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Cited by 225RNA Research and SplicingAdvanced Fluorescence Microscopy TechniquesRNA and protein synthesis mechanisms

The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells

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Horvathova, Ivana, Voigt, Franka, Kotrys, Anna V., Zhan, Yinxiu, Artus-Revel, Caroline G., Eglinger, Jan, Stadler, Michael B., Giorgetti, Luca +1 more·2017·Molecular Cell
DOI 10.1016/j.molcel.2017.09.030
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Abstract

RNA degradation plays a fundamental role in regulating gene expression. In order to characterize the spatiotemporal dynamics of RNA turnover in single cells, we developed a fluorescent biosensor based on dual-color, single-molecule RNA imaging that allows intact transcripts to be distinguished from stabilized degradation intermediates. Using this method, we measured mRNA decay in single cells and found that individual degradation events occur independently within the cytosol and are not enriched within processing bodies. We show that slicing of an mRNA targeted for endonucleolytic cleavage by the RNA-induced silencing complex can be observed in real time in living cells. This methodology provides a framework for investigating the entire life history of individual mRNAs from birth to death in single cells.

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  • Promoter ON/OFF transitions occur in the timescale of several minutes, considering that the time unit in the model is mRNA lifetime, expected to be around 1.5 h.

    “consistent with previous observations20, promoter ON/OFF transitions that occur in the timescale of several minutes (considering that the time unit in the model is mRNA lifetime, expected to be around 1.5 h)45 (Extended Data Fig. 4c, d).”

    From Nonlinear control of transcription through enhancer–promoter interactions (2022) · cites this paper as [45]

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  1. [1]1. Abrahamsson, S. ∙ Chen, J. ∙ Hajj, B. ... Fast multicolor 3D imaging using aberration-corrected multifocus microscopy Nat. Methods. 2013; 10:60-63 Crossref Scopus (21) PubMed Google Scholar
  2. [2]2. Anderson, P. ∙ Kedersha, N. ∙ Ivanov, P. Stress granules, P-bodies and cancer Biochim. Biophys. Acta. 2015; 1849:861-870 Crossref Scopus (301) PubMed Google Scholar
  3. [3]3. Banani, S.F. ∙ Lee, H.O. ∙ Hyman, A.A. ... Biomolecular condensates: organizers of cellular biochemistry Nat. Rev. Mol. Cell Biol. 2017; 18:285-298 Crossref Scopus (3258) PubMed Google Scholar
  4. [4]4. Beard, C. ∙ Hochedlinger, K. ∙ Plath, K. ... Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells Genesis. 2006; 44:23-28 Crossref Scopus (374) PubMed Google Scholar
  5. [5]5. Berg, H.C. Random Walks in Biology Princeton University Press, 1993 Google Scholar
  6. [6]6. Berthold, M.R. ∙ Cebron, N. ∙ Dill, F. ... KNIME - The Konstanz Information Miner: Version 2.0 and Beyond ACM SIGKDD Explorations Newsletter. 2009; 11:26-31 Crossref Google Scholar
  7. [7]7. Bhattacharyya, S.N. ∙ Habermacher, R. ∙ Martine, U. ... Relief of microRNA-mediated translational repression in human cells subjected to stress Cell. 2006; 125:1111-1124 Full Text Full Text (PDF) Scopus (1104) PubMed Google Scholar
  8. [8]8. Boehm, V. ∙ Gerbracht, J.V. ∙ Marx, M.C. ... Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences Nat. Commun. 2016; 7:13691 Crossref Scopus (22) PubMed Google Scholar
  9. [9]9. Brengues, M. ∙ Teixeira, D. ∙ Parker, R. Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies Science. 2005; 310:486-489 Crossref Scopus (621) PubMed Google Scholar
  10. [10]10. Chang, C.T. ∙ Bercovich, N. ∙ Loh, B. ... The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1 Nucleic Acids Res. 2014; 42:5217-5233 Crossref Scopus (80) PubMed Google Scholar
  11. [11]11. Chapman, E.G. ∙ Costantino, D.A. ∙ Rabe, J.L. ... The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production Science. 2014; 344:307-310 Crossref Scopus (188) PubMed Google Scholar
  12. [12]12. Chapman, E.G. ∙ Moon, S.L. ∙ Wilusz, J. ... RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA eLife. 2014; 3:e01892 Crossref Scopus (143) PubMed Google Scholar
  13. [13]13. Chen, J. ∙ Nikolaitchik, O. ∙ Singh, J. ... High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis Proc. Natl. Acad. Sci. USA. 2009; 106:13535-13540 Crossref Scopus (172) PubMed Google Scholar
  14. [14]14. Chu, C.Y. ∙ Rana, T.M. Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54 PLoS Biol. 2006; 4:e210 Crossref Scopus (427) PubMed Google Scholar
  15. [15]15. Cougot, N. ∙ Babajko, S. ∙ Séraphin, B. Cytoplasmic foci are sites of mRNA decay in human cells J. Cell Biol. 2004; 165:31-40 Crossref Scopus (520) PubMed Google Scholar
  16. [16]16. Daigle, N. ∙ Ellenberg, J. LambdaN-GFP: an RNA reporter system for live-cell imaging Nat. Methods. 2007; 4:633-636 Crossref Scopus (187) PubMed Google Scholar
  17. [17]17. Damgaard, C.K. ∙ Lykke-Andersen, J. Translational coregulation of 5’TOP mRNAs by TIA-1 and TIAR Genes Dev. 2011; 25:2057-2068 Crossref Scopus (177) PubMed Google Scholar
  18. [18]18. Decker, C.J. ∙ Parker, R. P-bodies and stress granules: possible roles in the control of translation and mRNA degradation Cold Spring Harb. Perspect. Biol. 2012; 4:a012286 Crossref Scopus (549) PubMed Google Scholar
  19. [19]19. Dunckley, T. ∙ Parker, R. The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif EMBO J. 1999; 18:5411-5422 Crossref Scopus (277) PubMed Google Scholar
  20. [20]20. Elkon, R. ∙ Zlotorynski, E. ∙ Zeller, K.I. ... Major role for mRNA stability in shaping the kinetics of gene induction BMC Genomics. 2010; 11:259 Crossref Scopus (82) PubMed Google Scholar
  21. [22]22. Franks, T.M. ∙ Lykke-Andersen, J. TTP and BRF proteins nucleate processing body formation to silence mRNAs with AU-rich elements Genes Dev. 2007; 21:719-735 Crossref Scopus (206) PubMed Google Scholar
  22. [23]23. Friedel, C.C. ∙ Dölken, L. ∙ Ruzsics, Z. ... Conserved principles of mammalian transcriptional regulation revealed by RNA half-life Nucleic Acids Res. 2009; 37:e115 Crossref Scopus (172) PubMed Google Scholar
  23. [24]24. Funakoshi, Y. ∙ Doi, Y. ∙ Hosoda, N. ... Mechanism of mRNA deadenylation: evidence for a molecular interplay between translation termination factor eRF3 and mRNA deadenylases Genes Dev. 2007; 21:3135-3148 Crossref Scopus (149) PubMed Google Scholar
  24. [25]25. Gagnon, K.T. ∙ Li, L. ∙ Chu, Y. ... RNAi factors are present and active in human cell nuclei Cell Rep. 2014; 6:211-221 Full Text Full Text (PDF) Scopus (303) PubMed Google Scholar
  25. [26]26. Garcia, J.F. ∙ Parker, R. MS2 coat proteins bound to yeast mRNAs block 5′ to 3′ degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system RNA. 2015; 21:1393-1395 Crossref Scopus (109) PubMed Google Scholar
  26. [27]27. Garneau, N.L. ∙ Wilusz, J. ∙ Wilusz, C.J. The highways and byways of mRNA decay Nat. Rev. Mol. Cell Biol. 2007; 8:113-126 Crossref Scopus (1027) PubMed Google Scholar
  27. [28]28. Gillespie, D.T. Exact Stochastic Simulation of Coupled Chemical Reactions J. Phys. Chem. 1977; 81:2340-2361 Crossref Scopus (7617) Google Scholar
  28. [29]29. Gowrishankar, G. ∙ Winzen, R. ∙ Dittrich-Breiholz, O. ... Inhibition of mRNA deadenylation and degradation by different types of cell stress Biol. Chem. 2006; 387:323-327 Crossref Scopus (34) PubMed Google Scholar
  29. [30]30. Grimm, J.B. ∙ English, B.P. ∙ Chen, J. ... A general method to improve fluorophores for live-cell and single-molecule microscopy Nat. Methods. 2015; 12:244-250 3, 250 Crossref Scopus (1040) PubMed Google Scholar
  30. [31]31. Halstead, J.M. ∙ Lionnet, T. ∙ Wilbertz, J.H. ... Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals Science. 2015; 347:1367-1671 Crossref Scopus (207) PubMed Google Scholar
  31. [32]32. Hao, S. ∙ Baltimore, D. The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules Nat. Immunol. 2009; 10:281-288 Crossref Scopus (402) PubMed Google Scholar
  32. [33]33. Heinrich, S. ∙ Sidler, C.L. ∙ Azzalin, C.M. ... Stem-loop RNA labeling can affect nuclear and cytoplasmic mRNA processing RNA. 2017; 23:134-141 Crossref Scopus (63) PubMed Google Scholar
  33. [34]34. Hilgers, V. ∙ Teixeira, D. ∙ Parker, R. Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae RNA. 2006; 12:1835-1845 Crossref Scopus (70) PubMed Google Scholar
  34. [35]35. Hocine, S. ∙ Raymond, P. ∙ Zenklusen, D. ... Single-molecule analysis of gene expression using two-color RNA labeling in live yeast Nat. Methods. 2013; 10:119-121 Crossref Scopus (236) PubMed Google Scholar
  35. [36]36. Isken, O. ∙ Maquat, L.E. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function Genes Dev. 2007; 21:1833-1856 Crossref Scopus (477) PubMed Google Scholar
  36. [37]37. Jain, S. ∙ Parker, R. The discovery and analysis of P Bodies Adv. Exp. Med. Biol. 2013; 768:23-43 Crossref Scopus (78) PubMed Google Scholar
  37. [38]38. Kedersha, N. ∙ Anderson, P. Mammalian stress granules and processing bodies Methods Enzymol. 2007; 431:61-81 Crossref Scopus (514) PubMed Google Scholar
  38. [39]39. Kieft, J.S. ∙ Rabe, J.L. ∙ Chapman, E.G. New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation RNA Biol. 2015; 12:1169-1177 Crossref Scopus (64) PubMed Google Scholar
  39. [40]40. Kramer, S. Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution Nucleic Acids Res. 2017; 45:e49 Crossref Scopus (18) PubMed Google Scholar
  40. [41]41. Leung, A.K. ∙ Calabrese, J.M. ∙ Sharp, P.A. Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules Proc. Natl. Acad. Sci. USA. 2006; 103:18125-18130 Crossref Scopus (311) PubMed Google Scholar
  41. [42]42. Lionnet, T. ∙ Czaplinski, K. ∙ Darzacq, X. ... A transgenic mouse for in vivo detection of endogenous labeled mRNA Nat. Methods. 2011; 8:165-170 Crossref Scopus (286) PubMed Google Scholar
  42. [43]43. Lykke-Andersen, J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay Mol. Cell. Biol. 2002; 22:8114-8121 Crossref Scopus (299) PubMed Google Scholar
  43. [44]44. Miller, C. ∙ Schwalb, B. ∙ Maier, K. ... Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast Mol. Syst. Biol. 2011; 7:458 Crossref Scopus (269) PubMed Google Scholar
  44. [45]45. Moon, S.L. ∙ Anderson, J.R. ∙ Kumagai, Y. ... A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability RNA. 2012; 18:2029-2040 Crossref Scopus (154) PubMed Google Scholar
  45. [46]46. Morisaki, T. ∙ Lyon, K. ∙ DeLuca, K.F. ... Real-time quantification of single RNA translation dynamics in living cells Science. 2016; 352:1425-1429 Crossref Scopus (254) PubMed Google Scholar
  46. [47]47. Otsu, N. A Threshold Selection Method from Grey-Level Histograms IEEE Trans. Syst. Man Cybern. 1979; 9:62-66 Crossref Google Scholar
  47. [48]48. Pichon, X. ∙ Bastide, A. ∙ Safieddine, A. ... Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells J. Cell Biol. 2016; 214:769-781 Crossref Scopus (120) PubMed Google Scholar
  48. [49]49. Rabani, M. ∙ Levin, J.Z. ∙ Fan, L. ... Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells Nat. Biotechnol. 2011; 29:436-442 Crossref Scopus (420) PubMed Google Scholar
  49. [50]50. Raj, A. ∙ van Oudenaarden, A. Nature, nurture, or chance: stochastic gene expression and its consequences Cell. 2008; 135:216-226 Full Text Full Text (PDF) Scopus (1867) PubMed Google Scholar
  50. [52]52. Schoenberg, D.R. ∙ Maquat, L.E. Regulation of cytoplasmic mRNA decay Nat. Rev. Genet. 2012; 13:246-259 Crossref Scopus (3) PubMed Google Scholar
  51. [53]53. Sheth, U. ∙ Parker, R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies Science. 2003; 300:805-808 Crossref Scopus (1070) PubMed Google Scholar
  52. [54]54. Stoecklin, G. ∙ Mayo, T. ∙ Anderson, P. ARE-mRNA degradation requires the 5′-3′ decay pathway EMBO Rep. 2006; 7:72-77 Crossref Scopus (197) PubMed Google Scholar
  53. [55]55. Tinevez, J.Y. ∙ Perry, N. ∙ Schindelin, J. ... TrackMate: An open and extensible platform for single-particle tracking Methods. 2017; 115:80-90 Crossref Scopus (1888) PubMed Google Scholar
  54. [56]56. Trcek, T. ∙ Larson, D.R. ∙ Moldón, A. ... Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast Cell. 2011; 147:1484-1497 Full Text Full Text (PDF) Scopus (200) PubMed Google Scholar
  55. [57]57. Trcek, T. ∙ Sato, H. ∙ Singer, R.H. ... Temporal and spatial characterization of nonsense-mediated mRNA decay Genes Dev. 2013; 27:541-551 Crossref Scopus (100) PubMed Google Scholar
  56. [58]58. van Dijk, E. ∙ Cougot, N. ∙ Meyer, S. ... Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures EMBO J. 2002; 21:6915-6924 Crossref Scopus (389) PubMed Google Scholar
  57. [59]59. Voigt, F., Eglinger, J., and Chao, J.A. (in press). Detection of the first round of translation: the TRICK assay. In RNA Detection, I. Gaspar, ed. (Springer). Google Scholar
  58. [60]60. Wang, C. ∙ Han, B. ∙ Zhou, R. ... Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells Cell. 2016; 165:990-1001 Full Text Full Text (PDF) Scopus (239) PubMed Google Scholar
  59. [61]61. Weidenfeld, I. ∙ Gossen, M. ∙ Löw, R. ... Inducible expression of coding and inhibitory RNAs from retargetable genomic loci Nucleic Acids Res. 2009; 37:e50 Crossref Scopus (60) PubMed Google Scholar
  60. [62]62. Wu, B. ∙ Miskolci, V. ∙ Sato, H. ... Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences Genes Dev. 2015; 29:876-886 Crossref Scopus (73) PubMed Google Scholar
  61. [63]63. Wu, B. ∙ Eliscovich, C. ∙ Yoon, Y.J. ... Translation dynamics of single mRNAs in live cells and neurons Science. 2016; 352:1430-1435 Crossref Scopus (330) PubMed Google Scholar
  62. [64]64. Yamagishi, R. ∙ Hosoda, N. ∙ Hoshino, S. Arsenite inhibits mRNA deadenylation through proteolytic degradation of Tob and Pan3 Biochem. Biophys. Res. Commun. 2014; 455:323-331 Crossref Scopus (8) PubMed Google Scholar
  63. [65]65. Yamashita, A. ∙ Chang, T.C. ∙ Yamashita, Y. ... Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover Nat. Struct. Mol. Biol. 2005; 12:1054-1063 Crossref Scopus (361) PubMed Google Scholar
  64. [66]66. Yan, X. ∙ Hoek, T.A. ∙ Vale, R.D. ... Dynamics of Translation of Single mRNA Molecules In Vivo Cell. 2016; 165:976-989 Full Text Full Text (PDF) Scopus (317) PubMed Google Scholar
  65. [67]67. Yen, J.C. ∙ Chang, F.J. ∙ Chang, S. A new criterion for automatic multilevel thresholding IEEE transactions on image processing: a publication of the IEEE Signal Processing Society. 1995; 4:370-378 Crossref Scopus (727) PubMed Google Scholar

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Authors
Horvathova, I., Voigt, F., Kotrys, A. V., Zhan, Y., Artus-Revel, C. G., Eglinger, J., Stadler, M. B., Giorgetti, L., & Chao, J. A.
Affiliations
  • Friedrich Miescher Institute (CH)
  • University of Basel (CH)
  • SIB Swiss Institute of Bioinformatics (CH)
Corresponding author
Chao, Jeffrey A.
ORCID
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2017-11
Volume
68
Issue
3
Pages
615-625.e9
ISSN
1097-2765 (ISSN-L)
DOI
10.1016/j.molcel.2017.09.030
OpenAlex
W2766829811
Cited by
225
References
68
Citations by year
2026: 11 · 2025: 28 · 2024: 24 · 2023: 26 · 2022: 24 · 2021: 28 · 2020: 30 · 2019: 26 · 2018: 25 · 2017: 3
FWCI
9.39
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Cell (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Novartis Research Foundation
  • Swiss National Science Foundation (31003A_156477)
  • SNF-NCCR RNA & Disease
  • SystemsX.ch/MetastasiX
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
mRNA turnover, RNA degradation, single-molecule RNA imaging, fluorescent biosensor, P-bodies, RNA-induced silencing complex, endonucleolytic cleavage
MeSH terms
Single Molecule Imaging, Gene Expression Regulation, HeLa Cells, Humans, Kinetics, Microscopy, Fluorescence, Models, Genetic, RNA, Messenger, Transfection, Genes, Reporter, Microscopy, Video, RNA Stability, Argonaute Proteins

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