51
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Rubtsova M, Naraykina Y, Vasilkova D, Meerson M, Zvereva M, Prassolov V, Lazarev V, Manuvera V, Kovalchuk S, Anikanov N, Butenko I, Pobeguts O, Govorun V, Dontsova O. Protein encoded in human telomerase RNA is involved in cell protective pathways. Nucleic Acids Res 2019; 46:8966-8977. [PMID: 30102362 PMCID: PMC6158713 DOI: 10.1093/nar/gky705] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/23/2018] [Indexed: 01/06/2023] Open
Abstract
Several studies have described functional peptides encoded in RNA that are considered to be noncoding. Telomerase RNA together with telomerase reverse transcriptase and regulatory proteins make up the telomerase complex, the major component of the telomere length-maintaining machinery. In contrast to protein subunits, telomerase RNA is expressed constitutively in most somatic cells where telomerase reverse transcriptase is absent. We show here that the transcript of human telomerase RNA codes a 121 amino acid protein (hTERP). The existence of hTERP was shown by immunoblotting, immunofluorescence microscopy and mass spectroscopy. Gain-of-function and loss-of-function experiments showed that hTERP protects cells from drug-induced apoptosis and participates in the processing of autophagosome. We suggest that hTERP regulates crosstalk between autophagy and apoptosis and is involved in cellular adaptation under stress conditions.
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Affiliation(s)
- Maria Rubtsova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yulia Naraykina
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Daria Vasilkova
- Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Mark Meerson
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Maria Zvereva
- Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Vasily Lazarev
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Valentin Manuvera
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Sergey Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Nickolay Anikanov
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Ivan Butenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Olga Pobeguts
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow 119992, Russia
| | - Olga Dontsova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Department of Chemistry, and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
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52
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Abstract
Human telomerase holoenzyme consists of the catalytic component TERT and the template RNA TERC. However, a network of accessory proteins plays key roles in its assembly, localization and stability. Defects in genes involved in telomerase biology affect the renewal of critical stem cell populations and cause disorders such as telomeropathies. Moreover, activation of telomerase in somatic cells allows neoplastic cells to proliferate indefinitely, thus contributing to tumorigenesis. For these reasons, identification of new players involved in telomerase regulation is crucial for the determination of novel therapeutic targets and biomarkers. In the very last years, increasing evidence describes components of the RNAi machinery as a new layer of complexity in human telomerase activity. In this review, we will discuss how AGO2 and other proteins which collaborate with AGO2 in RNAi pathway play a pivotal role in TERC stability and function.
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Affiliation(s)
- Ilaria Laudadio
- a Department of Molecular Medicine , "Sapienza" University of Rome , Rome , Italy
| | - Claudia Carissimi
- a Department of Molecular Medicine , "Sapienza" University of Rome , Rome , Italy
| | - Valerio Fulci
- a Department of Molecular Medicine , "Sapienza" University of Rome , Rome , Italy
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53
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Disruption of Telomerase RNA Maturation Kinetics Precipitates Disease. Mol Cell 2019; 74:688-700.e3. [PMID: 30930056 DOI: 10.1016/j.molcel.2019.02.033] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 01/16/2023]
Abstract
Mutations in RNA-processing enzymes are increasingly linked to human disease. Telomerase RNA and related noncoding RNAs require 3' end-processing steps, including oligoadenylation. Germline mutations in poly(A)ribonuclease (PARN) cause accumulation of extended human telomerase RNA (hTR) species and precipitate dyskeratosis congenita and pulmonary fibrosis. Here, we develop nascent RNAend-seq to measure processing rates of RNA precursors. We find that mature hTR derives from extended precursors but that in PARN-mutant cells hTR maturation kinetically stalls and unprocessed precursors are degraded. Loss of poly(A)polymerase PAPD5 in PARN-mutant cells accelerates hTR maturation and restores hTR processing, indicating that oligoadenylation and deadenylation set rates of hTR maturation. The H/ACA domain mediates hTR maturation by precisely defining the 3' end, recruiting poly(A)polymerase activity, and conferring sensitivity to PARN regulation. These data reveal a feedforward circuit in which post-transcriptional oligoadenylation controls RNA maturation kinetics. Similar alterations in RNA processing rates may contribute to mechanisms of RNA-based human disease.
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54
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Lee D, Park D, Park JH, Kim JH, Shin C. Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs. RNA (NEW YORK, N.Y.) 2019; 25:388-405. [PMID: 30591540 PMCID: PMC6380276 DOI: 10.1261/rna.069633.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 05/08/2023]
Abstract
The 3' ends of metazoan microRNAs (miRNAs) are initially defined by the RNase III enzymes during maturation, but subsequently experience extensive modifications by several enzymatic activities. For example, terminal nucleotidyltransferases (TENTs) elongate miRNAs by adding one or a few nucleotides to their 3' ends, which occasionally leads to differential regulation of miRNA stability or function. However, the catalytic entities that shorten miRNAs and the molecular consequences of such shortening are less well understood, especially in vertebrates. Here, we report that poly(A)-specific ribonuclease (PARN) sculpts the 3' ends of miRNAs in human cells. By generating PARN knockout cells and characterizing their miRNAome, we demonstrate that PARN digests the 3' extensions of miRNAs that are derived from the genome or attached by TENTs, thereby effectively reducing the length of miRNAs. Surprisingly, PARN-mediated shortening has little impact on miRNA stability, suggesting that this process likely operates to finalize miRNA maturation, rather than to initiate miRNA decay. PARN-mediated shortening is pervasive across most miRNAs and appears to be a conserved mechanism contributing to the 3' end formation of vertebrate miRNAs. Our findings add miRNAs to the expanding list of noncoding RNAs whose 3' end formation depends on PARN.
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Affiliation(s)
- Dooyoung Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Daechan Park
- Department of Biological Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong Heon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
- Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
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55
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Shukla S, Bjerke GA, Muhlrad D, Yi R, Parker R. The RNase PARN Controls the Levels of Specific miRNAs that Contribute to p53 Regulation. Mol Cell 2019; 73:1204-1216.e4. [PMID: 30770239 DOI: 10.1016/j.molcel.2019.01.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/08/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022]
Abstract
PARN loss-of-function mutations cause a severe form of the hereditary disease dyskeratosis congenita (DC). PARN deficiency affects the stability of non-coding RNAs such as human telomerase RNA (hTR), but these effects do not explain the severe disease in patients. We demonstrate that PARN deficiency affects the levels of numerous miRNAs in human cells. PARN regulates miRNA levels by stabilizing either mature or precursor miRNAs by removing oligo(A) tails added by the poly(A) polymerase PAPD5, which if remaining recruit the exonuclease DIS3L or DIS3L2 to degrade the miRNA. PARN knockdown destabilizes multiple miRNAs that repress p53 translation, which leads to an increase in p53 accumulation in a Dicer-dependent manner, thus explaining why PARN-defective patients show p53 accumulation. This work also reveals that DIS3L and DIS3L2 are critical 3' to 5' exonucleases that regulate miRNA stability, with the addition and removal of 3' end extensions controlling miRNA levels in the cell.
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Affiliation(s)
- Siddharth Shukla
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Glen A Bjerke
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rui Yi
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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56
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Rubtsova MP, Vasilkova DP, Moshareva MA, Malyavko AN, Meerson MB, Zatsepin TS, Naraykina YV, Beletsky AV, Ravin NV, Dontsova OA. Integrator is a key component of human telomerase RNA biogenesis. Sci Rep 2019; 9:1701. [PMID: 30737432 PMCID: PMC6368637 DOI: 10.1038/s41598-018-38297-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/17/2018] [Indexed: 11/27/2022] Open
Abstract
Telomeres are special DNA-protein structures that are located at the ends of linear eukaryotic chromosomes. The telomere length determines the proliferation potential of cells. Telomerase is a key component of the telomere length maintenance system. While telomerase is inactive in the majority of somatic cells, its activity determines the clonogenic potential of stem cells as a resource for tissue and organism regeneration. Reactivation of telomerase occurs during the process of immortalization in the majority of cancer cells. Telomerase is a ribonucleoprotein that contains telomerase reverse transcriptase and telomerase RNA components. The RNA processing mechanism of telomerase involves exosome trimming or degradation of the primary precursor. Recent data provide evidence that the competition between the processing and decay of telomerase RNA may regulate the amount of RNA at the physiological level. We show that termination of human telomerase RNA transcription is dependent on its promoter, which engages with the multisubunit complex Integrator to interact with RNA polymerase II and terminate transcription of the human telomerase RNA gene followed by further processing.
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Affiliation(s)
- M P Rubtsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143026, Russia. .,Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia.
| | - D P Vasilkova
- Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - M A Moshareva
- Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - A N Malyavko
- Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - M B Meerson
- Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - T S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143026, Russia.,Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - Y V Naraykina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143026, Russia.,Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - A V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - N V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - O A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143026, Russia. .,Lomonosov Moscow State University, Department of Chemistry, Faculty of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
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57
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Telomeres in Plants and Humans: Not So Different, Not So Similar. Cells 2019; 8:cells8010058. [PMID: 30654521 PMCID: PMC6356271 DOI: 10.3390/cells8010058] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/01/2023] Open
Abstract
Parallel research on multiple model organisms shows that while some principles of telomere biology are conserved among all eukaryotic kingdoms, we also find some deviations that reflect different evolutionary paths and life strategies, which may have diversified after the establishment of telomerase as a primary mechanism for telomere maintenance. Much more than animals, plants have to cope with environmental stressors, including genotoxic factors, due to their sessile lifestyle. This is, in principle, made possible by an increased capacity and efficiency of the molecular systems ensuring maintenance of genome stability, as well as a higher tolerance to genome instability. Furthermore, plant ontogenesis differs from that of animals in which tissue differentiation and telomerase silencing occur during early embryonic development, and the “telomere clock” in somatic cells may act as a preventive measure against carcinogenesis. This does not happen in plants, where growth and ontogenesis occur through the serial division of apical meristems consisting of a small group of stem cells that generate a linear series of cells, which differentiate into an array of cell types that make a shoot and root. Flowers, as generative plant organs, initiate from the shoot apical meristem in mature plants which is incompatible with the human-like developmental telomere shortening. In this review, we discuss differences between human and plant telomere biology and the implications for aging, genome stability, and cell and organism survival. In particular, we provide a comprehensive comparative overview of telomere proteins acting in humans and in Arabidopsis thaliana model plant, and discuss distinct epigenetic features of telomeric chromatin in these species.
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58
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The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN. Nat Commun 2018; 9:5430. [PMID: 30575725 PMCID: PMC6303318 DOI: 10.1038/s41467-018-07822-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/23/2018] [Indexed: 01/08/2023] Open
Abstract
Human telomerase RNA (hTR) is transcribed as a precursor that is then posttranscriptionally modified and processed. A fraction of the transcripts is oligoadenylated by TRAMP and either processed into the mature hTR or degraded by the exosome. Here, we characterize the processing of 3′ extended forms of varying length by PARN and RRP6. We show that tertiary RNA interactions unique to the longer transcripts favor RNA degradation, whereas H/ACA RNP assembly stimulates productive processing. Interestingly, the H/ACA complex actively promotes processing in addition to protecting the mature 3′ end. Processing occurs in two steps with longer forms first being trimmed by RRP6 and shorter forms then being processed by PARN. These results reveal how RNA structure and RNP assembly affect the kinetics of processing and degradation and ultimately determine the amount of functional telomerase produced in cells. Telomerase RNA (hTR) is transcribed as a 3′-extended precursor. Here the authors examine the processing of hTR precursors of various lengths and show that processing occurs in distinct steps involving different nucleases PARN and RRP6.
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59
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Kufel J, Grzechnik P. Small Nucleolar RNAs Tell a Different Tale. Trends Genet 2018; 35:104-117. [PMID: 30563726 DOI: 10.1016/j.tig.2018.11.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5' and 3' ends undergo processing to release mature, functional molecules. The maturation strategies of these noncoding RNAs in various organisms follow a similar pattern but employ different factors and are strictly correlated with genomic organisation of their genes.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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60
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Dionne KL, Bergeron D, Landry-Voyer AM, Bachand F. The 40S ribosomal protein uS5 (RPS2) assembles into an extraribosomal complex with human ZNF277 that competes with the PRMT3-uS5 interaction. J Biol Chem 2018; 294:1944-1955. [PMID: 30530495 DOI: 10.1074/jbc.ra118.004928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/27/2018] [Indexed: 02/06/2023] Open
Abstract
Ribosomal (r)-proteins are generally viewed as ubiquitous, constitutive proteins that simply function to maintain ribosome integrity. However, findings in the past decade have led to the idea that r-proteins have evolved specialized functions beyond the ribosome. For example, the 40S ribosomal protein uS5 (RPS2) is known to form an extraribosomal complex with the protein arginine methyltransferase PRMT3 that is conserved from fission yeast to humans. However, the full scope of uS5's extraribosomal functions, including whether uS5 interacts with any other proteins, is not known. In this study, we identify the conserved zinc finger protein 277 (ZNF277) as a new uS5-associated protein by using quantitative proteomics approaches in human cells. As previously shown for PRMT3, we found that ZNF277 uses a C2H2-type zinc finger domain to recognize uS5. Analysis of protein-protein interactions in living cells indicated that the ZNF277-uS5 complex is found in the cytoplasm and the nucleolus. Furthermore, we show that ZNF277 and PRMT3 compete for uS5 binding, because overexpression of PRMT3 inhibited the formation of the ZNF277-uS5 complex, whereas depletion of cellular ZNF277 resulted in increased levels of uS5-PRMT3. Notably, our results reveal that ZNF277 recognizes nascent uS5 in the course of mRNA translation, suggesting cotranslational assembly of the ZNF277-uS5 complex. Our findings thus unveil an intricate network of evolutionarily conserved protein-protein interactions involving extraribosomal uS5, suggesting a key role for uS5 beyond the ribosome.
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Affiliation(s)
- Kiersten L Dionne
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Danny Bergeron
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Anne-Marie Landry-Voyer
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François Bachand
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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61
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Tudek A, Lloret-Llinares M, Jensen TH. The multitasking polyA tail: nuclear RNA maturation, degradation and export. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0169. [PMID: 30397105 DOI: 10.1098/rstb.2018.0169] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
A polyA (pA) tail is an essential modification added to the 3' ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae, human cells and, when relevant, the fission yeast Schizosaccharomyces pombe Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3'-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in S. pombe and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
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62
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Aubert M, O'Donohue MF, Lebaron S, Gleizes PE. Pre-Ribosomal RNA Processing in Human Cells: From Mechanisms to Congenital Diseases. Biomolecules 2018; 8:biom8040123. [PMID: 30356013 PMCID: PMC6315592 DOI: 10.3390/biom8040123] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomal RNAs, the most abundant cellular RNA species, have evolved as the structural scaffold and the catalytic center of protein synthesis in every living organism. In eukaryotes, they are produced from a long primary transcript through an intricate sequence of processing steps that include RNA cleavage and folding and nucleotide modification. The mechanisms underlying this process in human cells have long been investigated, but technological advances have accelerated their study in the past decade. In addition, the association of congenital diseases to defects in ribosome synthesis has highlighted the central place of ribosomal RNA maturation in cell physiology regulation and broadened the interest in these mechanisms. Here, we give an overview of the current knowledge of pre-ribosomal RNA processing in human cells in light of recent progress and discuss how dysfunction of this pathway may contribute to the physiopathology of congenital diseases.
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Affiliation(s)
- Maxime Aubert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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63
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Larochelle M, Robert MA, Hébert JN, Liu X, Matteau D, Rodrigue S, Tian B, Jacques PÉ, Bachand F. Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nat Commun 2018; 9:4364. [PMID: 30341288 PMCID: PMC6195540 DOI: 10.1038/s41467-018-06546-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/30/2018] [Indexed: 11/09/2022] Open
Abstract
Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Here, we find that NNS-like transcription termination is not conserved in fission yeast. Rather, genome-wide analyses show global recruitment of mRNA 3' end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We also find that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.
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Affiliation(s)
- Marc Larochelle
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada
| | - Marc-Antoine Robert
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Jean-Nicolas Hébert
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Dominick Matteau
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Sébastien Rodrigue
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Pierre-Étienne Jacques
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada.
- Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, J1H5N4, Canada.
| | - François Bachand
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada.
- Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, J1H5N4, Canada.
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65
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Abstract
The nuclear RNA exosome is an essential and versatile machinery that regulates maturation and degradation of a huge plethora of RNA species. The past two decades have witnessed remarkable progress in understanding the whole picture of its RNA substrates and the structural basis of its functions. In addition to the exosome itself, recent studies focusing on associated co-factors have been elucidating how the exosome is directed towards specific substrates. Moreover, it has been gradually realized that loss-of-function of exosome subunits affect multiple biological processes such as the DNA damage response, R-loop resolution, maintenance of genome integrity, RNA export, translation and cell differentiation. In this review, we summarize the current knowledge of the mechanisms of nuclear exosome-mediated RNA metabolism and discuss their physiological significance.
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66
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Páez-Moscoso DJ, Pan L, Sigauke RF, Schroeder MR, Tang W, Baumann P. Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast. Nat Commun 2018; 9:587. [PMID: 29422664 PMCID: PMC5805746 DOI: 10.1038/s41467-017-02284-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/17/2017] [Indexed: 01/06/2023] Open
Abstract
Telomerase reverse transcriptase (TERT) and the non-coding telomerase RNA subunit (TR) constitute the core of telomerase. Here we now report that the putative F-box protein Pof8 is also a constitutive component of active telomerase in fission yeast. Pof8 functions in a hierarchical assembly pathway by promoting the binding of the Lsm2-8 complex to telomerase RNA, which in turn promotes binding of the catalytic subunit. Loss of Pof8 reduces TER1 stability, causes a severe assembly defect, and results in critically short telomeres. Structure profile searches identified similarities between Pof8 and telomerase subunits from ciliated protozoa, making Pof8 next to TERT the most widely conserved telomerase subunits identified to date.
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Affiliation(s)
| | - Lili Pan
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | | | | | - Wen Tang
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Peter Baumann
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA. .,Howard Hughes Medical Institute, Kansas City, MO, 64110, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, MO, 66160, USA. .,Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099, Mainz, Germany.
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67
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Montellese C, Montel-Lehry N, Henras AK, Kutay U, Gleizes PE, O'Donohue MF. Poly(A)-specific ribonuclease is a nuclear ribosome biogenesis factor involved in human 18S rRNA maturation. Nucleic Acids Res 2017; 45:6822-6836. [PMID: 28402503 PMCID: PMC5499762 DOI: 10.1093/nar/gkx253] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/03/2017] [Indexed: 01/28/2023] Open
Abstract
The poly-A specific ribonuclease (PARN), initially characterized for its role in mRNA catabolism, supports the processing of different types of non-coding RNAs including telomerase RNA. Mutations in PARN are linked to dyskeratosis congenita and pulmonary fibrosis. Here, we show that PARN is part of the enzymatic machinery that matures the human 18S ribosomal RNA (rRNA). Consistent with its nucleolar steady-state localization, PARN is required for 40S ribosomal subunit production and co-purifies with 40S subunit precursors. Depletion of PARN or expression of a catalytically-compromised PARN mutant results in accumulation of 3΄ extended 18S rRNA precursors. Analysis of these processing intermediates reveals a defect in 3΄ to 5΄ trimming of the internal transcribed spacer 1 (ITS1) region, subsequent to endonucleolytic cleavage at site E. Consistent with a function of PARN in exonucleolytic trimming of 18S-E pre-rRNA, recombinant PARN can process the corresponding ITS1 RNA fragment in vitro. Trimming of 18S-E pre-rRNA by PARN occurs in the nucleus, upstream of the final endonucleolytic cleavage by the endonuclease NOB1 in the cytoplasm. These results identify PARN as a new component of the ribosome biogenesis machinery in human cells. Defects in ribosome biogenesis could therefore underlie the pathologies linked to mutations in PARN.
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Affiliation(s)
| | - Nathalie Montel-Lehry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Ulrike Kutay
- Institut für Biochemie, ETH Zurich, Zurich CH-8093, Switzerland
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
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68
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Banerjee A, Vest KE, Pavlath GK, Corbett AH. Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing. Nucleic Acids Res 2017; 45:10706-10725. [PMID: 28977530 PMCID: PMC5737383 DOI: 10.1093/nar/gkx786] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/27/2017] [Indexed: 01/01/2023] Open
Abstract
The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of muscular dystrophy termed oculopharyngeal muscular dystrophy (OPMD). Despite the tissue-specific pathology that occurs in this disease, only recently have studies of PABPN1 begun to explore the role of this protein in skeletal muscle. We have used co-immunoprecipitation and mass spectrometry to identify proteins that interact with PABPN1 in mouse skeletal muscles. Among the interacting proteins we identified Matrin 3 (MATR3) as a novel protein interactor of PABPN1. The MATR3 gene is mutated in a form of distal myopathy and amyotrophic lateral sclerosis (ALS). We demonstrate, that like PABPN1, MATR3 is critical for myogenesis. Furthermore, MATR3 controls critical aspects of RNA processing including alternative polyadenylation and intron retention. We provide evidence that MATR3 also binds and regulates the levels of long non-coding RNA (lncRNA) Neat1 and together with PABPN1 is required for normal paraspeckle function. We demonstrate that PABPN1 and MATR3 are required for paraspeckles, as well as for adenosine to inosine (A to I) RNA editing of Ctn RNA in muscle cells. We provide a functional link between PABPN1 and MATR3 through regulation of a common lncRNA target with downstream impact on paraspeckle morphology and function. We extend our analysis to a mouse model of OPMD and demonstrate altered paraspeckle morphology in the presence of endogenous levels of alanine-expanded PABPN1. In this study, we report protein-binding partners of PABPN1, which could provide insight into novel functions of PABPN1 in skeletal muscle and identify proteins that could be sequestered with alanine-expanded PABPN1 in the nuclear aggregates found in OPMD.
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Affiliation(s)
- Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Katherine E Vest
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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69
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Telomerase RNA Imaging in Budding Yeast and Human Cells by Fluorescent In Situ Hybridization. Methods Mol Biol 2017. [PMID: 29043638 DOI: 10.1007/978-1-4939-7306-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Telomerase, the enzyme that elongates telomeres in most eukaryotes, is a ribonucleoprotein complex composed of a reverse transcriptase catalytic subunit (TERT in human, Est2 in the budding yeast S. cerevisiae), regulatory factors and a noncoding RNA called hTERC (in human) or TLC1 (in budding yeast). Telomerase trafficking is a major process in the biogenesis and regulation of telomerase action at telomeres. Due to its higher signal-to-noise ratio, imaging of the telomerase RNA moiety is frequently used to determine telomerase intracellular localization. Here we describe how to image telomerase RNA in human and yeast cells using fluorescence in situ hybridization.
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70
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Abstract
Numerous surveillance pathways sculpt eukaryotic transcriptomes by degrading unneeded, defective, and potentially harmful noncoding RNAs (ncRNAs). Because aberrant and excess ncRNAs are largely degraded by exoribonucleases, a key characteristic of these RNAs is an accessible, protein-free 5' or 3' end. Most exoribonucleases function with cofactors that recognize ncRNAs with accessible 5' or 3' ends and/or increase the availability of these ends. Noncoding RNA surveillance pathways were first described in budding yeast, and there are now high-resolution structures of many components of the yeast pathways and significant mechanistic understanding as to how they function. Studies in human cells are revealing the ways in which these pathways both resemble and differ from their yeast counterparts, and are also uncovering numerous pathways that lack equivalents in budding yeast. In this review, we describe both the well-studied pathways uncovered in yeast and the new concepts that are emerging from studies in mammalian cells. We also discuss the ways in which surveillance pathways compete with chaperone proteins that transiently protect nascent ncRNA ends from exoribonucleases, with partner proteins that sequester these ends within RNPs, and with end modification pathways that protect the ends of some ncRNAs from nucleases.
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Affiliation(s)
- Cedric Belair
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Frederick , Maryland 21702 , United States
| | - Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Frederick , Maryland 21702 , United States
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Frederick , Maryland 21702 , United States
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71
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PARN Modulates Y RNA Stability and Its 3'-End Formation. Mol Cell Biol 2017; 37:MCB.00264-17. [PMID: 28760775 DOI: 10.1128/mcb.00264-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 11/20/2022] Open
Abstract
Loss-of-function mutations in 3'-to-5' exoribonucleases have been implicated in hereditary human diseases. For example, PARN mutations cause a severe form of dyskeratosis congenita (DC), wherein PARN deficiency leads to human telomerase RNA instability. Since the DC phenotype in PARN patients is even more severe than that of loss-of-function alleles in telomerase components, we hypothesized that PARN would also be required for the stability of other RNAs. Here, we show that PARN depletion reduces the levels of abundant human Y RNAs, which might contribute to the severe phenotype of DC observed in patients. Depletion of PAPD5 or the cytoplasmic exonuclease DIS3L rescues the effect of PARN depletion on Y RNA levels, suggesting that PARN stabilizes Y RNAs by removing oligoadenylated tails added by PAPD5, which would otherwise recruit DIS3L for Y RNA degradation. Through deep sequencing of 3' ends, we provide evidence that PARN can also deadenylate the U6 and RMRP RNAs without affecting their levels. Moreover, we observed widespread posttranscriptional oligoadenylation, uridylation, and guanylation of U6 and Y RNA 3' ends, suggesting that in mammalian cells, the formation of a 3' end for noncoding RNAs can be a complex process governed by the activities of various 3'-end polymerases and exonucleases.
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72
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Warren AJ. Molecular basis of the human ribosomopathy Shwachman-Diamond syndrome. Adv Biol Regul 2017; 67:109-127. [PMID: 28942353 PMCID: PMC6710477 DOI: 10.1016/j.jbior.2017.09.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 01/05/2023]
Abstract
Mutations that target the ubiquitous process of ribosome assembly paradoxically cause diverse tissue-specific disorders (ribosomopathies) that are often associated with an increased risk of cancer. Ribosomes are the essential macromolecular machines that read the genetic code in all cells in all kingdoms of life. Following pre-assembly in the nucleus, precursors of the large 60S and small 40S ribosomal subunits are exported to the cytoplasm where the final steps in maturation are completed. Here, I review the recent insights into the conserved mechanisms of ribosome assembly that have come from functional characterisation of the genes mutated in human ribosomopathies. In particular, recent advances in cryo-electron microscopy, coupled with genetic, biochemical and prior structural data, have revealed that the SBDS protein that is deficient in the inherited leukaemia predisposition disorder Shwachman-Diamond syndrome couples the final step in cytoplasmic 60S ribosomal subunit maturation to a quality control assessment of the structural and functional integrity of the nascent particle. Thus, study of this fascinating disorder is providing remarkable insights into how the large ribosomal subunit is functionally activated in the cytoplasm to enter the actively translating pool of ribosomes.
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MESH Headings
- Bone Marrow Diseases/metabolism
- Bone Marrow Diseases/pathology
- Cryoelectron Microscopy
- Exocrine Pancreatic Insufficiency/metabolism
- Exocrine Pancreatic Insufficiency/pathology
- Humans
- Lipomatosis/metabolism
- Lipomatosis/pathology
- Mutation
- Proteins/genetics
- Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Shwachman-Diamond Syndrome
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Affiliation(s)
- Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK; The Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
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73
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Ishikawa H, Yoshikawa H, Izumikawa K, Miura Y, Taoka M, Nobe Y, Yamauchi Y, Nakayama H, Simpson RJ, Isobe T, Takahashi N. Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells. Nucleic Acids Res 2017; 45:3437-3447. [PMID: 27899605 PMCID: PMC5389690 DOI: 10.1093/nar/gkw1047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 10/24/2016] [Indexed: 11/14/2022] Open
Abstract
Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle. Knockdown of PARN or exogenous expression of an enzyme-dead PARN mutant (D28A) accumulated 18S-E in both the cytoplasm and nucleus. Moreover, expression of D28A accumulated 18S-E in Bystin-associated pre-40S particles, suggesting that the enzymatic activity of PARN is necessary for the release of 18S-E from Bystin-associated pre-40S particles. Finally, RNase H-based fragmentation analysis and 3΄-sequence analysis of 18S-E species present in cells expressing wild-type PARN or D28A suggested that PARN degrades the extended regions encompassing nucleotides 5-44 at the 3΄ end of mature 18S rRNA. Our results reveal a novel role for PARN in ribosome biogenesis in human cells.
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Affiliation(s)
- Hideaki Ishikawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Harunori Yoshikawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Keiichi Izumikawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yutaka Miura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Nakayama
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Richard J Simpson
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,La Trobe Institute for Molecular Science (LIMS), LIMS Building 1, Room 412 La Trobe University, Bundoora, Victoria 3086, Australia
| | - Toshiaki Isobe
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Nobuhiro Takahashi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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74
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Zinder JC, Lima CD. Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. Genes Dev 2017; 31:88-100. [PMID: 28202538 PMCID: PMC5322736 DOI: 10.1101/gad.294769.116] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Zinder and Lima highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes. The eukaryotic RNA exosome is an essential and conserved protein complex that can degrade or process RNA substrates in the 3′-to-5′ direction. Since its discovery nearly two decades ago, studies have focused on determining how the exosome, along with associated cofactors, achieves the demanding task of targeting particular RNAs for degradation and/or processing in both the nucleus and cytoplasm. In this review, we highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes.
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Affiliation(s)
- John C Zinder
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA.,Howard Hughes Medical Institute, New York, New York, 10065 USA
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75
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Tomecki R, Sikorski PJ, Zakrzewska-Placzek M. Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases. FEBS Lett 2017; 591:1801-1850. [PMID: 28524231 DOI: 10.1002/1873-3468.12682] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/14/2017] [Accepted: 05/15/2017] [Indexed: 12/17/2022]
Abstract
Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
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76
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Meola N, Jensen TH. Targeting the nuclear RNA exosome: Poly(A) binding proteins enter the stage. RNA Biol 2017; 14:820-826. [PMID: 28421898 DOI: 10.1080/15476286.2017.1312227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Centrally positioned in nuclear RNA metabolism, the exosome deals with virtually all transcript types. This 3'-5' exo- and endo-nucleolytic degradation machine is guided to its RNA targets by adaptor proteins that enable substrate recognition. Recently, the discovery of the 'Poly(A) tail exosome targeting (PAXT)' connection as an exosome adaptor to human nuclear polyadenylated transcripts has relighted the interest of poly(A) binding proteins (PABPs) in both RNA productive and destructive processes.
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Affiliation(s)
- Nicola Meola
- a Department of Molecular Biology and Genetics , Aarhus University , Aarhus C , Denmark
| | - Torben Heick Jensen
- a Department of Molecular Biology and Genetics , Aarhus University , Aarhus C , Denmark
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77
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Kühn U, Buschmann J, Wahle E. The nuclear poly(A) binding protein of mammals, but not of fission yeast, participates in mRNA polyadenylation. RNA (NEW YORK, N.Y.) 2017; 23:473-482. [PMID: 28096519 PMCID: PMC5340911 DOI: 10.1261/rna.057026.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 01/04/2017] [Indexed: 05/22/2023]
Abstract
The nuclear poly(A) binding protein (PABPN1) has been suggested, on the basis of biochemical evidence, to play a role in mRNA polyadenylation by strongly increasing the processivity of poly(A) polymerase. While experiments in metazoans have tended to support such a role, the results were not unequivocal, and genetic data show that the S. pombe ortholog of PABPN1, Pab2, is not involved in mRNA polyadenylation. The specific model in which PABPN1 increases the rate of poly(A) tail elongation has never been examined in vivo. Here, we have used 4-thiouridine pulse-labeling to examine the lengths of newly synthesized poly(A) tails in human cells. Knockdown of PABPN1 strongly reduced the synthesis of full-length tails of ∼250 nucleotides, as predicted from biochemical data. We have also purified S. pombe Pab2 and the S. pombe poly(A) polymerase, Pla1, and examined their in vitro activities. Whereas PABPN1 strongly increases the activity of its cognate poly(A) polymerase in vitro, Pab2 was unable to stimulate Pla1 to any significant extent. Thus, in vitro and in vivo data are consistent in supporting a role of PABPN1 but not S. pombe Pab2 in the polyadenylation of mRNA precursors.
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Affiliation(s)
- Uwe Kühn
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Juliane Buschmann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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78
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Xie J, Chen Z, Zhang X, Chen H, Guan W. Identification of an RNase that preferentially cleaves A/G nucleotides. Sci Rep 2017; 7:45207. [PMID: 28322335 PMCID: PMC5359670 DOI: 10.1038/srep45207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/20/2017] [Indexed: 02/02/2023] Open
Abstract
Ribonucleases play an important role in the RNA metabolism which is critical for the localization, stability and function of mature RNA transcripts. More and more ribonucleases were discovered in recent years with the progress of technology. In the present study, we found that the uncharacterized C19orf43, a novel interacting protein of human telomerase RNA (hTR), digested T7 transcribed RNA, total cellular RNA and RNA oligos but not DNA. Thus we named this new RNase as hTRIR (human telomerase RNA interacting RNase). Genetic analysis showed that hTRIR is conserved among eukaryotic species and widely expressed in different cell lines. The RNase activity of hTRIR works in a broad temperature and pH range while divalent cations are not required. The conserved C-terminus of C19orf43 is necessary for its activity. Finally, we found that hTRIR cleaves all four unpaired RNA nucleotides from 5′ end or 3′ end with higher efficiency for purine bases, which suggested that hTRIR is an exoribonuclease. Taken together, our study showed the first evidence of the novel function of hTRIR in vitro, which provides clue to study the regulatory mechanism of hTR homeostasis in vivo.
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Affiliation(s)
- Jumin Xie
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Honghe Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
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79
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Abstract
Telomerase is the essential reverse transcriptase required for linear chromosome maintenance in most eukaryotes. Telomerase supplements the tandem array of simple-sequence repeats at chromosome ends to compensate for the DNA erosion inherent in genome replication. The template for telomerase reverse transcriptase is within the RNA subunit of the ribonucleoprotein complex, which in cells contains additional telomerase holoenzyme proteins that assemble the active ribonucleoprotein and promote its function at telomeres. Telomerase is distinct among polymerases in its reiterative reuse of an internal template. The template is precisely defined, processively copied, and regenerated by release of single-stranded product DNA. New specificities of nucleic acid handling that underlie the catalytic cycle of repeat synthesis derive from both active site specialization and new motif elaborations in protein and RNA subunits. Studies of telomerase provide unique insights into cellular requirements for genome stability, tissue renewal, and tumorigenesis as well as new perspectives on dynamic ribonucleoprotein machines.
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Affiliation(s)
- R Alex Wu
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
| | - Jacob M Vogan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
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80
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Meola N, Domanski M, Karadoulama E, Chen Y, Gentil C, Pultz D, Vitting-Seerup K, Lykke-Andersen S, Andersen JS, Sandelin A, Jensen TH. Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts. Mol Cell 2016; 64:520-533. [PMID: 27871484 DOI: 10.1016/j.molcel.2016.09.025] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/18/2016] [Accepted: 09/20/2016] [Indexed: 12/20/2022]
Abstract
The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its co-factor Mtr4p/hMTR4, which links to RNA-binding protein adaptors. One example is the trimeric human nuclear exosome targeting (NEXT) complex, which is composed of hMTR4, the Zn-finger protein ZCCHC8, and the RNA-binding factor RBM7. NEXT primarily targets early and unprocessed transcripts, which demands a rationale for how the nuclear exosome recognizes processed RNAs. Here, we describe the poly(A) tail exosome targeting (PAXT) connection, which comprises the ZFC3H1 Zn-knuckle protein as a central link between hMTR4 and the nuclear poly(A)-binding protein PABPN1. Individual depletion of ZFC3H1 and PABPN1 results in the accumulation of common transcripts that are generally both longer and more extensively polyadenylated than NEXT substrates. Importantly, ZFC3H1/PABPN1 and ZCCHC8/RBM7 contact hMTR4 in a mutually exclusive manner, revealing that the exosome targets nuclear transcripts of different maturation status by substituting its hMTR4-associating adaptors.
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Affiliation(s)
- Nicola Meola
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
| | - Michal Domanski
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
| | - Evdoxia Karadoulama
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark; The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloesvej 5, DK-2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloesvej 5, DK-2200 Copenhagen, Denmark
| | - Coline Gentil
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
| | - Dennis Pultz
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloesvej 5, DK-2200 Copenhagen, Denmark
| | - Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloesvej 5, DK-2200 Copenhagen, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark.
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81
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Ketele A, Kiss T, Jády BE. Human intron-encoded AluACA RNAs and telomerase RNA share a common element promoting RNA accumulation. RNA Biol 2016; 13:1274-1285. [PMID: 27726486 PMCID: PMC5207380 DOI: 10.1080/15476286.2016.1239689] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Mammalian cells express hundreds of intron-encoded box H/ACA RNAs which fold into a common hairpin-hinge-hairpin-tail structure, interact with 4 evolutionarily conserved proteins, dyskerin, Nop10, Nhp2 and Gar1, and function mainly in RNA pseudouridylation. The human telomerase H/ACA RNA (hTR) directs telomeric DNA synthesis and it carries a 5'-terminal domain encompassing the telomeric template sequence. The primary hTR transcript is synthesized from an independent gene by RNA polymerase II and undergoes 3' end processing controlled by the 3'-terminal H/ACA domain. The apical stem-loop of the 3' hairpin of hTR carries a unique biogenesis-promoting element, the BIO motif that promotes hTR processing and RNP assembly. AluACA RNAs represent a distinct class of human H/ACA RNAs; they are processed from intronic Alu repetitive sequences. As compared to canonical H/ACA RNAs, the AluACA RNAs carry unusually short or long 5' hairpins and generally, they accumulate at low levels. Here, we demonstrate that the suboptimal 5' hairpins are responsible for the weak expression of AluACA RNAs. We also show that AluACA RNAs frequently carry a processing/stabilization element that is structurally and functionally indistinguishable from the hTR BIO motif. Both hTR and AluACA biogenesis-promoting elements are located in the terminal stem-loop of the 3'-terminal H/ACA hairpin, they show perfect structural conservation and are functionally interchangeable in in vivo RNA processing reactions. Our results demonstrate that the BIO motif, instead of being confined to hTR, is a more general H/ACA RNP biogenesis-facilitating element that can also promote processing/assembly of intron-encoded AluACA RNPs.
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Affiliation(s)
- Amandine Ketele
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Center de Biologie Intégrative, Université Paul Sabatier , Toulouse Cedex 9, France
| | - Tamás Kiss
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Center de Biologie Intégrative, Université Paul Sabatier , Toulouse Cedex 9, France.,b Biological Research Center, Hungarian Academy of Sciences , Szeged , Hungary
| | - Beáta E Jády
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Center de Biologie Intégrative, Université Paul Sabatier , Toulouse Cedex 9, France
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82
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Hebert MD, Poole AR. Towards an understanding of regulating Cajal body activity by protein modification. RNA Biol 2016; 14:761-778. [PMID: 27819531 DOI: 10.1080/15476286.2016.1243649] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The biogenesis of small nuclear ribonucleoproteins (snRNPs), small Cajal body-specific RNPs (scaRNPs), small nucleolar RNPs (snoRNPs) and the telomerase RNP involves Cajal bodies (CBs). Although many components enriched in the CB contain post-translational modifications (PTMs), little is known about how these modifications impact individual protein function within the CB and, in concert with other modified factors, collectively regulate CB activity. Since all components of the CB also reside in other cellular locations, it is also important that we understand how PTMs affect the subcellular localization of CB components. In this review, we explore the current knowledge of PTMs on the activity of proteins known to enrich in CBs in an effort to highlight current progress as well as illuminate paths for future investigation.
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Affiliation(s)
- Michael D Hebert
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Aaron R Poole
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
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83
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MacNeil DE, Bensoussan HJ, Autexier C. Telomerase Regulation from Beginning to the End. Genes (Basel) 2016; 7:genes7090064. [PMID: 27649246 PMCID: PMC5042394 DOI: 10.3390/genes7090064] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022] Open
Abstract
The vast body of literature regarding human telomere maintenance is a true testament to the importance of understanding telomere regulation in both normal and diseased states. In this review, our goal was simple: tell the telomerase story from the biogenesis of its parts to its maturity as a complex and function at its site of action, emphasizing new developments and how they contribute to the foundational knowledge of telomerase and telomere biology.
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Affiliation(s)
- Deanna Elise MacNeil
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
| | - Hélène Jeanne Bensoussan
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
| | - Chantal Autexier
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
- Department of Experimental Medicine, McGill University, 1110 Pins Avenue West, Room 101, Montréal, QC H3A 1A3, Canada.
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84
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Anastasakis D, Skeparnias I, Shaukat AN, Grafanaki K, Kanellou A, Taraviras S, Papachristou DJ, Papakyriakou A, Stathopoulos C. Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete expression during early development. Nucleic Acids Res 2016; 44:8908-8920. [PMID: 27515512 PMCID: PMC5062988 DOI: 10.1093/nar/gkw709] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/02/2016] [Indexed: 12/28/2022] Open
Abstract
PNLDC1 is a homologue of poly(A) specific ribonuclease (PARN), a known deadenylase with additional role in processing of non-coding RNAs. Both enzymes were reported recently to participate in piRNA biogenesis in silkworm and C. elegans, respectively. To get insights on the role of mammalian PNLDC1, we characterized the human and mouse enzymes. PNLDC1 shows limited conservation compared to PARN and represents an evolutionary related but distinct group of enzymes. It is expressed specifically in mouse embryonic stem cells, human and mouse testes and during early mouse embryo development, while it fades during differentiation. Its expression in differentiated cells, is suppressed through methylation of its promoter by the de novo methyltransferase DNMT3B. Both enzymes are localized mainly in the ER and exhibit in vitro specificity restricted solely to 3′ RNA or DNA polyadenylates. Knockdown of Pnldc1 in mESCs and subsequent NGS analysis showed that although the expression of the remaining deadenylases remains unaffected, it affects genes involved mainly in reprogramming, cell cycle and translational regulation. Mammalian PNLDC1 is a novel deadenylase expressed specifically in cell types which share regulatory mechanisms required for multipotency maintenance. Moreover, it could be involved both in posttranscriptional regulation through deadenylation and genome surveillance during early development.
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Affiliation(s)
- Dimitrios Anastasakis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | | | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Alexandra Kanellou
- Department of Physiology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Dionysios J Papachristou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Athanasios Papakyriakou
- Laboratory of Chemical Biology, National Centre for Scientific Research 'Demokritos', 15341 Athens, Greece
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85
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Klein P, Oloko M, Roth F, Montel V, Malerba A, Jarmin S, Gidaro T, Popplewell L, Perie S, Lacau St Guily J, de la Grange P, Antoniou MN, Dickson G, Butler-Browne G, Bastide B, Mouly V, Trollet C. Nuclear poly(A)-binding protein aggregates misplace a pre-mRNA outside of SC35 speckle causing its abnormal splicing. Nucleic Acids Res 2016; 44:10929-10945. [PMID: 27507886 PMCID: PMC5159528 DOI: 10.1093/nar/gkw703] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 07/25/2016] [Accepted: 07/29/2016] [Indexed: 11/21/2022] Open
Abstract
A short abnormal polyalanine expansion in the polyadenylate-binding protein nuclear-1 (PABPN1) protein causes oculopharyngeal muscular dystrophy (OPMD). Mutated PABPN1 proteins accumulate as insoluble intranuclear aggregates in muscles of OPMD patients. While the roles of PABPN1 in nuclear polyadenylation and regulation of alternative poly(A) site choice have been established, the molecular mechanisms which trigger pathological defects in OPMD and the role of aggregates remain to be determined. Using exon array, for the first time we have identified several splicing defects in OPMD. In particular, we have demonstrated a defect in the splicing regulation of the muscle-specific Troponin T3 (TNNT3) mutually exclusive exons 16 and 17 in OPMD samples compared to controls. This splicing defect is directly linked to the SC35 (SRSF2) splicing factor and to the presence of nuclear aggregates. As reported here, PABPN1 aggregates are able to trap TNNT3 pre-mRNA, driving it outside nuclear speckles, leading to an altered SC35-mediated splicing. This results in a decreased calcium sensitivity of muscle fibers, which could in turn plays a role in muscle pathology. We thus report a novel mechanism of alternative splicing deregulation that may play a role in various other diseases with nuclear inclusions or foci containing an RNA binding protein.
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Affiliation(s)
- Pierre Klein
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France
| | - Martine Oloko
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France
| | - Fanny Roth
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France
| | - Valérie Montel
- Univ. Lille - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, équipe APMS, F-59000 Lille, France
| | - Alberto Malerba
- School of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Susan Jarmin
- School of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Teresa Gidaro
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France
| | - Linda Popplewell
- School of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Sophie Perie
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France.,Department of Otolaryngology-Head and Neck Surgery, University Pierre-et-Marie-Curie, Paris VI, Tenon Hospital, Assistance Publique des Hopitaux de Paris, Paris, France
| | - Jean Lacau St Guily
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France.,Department of Otolaryngology-Head and Neck Surgery, University Pierre-et-Marie-Curie, Paris VI, Tenon Hospital, Assistance Publique des Hopitaux de Paris, Paris, France
| | | | - Michael N Antoniou
- King's College London School of Medicine, Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Guy's Hospital, London, UK
| | - George Dickson
- School of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Gillian Butler-Browne
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France
| | - Bruno Bastide
- Univ. Lille - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, équipe APMS, F-59000 Lille, France
| | - Vincent Mouly
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France
| | - Capucine Trollet
- Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche en Myologie, INSERM UMRS974, CNRS FRE3617, Institut de Myologie, 47 bd de l'Hôpital, 75013 Paris, France
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86
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Boyraz B, Moon DH, Segal M, Muosieyiri MZ, Aykanat A, Tai AK, Cahan P, Agarwal S. Posttranscriptional manipulation of TERC reverses molecular hallmarks of telomere disease. J Clin Invest 2016; 126:3377-82. [PMID: 27482890 DOI: 10.1172/jci87547] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022] Open
Abstract
The telomerase RNA component (TERC) is a critical determinant of cellular self-renewal. Poly(A)-specific ribonuclease (PARN) is required for posttranscriptional maturation of TERC. PARN mutations lead to incomplete 3' end processing and increased destruction of nascent TERC RNA transcripts, resulting in telomerase deficiency and telomere diseases. Here, we determined that overexpression of TERC increased telomere length in PARN-deficient cells and hypothesized that decreasing posttranscriptional 3' oligo-adenylation of TERC would counteract the deleterious effects of PARN mutations. Inhibition of the noncanonical poly(A) polymerase PAP-associated domain-containing 5 (PAPD5) increased TERC levels in PARN-mutant patient cells. PAPD5 inhibition was also associated with increases in TERC stability, telomerase activity, and telomere elongation. Our results demonstrate that manipulating posttranscriptional regulatory pathways may be a potential strategy to reverse the molecular hallmarks of telomere disease.
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87
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Podlevsky JD, Li Y, Chen JJL. The functional requirement of two structural domains within telomerase RNA emerged early in eukaryotes. Nucleic Acids Res 2016; 44:9891-9901. [PMID: 27378779 PMCID: PMC5175330 DOI: 10.1093/nar/gkw605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/30/2022] Open
Abstract
Telomerase emerged during evolution as a prominent solution to the eukaryotic linear chromosome end-replication problem. Telomerase minimally comprises the catalytic telomerase reverse transcriptase (TERT) and telomerase RNA (TR) that provides the template for telomeric DNA synthesis. While the TERT protein is well-conserved across taxa, TR is highly divergent amongst distinct groups of species. Herein, we have identified the essential functional domains of TR from the basal eukaryotic species Trypanosoma brucei, revealing the ancestry of TR comprising two distinct structural core domains that can assemble in trans with TERT and reconstitute active telomerase enzyme in vitro. The upstream essential domain of T. brucei TR, termed the template core, constitutes three short helices in addition to the 11-nt template. Interestingly, the trypanosome template core domain lacks the ubiquitous pseudoknot found in all known TRs, suggesting later evolution of this critical structural element. The template-distal domain is a short stem-loop, termed equivalent CR4/5 (eCR4/5). While functionally similar to vertebrate and fungal CR4/5, trypanosome eCR4/5 is structurally distinctive, lacking the essential P6.1 stem-loop. Our functional study of trypanosome TR core domains suggests that the functional requirement of two discrete structural domains is a common feature of TRs and emerged early in telomerase evolution.
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Affiliation(s)
- Joshua D Podlevsky
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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88
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Abstract
Telomerase is the eukaryotic solution to the ‘end-replication problem’ of linear chromosomes by synthesising the highly repetitive DNA constituent of telomeres, the nucleoprotein cap that protects chromosome termini. Functioning as a ribonucleoprotein (RNP) enzyme, telomerase is minimally composed of the highly conserved catalytic telomerase reverse transcriptase (TERT) and essential telomerase RNA (TR) component. Beyond merely providing the template for telomeric DNA synthesis, TR is an innate telomerase component and directly facilitates enzymatic function. TR accomplishes this by having evolved structural elements for stable assembly with the TERT protein and the regulation of the telomerase catalytic cycle. Despite its prominence and prevalence, TR has profoundly diverged in length, sequence, and biogenesis pathway among distinct evolutionary lineages. This diversity has generated numerous structural and mechanistic solutions for ensuring proper RNP formation and high fidelity telomeric DNA synthesis. Telomerase provides unique insights into RNA and protein coevolution within RNP enzymes.
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Affiliation(s)
- Joshua D Podlevsky
- a School of Molecular Sciences, Arizona State University , Tempe , AZ , USA
| | - Julian J-L Chen
- a School of Molecular Sciences, Arizona State University , Tempe , AZ , USA
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89
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Shukla S, Parker R. Hypo- and Hyper-Assembly Diseases of RNA-Protein Complexes. Trends Mol Med 2016; 22:615-628. [PMID: 27263464 DOI: 10.1016/j.molmed.2016.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 12/14/2022]
Abstract
A key aspect of cellular function is the proper assembly and utilization of ribonucleoproteins (RNPs). Recent studies have shown that hyper- or hypo-assembly of various RNPs can lead to human diseases. Defects in the formation of RNPs lead to 'RNP hypo-assembly diseases', which can be caused by RNA degradation outcompeting RNP assembly. By contrast, excess RNP assembly, either in higher order RNP granules, or due to the expression of repeat-containing RNAs, can lead to 'RNP hyper-assembly diseases'. Here, we discuss the most recent advances in understanding the cause of disease onset, as well as potential therapies from the aspect of modulating RNP assembly in the cell, which presents a novel route to the treatment of these diseases.
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Affiliation(s)
- Siddharth Shukla
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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90
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Inhibition of telomerase RNA decay rescues telomerase deficiency caused by dyskerin or PARN defects. Nat Struct Mol Biol 2016; 23:286-92. [PMID: 26950371 PMCID: PMC4830462 DOI: 10.1038/nsmb.3184] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/05/2016] [Indexed: 01/20/2023]
Abstract
Mutations in the human telomerase RNA component (hTR), the telomerase ribonucleoprotein component dyskerin (DKC1) and the poly(A) RNase (PARN) can lead to reduced levels of hTR and to dyskeratosis congenita (DC). However, the enzymes and mechanisms responsible for hTR degradation are unknown. We demonstrate that defects in dyskerin binding lead to hTR degradation by PAPD5-mediated oligoadenylation, which promotes 3'-to-5' degradation by EXOSC10, as well as decapping and 5'-to-3' decay by the cytoplasmic DCP2 and XRN1 enzymes. PARN increased hTR levels by deadenylating hTR, thereby limiting its degradation by EXOSC10. Telomerase activity and proper hTR localization in dyskerin- or PARN-deficient cells were rescued by knockdown of DCP2 and/or EXOSC10. Prevention of hTR RNA decay also led to a rescue of localization of DC-associated hTR mutants. These results suggest that inhibition of RNA decay pathways might be a useful therapy for some telomere pathologies.
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91
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Tseng CK, Wang HF, Burns A, Schroeder M, Gaspari M, Baumann P. Human Telomerase RNA Processing and Quality Control. Cell Rep 2015; 13:2232-43. [DOI: 10.1016/j.celrep.2015.10.075] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/02/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022] Open
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