Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Howard E Henderson
- Department of Chemical Pathology and the School of Adolescent Health, Red Cross Children's Hospital, University of Cape Town, Cape Town, South Africa
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41
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Bjork P, Baurén G, Gelius B, Wrange O, Wieslander L. The Chironomus tentans translation initiation factor eIF4H is present in the nucleus but does not bind to mRNA until the mRNA reaches the cytoplasmic perinuclear region. J Cell Sci 2003; 116:4521-32. [PMID: 14576346 DOI: 10.1242/jcs.00766] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the cell nucleus, precursors to mRNA, pre-mRNAs, associate with a large number of proteins and are processed to mRNA-protein complexes, mRNPs. The mRNPs are then exported to the cytoplasm and the mRNAs are translated into proteins. The mRNAs containing in-frame premature stop codons are recognized and degraded in the nonsense-mediated mRNA decay process. This mRNA surveillence may also occur in the nucleus and presumably involves components of the translation machinery. Several translation factors have been detected in the nucleus, but their functional relationship to the dynamic protein composition of pre-mRNPs and mRNPs in the nucleus is still unclear.
Here, we have identified and characterized the translation initiation factor eIF4H in the dipteran Chironomus tentans. In the cytoplasm, Ct-eIF4H is associated with poly(A+) RNA in polysomes. We show that a minor fraction of Ct-eIF4H enters the nucleus. This fraction is independent on the level of transcription. CteIF4H could not be detected in gene-specific pre-mRNPs or mRNPs, nor in bulk mRNPs in the nucleus. Our immunoelectron microscopy data suggest that Ct-eIF4H associates with mRNP in the cytoplasmic perinuclear region, immediately as the mRNP exits from the nuclear pore complex.
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Affiliation(s)
- Petra Bjork
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-106 91 Stockholm, Sweden
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42
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Alonso CR, Akam M. A Hox gene mutation that triggers nonsense-mediated RNA decay and affects alternative splicing during Drosophila development. Nucleic Acids Res 2003; 31:3873-80. [PMID: 12853602 PMCID: PMC167643 DOI: 10.1093/nar/gkg482] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2003] [Accepted: 05/07/2003] [Indexed: 11/14/2022] Open
Abstract
Nonsense mutations are usually assumed to affect protein function by generating truncated protein products. Nonetheless, it is now clear that these mutations affect not just protein synthesis but also messenger RNA stability. The surveillance mechanism responsible for the detection and degradation of 'nonsense' RNA messages is termed nonsense-mediated RNA decay (NMD). Essential biochemical components of the NMD machinery have been defined in several species. Here we identify the Drosophila orthologue of one of these factors, Upf1, and document its expression during embryogenesis. To test whether NMD acts during Drosophila development, we make use of a mutation that introduces a stop codon into a variably spliced exon of the Hox gene Ultrabithorax (Ubx). Using real-time quantitative RT-PCR we demonstrate that Ubx transcripts containing the premature stop codon are expressed at lower levels than their wild type counterpart. Unexpectedly, we also find that the same mutation significantly increases the levels of a Ubx splicing isoform that lacks the exon containing the premature termination codon. These findings indicate that NMD is operational during Drosophila development and suggest that nonsense mutations may affect development by altering the spectrum of splicing products formed, as well as by reducing or eliminating protein synthesis.
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Affiliation(s)
- Claudio R Alonso
- Laboratory for Development and Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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43
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Kolpakova E, Rusten TE, Olsnes S. Characterization and tissue expression of acidic fibroblast growth factor binding protein homologue in Drosophila melanogaster. Gene 2003; 310:185-91. [PMID: 12801646 DOI: 10.1016/s0378-1119(03)00550-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have earlier reported a Drosophila protein, which aligned significantly with the amino acid sequence of the human acidic fibroblast growth factor intracellular binding protein (FIBP). In attempts to further elucidate the function of FIBP and its putative role in fibroblast growth factor (FGF) signaling we have cloned and characterized FIBP from Drosophila melanogaster (DrFIBP). Using comparative sequence analysis of Drosophila and human FIBP genes we demonstrate a remarkable conservation of their structural architecture suggesting that FIBP from vertebrates and insects are genuine homologues. Reverse transcriptase polymerase chain reaction analysis of FIBP mRNA from Drosophila revealed differential splicing by intron retention resulting in the production of three distinct FIBP transcripts. The retention of the intronic sequences introduces termination codons within the mature FIBP mRNA leading to premature termination of translation. Analysis of FIBP mRNA distribution in the fruit fly suggests that DrFIBP, like its mammalian homologue, is an abundant protein whose expression is maintained during embryonic, larval and adult stages. The spatial expression pattern investigated by whole mount embryo immunostaining reveals expression of FIBP in the developing tracheal system and in ventral midline cells, two known sites of FGF signaling in the fruit fly.
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MESH Headings
- Alternative Splicing
- Animals
- Blotting, Northern
- Carrier Proteins/genetics
- DNA/chemistry
- DNA/genetics
- DNA/isolation & purification
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila melanogaster/embryology
- Drosophila melanogaster/genetics
- Drosophila melanogaster/growth & development
- Embryo, Nonmammalian/metabolism
- Embryonic Development
- Exons
- Gene Expression Regulation, Developmental
- Genes, Insect/genetics
- Immunohistochemistry
- Intracellular Signaling Peptides and Proteins
- Introns
- Molecular Sequence Data
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Elona Kolpakova
- Department of Biochemistry, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, N-0310, Oslo, Norway
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44
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Abstract
Recently, several reports have been published in support of the idea that protein synthesis occurs in both the nucleus and the cytoplasm. This proposal has generated a great deal of excitement because, if true, it would mean that our thinking about the compartmentalization of cell functions would have to be re-evaluated. The significance and broad implications of this phenomenon require that the experimental evidence used to support it be carefully evaluated. Here, we critique the published evidence in support of, or in opposition to, the question of whether translation occurs in the nucleus. Arguments in support of nuclear translation focus on three issues: (1) the presence of translation factors and ribosomal components in the nucleus, and their recruitment to sites of transcription; (2) amino acid incorporation in isolated nuclei and in nuclei under conditions that should not permit protein import; and (3) the fact that nuclear translation would account for observations that are otherwise difficult to explain. Arguments against nuclear translation emphasize the absence (or low abundance) from nuclei of many translation factors; the likely inactivity of nascent ribosomes; and the loss of translation activity as nuclei are purified from contaminating cytoplasm. In our opinion, all of the experiments on nuclear translation published to date lack critical controls and, therefore, are not compelling; also, traditional mechanisms can explain the observations for which nuclear translation has been invoked. Thus, while we cannot rule out nuclear translation, in the absence of better supporting data we are reluctant to believe it occurs.
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Affiliation(s)
- James E Dahlberg
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, 53706, USA.
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45
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Bohnsack MT, Regener K, Schwappach B, Saffrich R, Paraskeva E, Hartmann E, Görlich D. Exp5 exports eEF1A via tRNA from nuclei and synergizes with other transport pathways to confine translation to the cytoplasm. EMBO J 2002; 21:6205-15. [PMID: 12426392 PMCID: PMC137205 DOI: 10.1093/emboj/cdf613] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2002] [Revised: 09/16/2002] [Accepted: 09/24/2002] [Indexed: 11/13/2022] Open
Abstract
Importin beta-type transport receptors mediate the vast majority of transport pathways between cell nucleus and cytoplasm. We identify here the translation elongation factor 1A (eEF1A) as the predominant nuclear export substrate of RanBP21/exportin 5 (Exp5). This cargo-exportin interaction is rather un usual in that eEF1A binds the exportin not directly, but instead via aminoacylated tRNAs. Exp5 thus represents the second directly RNA-binding exportin and mediates tRNA export in parallel with exportin-t. It was suggested recently that 10-15% of the cellular translation would occur in the nucleus. Our data rule out such a scenario and instead suggest that nuclear translation is actively suppressed by the nuclear export machinery. We found that the vast majority of translation initiation factors (eIF2, eIF2B, eIF3, eIF4A1, eIF5 and eIF5B), all three elongation factors (eEF1A, eEF1B and eEF2) and the termination factor eRF1 are strictly excluded from nuclei. Besides Exp5 and importin 13, CRM1 and as yet unidentified exportins also contribute to the depletion of translation factors from nuclei.
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Affiliation(s)
- Markus T. Bohnsack
- ZMBH, INF 282, DKFZ, INF 280, D-69120 Heidelberg and Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany Present address: Department of Medicine, University of Thessaly, Greece Corresponding author e-mail:
| | - Kathrin Regener
- ZMBH, INF 282, DKFZ, INF 280, D-69120 Heidelberg and Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany Present address: Department of Medicine, University of Thessaly, Greece Corresponding author e-mail:
| | - Blanche Schwappach
- ZMBH, INF 282, DKFZ, INF 280, D-69120 Heidelberg and Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany Present address: Department of Medicine, University of Thessaly, Greece Corresponding author e-mail:
| | - Rainer Saffrich
- ZMBH, INF 282, DKFZ, INF 280, D-69120 Heidelberg and Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany Present address: Department of Medicine, University of Thessaly, Greece Corresponding author e-mail:
| | - Efrosyni Paraskeva
- ZMBH, INF 282, DKFZ, INF 280, D-69120 Heidelberg and Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany Present address: Department of Medicine, University of Thessaly, Greece Corresponding author e-mail:
| | - Enno Hartmann
- ZMBH, INF 282, DKFZ, INF 280, D-69120 Heidelberg and Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany Present address: Department of Medicine, University of Thessaly, Greece Corresponding author e-mail:
| | - Dirk Görlich
- ZMBH, INF 282, DKFZ, INF 280, D-69120 Heidelberg and Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany Present address: Department of Medicine, University of Thessaly, Greece Corresponding author e-mail:
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Wang J, Chang YF, Hamilton JI, Wilkinson MF. Nonsense-associated altered splicing: a frame-dependent response distinct from nonsense-mediated decay. Mol Cell 2002; 10:951-7. [PMID: 12419238 DOI: 10.1016/s1097-2765(02)00635-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nonsense-associated altered splicing (NAS) is a putative correction response that upregulates alternatively spliced transcripts that have skipped offending premature termination codons (PTCs). Here, we examined whether NAS has characteristics in common with nonsense-mediated decay (NMD), a surveillance mechanism that degrades PTC-bearing mRNAs. We discovered that although NAS shared the need for a Kozak AUG to define frame, it differed from NMD. NAS was not affected by depletion of the NMD protein hUPF2, and it functioned independently of RNA stabilization. We identified an alternatively spliced transcript acted upon by both NAS and NMD, indicating that these two mechanisms are not mutually exclusive. Our results suggest that NAS and NMD are distinct mechanisms despite being triggered by the same signal.
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Affiliation(s)
- Jun Wang
- Department of Immunology, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA
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47
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Maquat LE. NASty effects on fibrillin pre-mRNA splicing: another case of ESE does it, but proposals for translation-dependent splice site choice live on. Genes Dev 2002; 16:1743-53. [PMID: 12130534 DOI: 10.1101/gad.1014502] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.
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