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Annual Review of Biophysics

Volume 53, 2024

Translation Dynamics of Single mRNAs in Live Cells

Abstract

The translation of messenger RNA (mRNA) into proteins represents the culmination of gene expression. Recent technological advances have revolutionized our ability to investigate this process with unprecedented precision, enabling the study of translation at the single-molecule level in real time within live cells. In this review, we provide an overview of single-mRNA translation reporters. We focus on the core technology, as well as the rapid development of complementary probes, tags, and accessories that enable the visualization and quantification of a wide array of translation dynamics. We then highlight notable studies that have utilized these reporters in model systems to address key biological questions. The high spatiotemporal resolution of these studies is shedding light on previously unseen phenomena, uncovering the full heterogeneity and complexity of translational regulation.

Keyword(s): central dogma, fluorescence microscopy, gene expression, intrabodies, live-cell imaging, messenger RNA, mRNA, single-molecule tracking, translation
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/content/journals/10.1146/annurev-biophys-030822-034116
2024-07-16
2024-10-03
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Literature Cited

  1. 1.
    Adivarahan S, Livingston N, Nicholson B, Rahman S, Wu B, et al. 2018.. Spatial organization of single mRNPs at different stages of the gene expression pathway. . Mol. Cell 72:(4):727–38.e5
     [Crossref] [Google Scholar]
  2. 2.
    Aguilera LU, Raymond W, Fox ZR, May M, Djokic E, et al. 2019.. Computational design and interpretation of single-RNA translation experiments. . PLOS Comput. Biol. 15:(10):e1007425
     [Crossref] [Google Scholar]
  3. 3.
    Ai H, Olenych SG, Wong P, Davidson MW, Campbell RE. 2008.. Hue-shifted monomeric variants of Clavularia cyan fluorescent protein: identification of the molecular determinants of color and applications in fluorescence imaging. . BMC Biol. 6::13
     [Crossref] [Google Scholar]
  4. 4.
    Barondeau DP, Putnam CD, Kassmann CJ, Tainer JA, Getzoff ED. 2003.. Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. . PNAS 100:(21):12111–16
     [Crossref] [Google Scholar]
  5. 5.
    Barrington CL, Koch AL, Galindo G, Larkin-Gero E, Morrison EJ, et al. 2022.. Synonymous codon usage regulates translation initiation. . bioRxiv 2022.05.13.491887. https://doi.org/10.1101/2022.05.13.491887
  6. 6.
    Baymiller M, Moon SL. 2023.. Stress granules as causes and consequences of translation suppression. . Antioxid. Redox Signal. 39:(4–6):390–409
     [Crossref] [Google Scholar]
  7. 7.
    Bellec M, Chen R, Dhayni J, Favard C, Trullo A, et al. 2023.. Boosting the toolbox for live imaging of translation. . bioRxiv 2023.02.25.529998. https://doi.org10.1101/2023.02.25.529998
  8. 8.
    Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM. 1998.. Localization of ASH1 mRNA particles in living yeast. . Mol. Cell 2:(4):437–45
     [Crossref] [Google Scholar]
  9. 9.
    Blake LA, Liu Y, Inoue T, Wu B. 2023.. A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies. . bioRxiv 2023.04.26.538452. https://doi.org/10.1101/2023.04.26.538452
  10. 10.
    Blobel G, Sabatini D. 1971.. Dissociation of mammalian polyribosomes into subunits by puromycin. . PNAS 68:(2):390–94
     [Crossref] [Google Scholar]
  11. 11.
    Boersma S, Khuperkar D, Verhagen BM, Sonneveld S, Grimm JB, et al. 2019.. Multi-color single-molecule imaging uncovers extensive heterogeneity in mRNA decoding. . Cell 178:(2):45872.e19
     [Crossref] [Google Scholar]
  12. 12.
    Boersma S, Rabouw HH, Bruurs LJ, Pavlovič T, van Vliet AL, et al. 2020.. Translation and replication dynamics of single RNA viruses. . Cell 183:(7):1930–45.e23
     [Crossref] [Google Scholar]
  13. 13.
    Braselmann E, Palmer AE. 2020.. A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells. . Methods Enzymol. 641::343–72
     [Crossref] [Google Scholar]
  14. 14.
    Braselmann E, Rathbun C, Richards EM, Palmer AE. 2020.. Illuminating RNA biology: tools for imaging RNA in live mammalian cells. . Cell Chem. Biol. 27:(8):891–903
     [Crossref] [Google Scholar]
  15. 15.
    Braselmann E, Stasevich TJ, Lyon K, Batey RT, Palmer AE. 2019.. Detection and quantification of single mRNA dynamics with the Riboglow fluorescent RNA tag. . bioRxiv 701649. https://doi.org/10.1101/701649
  16. 16.
    Braselmann E, Wierzba AJ, Polaski JT, Chromiński M, Holmes ZE, et al. 2018.. A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells. . Nat. Chem. Biol. 14:(10):964–71
     [Crossref] [Google Scholar]
  17. 17.
    Bruurs LJM, Müller M, Schipper JG, Rabouw HH, Boersma S, et al. 2022.. Heterogeneity in viral replication dynamics shapes the antiviral response. . bioRxiv 2022.06.08.495262. https://doi.org/10.1101/2022.06.08.495262
  18. 18.
    Buxbaum AR, Haimovich G, Singer RH. 2015.. In the right place at the right time: visualizing and understanding mRNA localization. . Nat. Rev. Mol. Cell Biol. 16:(2):95–109
     [Crossref] [Google Scholar]
  19. 19.
    Cajigas IJ, Tushev G, Will TJ, tom Dieck S, Fuerst N, Schuman EM. 2012.. The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging. . Neuron 74:(3):453–66
     [Crossref] [Google Scholar]
  20. 20.
    Campbell BC, Nabel EM, Murdock MH, Lao-Peregrin C, Tsoulfas P, et al. 2020.. mGreenLantern: a bright monomeric fluorescent protein with rapid expression and cell filling properties for neuronal imaging. . PNAS 117:(48):30710–21
     [Crossref] [Google Scholar]
  21. 21.
    Cawte AD, Iino H, Unrau PJ, Rueda DS. 2022.. Single-molecule RNA imaging using Mango II arrays. . Methods Mol. Biol. 2404::267–80
     [Crossref] [Google Scholar]
  22. 22.
    Cawte AD, Unrau PJ, Rueda DS. 2020.. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays. . Nat. Commun. 11::1283
     [Crossref] [Google Scholar]
  23. 23.
    Chao JA, Patskovsky Y, Almo SC, Singer RH. 2008.. Structural basis for the coevolution of a viral RNA-protein complex. . Nat. Struct. Mol. Biol. 15:(1):103–5
     [Crossref] [Google Scholar]
  24. 24.
    Chao JA, Yoon YJ, Singer RH. 2012.. Imaging translation in single cells using fluorescent microscopy. . Cold Spring Harb. Perspect. Biol. 4:(11):a012310
     [Crossref] [Google Scholar]
  25. 25.
    Chen J, Liu Y, Wu B, Nikolaitchik OA, Mohan PR, et al. 2020.. Visualizing the translation and packaging of HIV-1 full-length RNA. . PNAS 117:(11):6145–55
     [Crossref] [Google Scholar]
  26. 26.
    Chouaib R, Safieddine A, Pichon X, Imbert A, Kwon OS, et al. 2020.. A dual protein-mRNA localization screen reveals compartmentalized translation and widespread co-translational RNA targeting. . Dev. Cell 54:(6):773–91.e5
     [Crossref] [Google Scholar]
  27. 27.
    Christensen AK, Bourne CM. 1999.. Shape of large bound polysomes in cultured fibroblasts and thyroid epithelial cells. . Anat. Rec. 255:(2):116–29
     [Crossref] [Google Scholar]
  28. 28.
    Chubb JR, Trcek T, Shenoy SM, Singer RH. 2006.. Transcriptional pulsing of a developmental gene. . Curr. Biol. 16:(10):1018–25
     [Crossref] [Google Scholar]
  29. 29.
    Cialek CA, Galindo G, Koch AL, Saxton MN, Stasevich TJ. 2021.. Bead loading proteins and nucleic acids into adherent human cells. . J. Vis. Exp. 172::e62559
     [Google Scholar]
  30. 30.
    Cialek CA, Galindo G, Morisaki T, Zhao N, Montgomery TA, Stasevich TJ. 2022.. Imaging translational control by Argonaute with single-molecule resolution in live cells. . Nat. Commun. 13::3345
     [Crossref] [Google Scholar]
  31. 31.
    Cioni J-M, Lin JQ, Holtermann AV, Koppers M, Jakobs MAH, et al. 2019.. Late endosomes act as mRNA translation platforms and sustain mitochondria in axons. . Cell 176:(1–2):56–72.e15
     [Crossref] [Google Scholar]
  32. 32.
    Cohen B, Altman T, Golani-Armon A, Savulescu AF, Ibraheem A, et al. 2022.. Co-transport of the nuclear-encoded Cox7c mRNA with mitochondria along axons occurs through a coding-region-dependent mechanism. . J. Cell Sci. 135:(16):jcs259436
     [Crossref] [Google Scholar]
  33. 33.
    Costantini LM, Fossati M, Francolini M, Snapp EL. 2012.. Assessing the tendency of fluorescent proteins to oligomerize under physiologic conditions. . Traffic 13:(5):643–49
     [Crossref] [Google Scholar]
  34. 34.
    Coulon A, Larson DR. 2016.. Fluctuation analysis: dissecting transcriptional kinetics with signal theory. . Methods Enzymol. 572::159–91
     [Crossref] [Google Scholar]
  35. 35.
    Daigle N, Ellenberg J. 2007.. LambdaN-GFP: an RNA reporter system for live-cell imaging. . Nat. Methods 4:(8):633–36
     [Crossref] [Google Scholar]
  36. 36.
    Das S, Lituma PJ, Castillo PE, Singer RH. 2023.. Maintenance of a short-lived protein required for long-term memory involves cycles of transcription and local translation. . Neuron 111:(13):2051–64.e6
     [Crossref] [Google Scholar]
  37. 37.
    Dave P, Roth G, Griesbach E, Mateju D, Hochstoeger T, Chao JA. 2023.. Single-molecule imaging reveals translation-dependent destabilization of mRNAs. . Mol. Cell 83:(4):589–606.e6
     [Crossref] [Google Scholar]
  38. 38.
    Davis L, Dou P, DeWit M, Kater SB. 1992.. Protein synthesis within neuronal growth cones. . J. Neurosci. 12:(12):4867–77
     [Crossref] [Google Scholar]
  39. 39.
    Dieterich DC, Hodas JJL, Gouzer G, Shadrin IY, Ngo JT, et al. 2010.. In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons. . Nat. Neurosci. 13:(7):897–905
     [Crossref] [Google Scholar]
  40. 40.
    Dolgosheina EV, Jeng SCY, Panchapakesan SSS, Cojocaru R, Chen PSK, et al. 2014.. RNA Mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. . ACS Chem. Biol. 9:(10):2412–20
     [Crossref] [Google Scholar]
  41. 41.
    Dufourt J, Bellec M, Trullo A, Dejean M, De Rossi S, et al. 2021.. Imaging translation dynamics in live embryos reveals spatial heterogeneities. . Science 372:(6544):840–44
     [Crossref] [Google Scholar]
  42. 42.
    Enam SU, Zinshteyn B, Goldman DH, Cassani M, Livingston NM, et al. 2020.. Puromycin reactivity does not accurately localize translation at the subcellular level. . eLife 9::e60303
     [Crossref] [Google Scholar]
  43. 43.
    Fusco D, Accornero N, Lavoie B, Shenoy SM, Blanchard J-M, et al. 2003.. Single mRNA molecules demonstrate probabilistic movement in living mammalian cells. . Curr. Biol. 13:(2):161–67
     [Crossref] [Google Scholar]
  44. 44.
    Gao J, Liao J, Yang G-Y. 2009.. CAAX-box protein, prenylation process and carcinogenesis. . Am. J. Transl. Res. 1:(3):312–25
     [Google Scholar]
  45. 45.
    Garcia JF, Parker R. 2015.. 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 21:(8):1393–95
     [Crossref] [Google Scholar]
  46. 46.
    Garcia JF, Parker R. 2016.. Ubiquitous accumulation of 3′ mRNA decay fragments in Saccharomyces cerevisiae mRNAs with chromosomally integrated MS2 arrays. . RNA 22:(5):657–59
     [Crossref] [Google Scholar]
  47. 47.
    Gasparski AN, Mason DE, Moissoglu K, Mili S. 2022.. Regulation and outcomes of localized RNA translation. . Wiley Interdiscip. Rev. RNA 13:(6):e1721
     [Crossref] [Google Scholar]
  48. 48.
    Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. 2023.. mRNA location and translation rate determine protein targeting to dual destinations. . Mol. Cell 83:(15):2726–38.e9
     [Crossref] [Google Scholar]
  49. 49.
    Glock C, Biever A, Tushev G, Nassim-Assir B, Kao A, et al. 2021.. The translatome of neuronal cell bodies, dendrites, and axons. . PNAS 118:(43):e2113929118
     [Crossref] [Google Scholar]
  50. 50.
    Goldman DH, Livingston NM, Movsik J, Wu B, Green R. 2021.. Live-cell imaging reveals kinetic determinants of quality control triggered by ribosome stalling. . Mol. Cell 81:(8):1830–40.e8
     [Crossref] [Google Scholar]
  51. 51.
    Gómez-Puerta S, Ferrero R, Hochstoeger T, Zubiri I, Chao J, et al. 2022.. Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1α. . eLife 11::e75580
     [Crossref] [Google Scholar]
  52. 52.
    Götzke H, Kilisch M, Martínez-Carranza M, Sograte-Idrissi S, Rajavel A, et al. 2019.. The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications. . Nat. Commun. 10::4403
     [Crossref] [Google Scholar]
  53. 53.
    Grimm JB, English BP, Chen J, Slaughter JP, Zhang Z, et al. 2015.. A general method to improve fluorophores for live-cell and single-molecule microscopy. . Nat. Methods 12:(3):244–50
     [Crossref] [Google Scholar]
  54. 54.
    Grimm JB, Muthusamy AK, Liang Y, Brown TA, Lemon WC, et al. 2017.. A general method to fine-tune fluorophores for live-cell and in vivo imaging. . Nat. Methods 14:(10):987–94
     [Crossref] [Google Scholar]
  55. 55.
    Hafner A-S, Donlin-Asp PG, Leitch B, Herzog E, Schuman EM. 2019.. Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments. . Science 364:(6441):eaau3644
     [Crossref] [Google Scholar]
  56. 56.
    Haimovich G, Zabezhinsky D, Haas B, Slobodin B, Purushothaman P, et al. 2016.. Use of the MS2 aptamer and coat protein for RNA localization in yeast: a response to “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 22:(5):660–66
     [Crossref] [Google Scholar]
  57. 57.
    Hancock JF, Cadwallader K, Paterson H, Marshall CJ. 1991.. A CAAX or a CAAL motif and a second signal are sufficient for plasma membrane targeting of ras proteins. . EMBO J. 10:(13):4033–39
     [Crossref] [Google Scholar]
  58. 58.
    Harbauer AB, Hees JT, Wanderoy S, Segura I, Gibbs W, et al. 2022.. Neuronal mitochondria transport Pink1 mRNA via synaptojanin 2 to support local mitophagy. . Neuron 110:(9):1516–31.e9
     [Crossref] [Google Scholar]
  59. 59.
    Heinrich S, Sidler CL, Azzalin CM, Weis K. 2017.. Stem-loop RNA labeling can affect nuclear and cytoplasmic mRNA processing. . RNA 23:(2):134–41
     [Crossref] [Google Scholar]
  60. 60.
    Higuchi Y, Ashwin P, Roger Y, Steinberg G. 2014.. Early endosome motility spatially organizes polysome distribution. . J. Cell Biol. 204:(3):343–57
     [Crossref] [Google Scholar]
  61. 61.
    Hobson BD, Kong L, Angelo MF, Lieberman OJ, Mosharov EV, et al. 2022.. Subcellular and regional localization of mRNA translation in midbrain dopamine neurons. . Cell Rep. 38:(2):110208
     [Crossref] [Google Scholar]
  62. 62.
    Hobson BD, Kong L, Hartwick EW, Gonzalez RL, Sims PA. 2020.. Elongation inhibitors do not prevent the release of puromycylated nascent polypeptide chains from ribosomes. . eLife 9::e60048
     [Crossref] [Google Scholar]
  63. 63.
    Hocine S, Vera M, Zenklusen D, Singer RH. 2015.. Promoter-autonomous functioning in a controlled environment using single molecule FISH. . Sci. Rep. 5::9934
     [Crossref] [Google Scholar]
  64. 64.
    Hoek TA, Khuperkar D, Lindeboom RG, Sonneveld S, Verhagen BM, et al. 2019.. Single-molecule imaging uncovers rules governing nonsense-mediated mRNA decay. . Mol. Cell 75:(2):324–39.e11
     [Crossref] [Google Scholar]
  65. 65.
    Hopp TP, Prickett KS, Price VL, Libby RT, March CJ, et al. 1988.. A short polypeptide marker sequence useful for recombinant protein identification and purification. . Nat. Biotechnol. 6:(10):1204–10
     [Crossref] [Google Scholar]
  66. 66.
    Horvathova I, Voigt F, Kotrys AV, Zhan Y, Artus-Revel CG, et al. 2017.. The dynamics of mRNA turnover revealed by single-molecule imaging in single cells. . Mol. Cell 68:(3):615–25.e9
     [Crossref] [Google Scholar]
  67. 67.
    Ingolia NT, Lareau LF, Weissman JS. 2011.. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. . Cell 147:(4):789–802
     [Crossref] [Google Scholar]
  68. 68.
    Jaramillo AM, Weil TT, Goodhouse J, Gavis ER, Schupbach T. 2008.. The dynamics of fluorescently labeled endogenous gurken mRNA in Drosophila. . J. Cell Sci. 121:(6):887–94
     [Crossref] [Google Scholar]
  69. 69.
    Jumper J, Evans R, Pritzel A, Green T, Figurnov M, et al. 2021.. Highly accurate protein structure prediction with AlphaFold. . Nature 596:(7873):583–89
     [Crossref] [Google Scholar]
  70. 70.
    Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S, Ramakrishnan V, Hegde RS. 2018.. ZNF598 is a quality control sensor of collided ribosomes. . Mol. Cell 72:(3):469–81.e7
     [Crossref] [Google Scholar]
  71. 71.
    Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, et al. 2016.. Mapping translation “hot-spots” in live cells by tracking single molecules of mRNA and ribosomes. . eLife 5::e10415
     [Crossref] [Google Scholar]
  72. 72.
    Khong A, Parker R. 2018.. mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction. . J. Cell Biol. 217:(12):4124–40
     [Crossref] [Google Scholar]
  73. 73.
    Kim B, Seol J, Kim YK, Lee J-B. 2023.. Single-molecule visualization of mRNA circularization during translation. . Exp. Mol. Med. 55::283–89
     [Crossref] [Google Scholar]
  74. 74.
    Kobayashi H, Singer RH. 2022.. Single-molecule imaging of microRNA-mediated gene silencing in cells. . Nat. Commun. 13::1435
     [Crossref] [Google Scholar]
  75. 75.
    Koch A, Aguilera L, Morisaki T, Munsky B, Stasevich TJ. 2020.. Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells. . Nat. Struct. Mol. Biol. 27:(12):1095–104
     [Crossref] [Google Scholar]
  76. 76.
    Lam AJ, St-Pierre F, Gong Y, Marshall JD, Cranfill PJ, et al. 2012.. Improving FRET dynamic range with bright green and red fluorescent proteins. . Nat. Methods 9:(10):1005–12
     [Crossref] [Google Scholar]
  77. 77.
    Lambert GG, Depernet H, Gotthard G, Schultz DT, Navizet I, et al. 2020.. Aequorea's secrets revealed: new fluorescent proteins with unique properties for bioimaging and biosensing. . PLOS Biol. 18:(11):e3000936
     [Crossref] [Google Scholar]
  78. 78.
    Lange S, Katayama Y, Schmid M, Burkacky O, Bräuchle C, et al. 2008.. Simultaneous transport of different localized mRNA species revealed by live-cell imaging. . Traffic 9:(8):1256–67
     [Crossref] [Google Scholar]
  79. 79.
    Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. 2011.. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. . Science 332:(6028):475–78
     [Crossref] [Google Scholar]
  80. 80.
    Li W, Maekiniemi A, Sato H, Osman C, Singer RH. 2022.. An improved imaging system that corrects MS2-induced RNA destabilization. . Nat. Methods 19:(12):1558–62
     [Crossref] [Google Scholar]
  81. 81.
    Liao Y-C, Fernandopulle MS, Wang G, Choi H, Hao L, et al. 2019.. RNA granules hitchhike on lysosomes for long-distance transport, using Annexin A11 as a molecular tether. . Cell 179:(1):147–64.e20
     [Crossref] [Google Scholar]
  82. 82.
    Lionnet T, Czaplinski K, Darzacq X, Shav-Tal Y, Wells AL, et al. 2011.. A transgenic mouse for in vivo detection of endogenous labeled mRNA. . Nat. Methods 8:(2):165–70
     [Crossref] [Google Scholar]
  83. 83.
    Liu Y, Zhao N, Kanemaki MT, Yamamoto Y, Sadamura Y, et al. 2021.. Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells. . Genes Cells 26:(11):905–26
     [Crossref] [Google Scholar]
  84. 84.
    Livingston NM, Kwon J, Valera O, Saba JA, Sinha NK, et al. 2023.. Bursting translation on single mRNAs in live cells. . Mol. Cell 83:(13):2276–89.e11
     [Crossref] [Google Scholar]
  85. 85.
    López-Erauskin J, Tadokoro T, Baughn MW, Myers B, McAlonis-Downes M, et al. 2018.. ALS/FTD-linked mutation in FUS suppresses intra-axonal protein synthesis and drives disease without nuclear loss-of-function of FUS. . Neuron 100:(4):816–30.e7
     [Crossref] [Google Scholar]
  86. 86.
    Lyon K, Aguilera LU, Morisaki T, Munsky B, Stasevich TJ. 2019.. Live-cell single RNA imaging reveals bursts of translational frameshifting. . Mol. Cell 75:(1):172–83.e9
     [Crossref] [Google Scholar]
  87. 87.
    Lyon K, Stasevich TJ. 2017.. Imaging translational and post-translational gene regulatory dynamics in living cells with antibody-based probes. . Trends Genet. 33:(5):322–35
     [Crossref] [Google Scholar]
  88. 88.
    Mateju D, Chao JA. 2022.. Stress granules: regulators or by-products?. FEBS J. 289:(2):363–73
     [Crossref] [Google Scholar]
  89. 89.
    Mateju D, Eichenberger B, Voigt F, Eglinger J, Roth G, Chao JA. 2020.. Single-molecule imaging reveals translation of mRNAs localized to stress granules. . Cell 183:(7):1801–12.e13
     [Crossref] [Google Scholar]
  90. 90.
    Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. 2022.. ColabFold: making protein folding accessible to all. . Nat. Methods 19:(6):679–82
     [Crossref] [Google Scholar]
  91. 91.
    Moon SL, Morisaki T, Khong A, Lyon K, Parker R, Stasevich TJ. 2019.. Multicolour single-molecule tracking of mRNA interactions with RNP granules. . Nat. Cell Biol. 21:(2):162–68
     [Crossref] [Google Scholar]
  92. 92.
    Moon SL, Morisaki T, Stasevich TJ, Parker R. 2020.. Coupling of translation quality control and mRNA targeting to stress granules. . J. Cell Biol. 219:(8):e202004120
     [Crossref] [Google Scholar]
  93. 93.
    Mor A, Suliman S, Ben-Yishay R, Yunger S, Brody Y, Shav-Tal Y. 2010.. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. . Nat. Cell Biol. 12:(6):543–52
     [Crossref] [Google Scholar]
  94. 94.
    Morisaki T, Lyon K, DeLuca KF, DeLuca JG, English BP, et al. 2016.. Real-time quantification of single RNA translation dynamics in living cells. . Science 352:(6292):1425–29
     [Crossref] [Google Scholar]
  95. 95.
    Morisaki T, Stasevich TJ. 2018.. Quantifying single mRNA translation kinetics in living cells. . Cold Spring Harb. Perspect. Biol. 10:(11):a032078
     [Crossref] [Google Scholar]
  96. 96.
    Murakawa T, Nakamura T, Kawaguchi K, Murayama F, Zhao N, et al. 2022.. A Drosophila toolkit for HA-tagged proteins unveils a block in autophagy flux in the last instar larval fat body. . Development 149:(6):dev200243
     [Crossref] [Google Scholar]
  97. 97.
    Muyldermans S, Baral TN, Retamozzo VC, De Baetselier P, De Genst E, et al. 2009.. Camelid immunoglobulins and nanobody technology. . Vet. Immunol. Immunopathol. 128:(1–3):178–83
     [Crossref] [Google Scholar]
  98. 98.
    Park HY, Lim H, Yoon YJ, Follenzi A, Nwokafor C, et al. 2014.. Visualization of dynamics of single endogenous mRNA labeled in live mouse. . Science 343:(6169):422–24
     [Crossref] [Google Scholar]
  99. 99.
    Peabody DS. 1990.. Translational repression by bacteriophage MS2 coat protein expressed from a plasmid. A system for genetic analysis of a protein-RNA interaction. . J. Biol. Chem. 265:(10):5684–89
     [Crossref] [Google Scholar]
  100. 100.
    Pédelacq J-D, Cabantous S, Tran T, Terwilliger TC, Waldo GS. 2006.. Engineering and characterization of a superfolder green fluorescent protein. . Nat. Biotechnol. 24:(1):79–88
     [Crossref] [Google Scholar]
  101. 101.
    Pichon X, Bastide A, Safieddine A, Chouaib R, Samacoits A, et al. 2016.. Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells. . J. Cell Biol. 214:(6):769–81
     [Crossref] [Google Scholar]
  102. 102.
    Pichon X, Robert M-C, Bertrand E, Singer RH, Tutucci E. 2020.. New generations of MS2 variants and MCP fusions to detect single mRNAs in living eukaryotic cells. . Methods Mol. Biol. 2166::121–44
     [Crossref] [Google Scholar]
  103. 103.
    Rangaraju V, Lauterbach M, Schuman EM. 2019.. Spatially stable mitochondrial compartments fuel local translation during plasticity. . Cell 176:(1–2):73–84.e15
     [Crossref] [Google Scholar]
  104. 104.
    Raymond WS, Ghaffari S, Aguilera LU, Ron E, Morisaki T, et al. 2023.. Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments. . Front. Cell Dev. Biol. 11::1151318
     [Crossref] [Google Scholar]
  105. 105.
    Ruijtenberg S, Sonneveld S, Cui TJ, Logister I, de Steenwinkel D, et al. 2020.. mRNA structural dynamics shape Argonaute-target interactions. . Nat. Struct. Mol. Biol. 27:(9):790–801
     [Crossref] [Google Scholar]
  106. 106.
    Safieddine A, Coleno E, Salloum S, Imbert A, Traboulsi A-M, et al. 2021.. A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport. . Nat. Commun. 12::1352
     [Crossref] [Google Scholar]
  107. 107.
    Sato H, Das S, Singer RH, Vera M. 2020.. Imaging of DNA and RNA in living eukaryotic cells to reveal spatiotemporal dynamics of gene expression. . Annu. Rev. Biochem. 89::159–87
     [Crossref] [Google Scholar]
  108. 108.
    Sato Y, Kujirai T, Arai R, Asakawa H, Ohtsuki C, et al. 2016.. A genetically encoded probe for live-cell imaging of H4K20 monomethylation. . J. Mol. Biol. 428:(20):3885–902
     [Crossref] [Google Scholar]
  109. 109.
    Schmidt A, Gao G, Little SR, Jalihal AP, Walter NG. 2020.. Following the messenger: recent innovations in live cell single molecule fluorescence imaging. . Wiley Interdiscip. Rev. RNA 11:(4):e1587
     [Crossref] [Google Scholar]
  110. 110.
    Sepulveda G, Antkowiak M, Brust-Mascher I, Mahe K, Ou T, et al. 2018.. Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation in vertebrates. . eLife 7::e34959
     [Crossref] [Google Scholar]
  111. 111.
    Shaner NC, Lambert GG, Chammas A, Ni Y, Cranfill PJ, et al. 2013.. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. . Nat. Methods 10:(5):407–9
     [Crossref] [Google Scholar]
  112. 112.
    Shigeoka T, Jung H, Jung J, Turner-Bridger B, Ohk J, et al. 2016.. Dynamic axonal translation in developing and mature visual circuits. . Cell 166:(1):181–92
     [Crossref] [Google Scholar]
  113. 113.
    Slubowski CJ, Funk AD, Roesner JM, Paulissen SM, Huang LS. 2015.. Plasmids for C-terminal tagging in Saccharomyces cerevisiae that contain improved GFP proteins, Envy and Ivy. . Yeast 32:(4):379–87
     [Crossref] [Google Scholar]
  114. 114.
    Sonenberg N, Hinnebusch AG. 2009.. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. . Cell 136:(4):731–45
     [Crossref] [Google Scholar]
  115. 115.
    Swaminathan R, Hoang CP, Verkman AS. 1997.. Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. . Biophys. J. 72:(4):1900–7
     [Crossref] [Google Scholar]
  116. 116.
    Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD. 2014.. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. . Cell 159:(3):635–46
     [Crossref] [Google Scholar]
  117. 117.
    Tingey M, Schnell SJ, Yu W, Saredy J, Junod S, et al. 2022.. Technologies enabling single-molecule super-resolution imaging of mRNA. . Cells 11:(19):3079
     [Crossref] [Google Scholar]
  118. 118.
    Tocchini C, Rohner M, Guerard L, Ray P, Von Stetina SE, Mango SE. 2021.. Translation-dependent mRNA localization to Caenorhabditis elegans adherens junctions. . Development 148:(24):dev200027
     [Crossref] [Google Scholar]
  119. 119.
    Tokunaga M, Imamoto N, Sakata-Sogawa K. 2008.. Highly inclined thin illumination enables clear single-molecule imaging in cells. . Nat. Methods 5:(2):159–61
     [Crossref] [Google Scholar]
  120. 120.
    Tsirkas I, Zur T, Dovrat D, Cohen A, Ravkaie L, Aharoni A. 2022.. Protein fluorescent labeling in live yeast cells using scFv-based probes. . Cell Rep. Methods 2:(12):100357
     [Crossref] [Google Scholar]
  121. 121.
    Tutucci E, Livingston NM, Singer RH, Wu B. 2018.. Imaging mRNA in vivo, from birth to death. . Annu. Rev. Biophys. 47::85–106
     [Crossref] [Google Scholar]
  122. 122.
    Tutucci E, Vera M, Biswas J, Garcia J, Parker R, Singer RH. 2018.. An improved MS2 system for accurate reporting of the mRNA life cycle. . Nat. Methods 15:(1):81–89
     [Crossref] [Google Scholar]
  123. 123.
    Valbuena FM, Fitzgerald I, Strack RL, Andruska N, Smith L, Glick BS. 2020.. A photostable monomeric superfolder green fluorescent protein. . Traffic 21:(8):534–44
     [Crossref] [Google Scholar]
  124. 124.
    Vedula P, Kurosaka S, MacTaggart B, Ni Q, Papoian G, et al. 2021.. Different translation dynamics of β- and γ-actin regulates cell migration. . eLife 10::e68712
     [Crossref] [Google Scholar]
  125. 125.
    Vicens Q, Kieft JS, Rissland OS. 2018.. Revisiting the closed-loop model and the nature of mRNA 5′-3′ communication. . Mol. Cell 72:(5):805–12
     [Crossref] [Google Scholar]
  126. 126.
    Vigano MA, Ell C-M, Kustermann MMM, Aguilar G, Matsuda S, et al. 2021.. Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster. . Development 148:(6):dev191700
     [Crossref] [Google Scholar]
  127. 127.
    Vinter DJ, Hoppe C, Minchington TG, Sutcliffe C, Ashe HL. 2021.. Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. . Development 148:(18):dev196121
     [Crossref] [Google Scholar]
  128. 128.
    Viswanathan S, Williams ME, Bloss EB, Stasevich TJ, Speer CM, et al. 2015.. High-performance probes for light and electron microscopy. . Nat. Methods 12:(6):568–76
     [Crossref] [Google Scholar]
  129. 129.
    Voigt F, Zhang H, Cui XA, Triebold D, Liu AX, et al. 2017.. Single-molecule quantification of translation-dependent association of mRNAs with the endoplasmic reticulum. . Cell Rep. 21:(13):3740–53
     [Crossref] [Google Scholar]
  130. 130.
    Volkov IL, Lundin E, Kipper K, Metelev M, Zikrin S, Johansson M. 2022.. Spatiotemporal kinetics of the SRP pathway in live E. coli cells. . PNAS 119:(38):e2204038119
     [Crossref] [Google Scholar]
  131. 131.
    Wang C, Han B, Zhou R, Zhuang X. 2016.. Real-time imaging of translation on single mRNA transcripts in live cells. . Cell 165:(4):990–1001
     [Crossref] [Google Scholar]
  132. 132.
    Wilbertz JH, Voigt F, Horvathova I, Roth G, Zhan Y, Chao JA. 2019.. Single-molecule imaging of mRNA localization and regulation during the integrated stress response. . Mol. Cell 73:(5):946–58.e7
     [Crossref] [Google Scholar]
  133. 133.
    Wilson IA, Niman HL, Houghten RA, Cherenson AR, Connolly ML, Lerner RA. 1984.. The structure of an antigenic determinant in a protein. . Cell 37:(3):767–78
     [Crossref] [Google Scholar]
  134. 134.
    Winkenbach LP, Parker DM, Williams RTP, Nishimura EO. 2022.. The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo. . Development 149:(22):dev200930
     [Crossref] [Google Scholar]
  135. 135.
    Wongso D, Dong J, Ueda H, Kitaguchi T. 2017.. Flashbody: a next generation fluobody with fluorescence intensity enhanced by antigen binding. . Anal. Chem. 89:(12):6719–25
     [Crossref] [Google Scholar]
  136. 136.
    Wu B, Eliscovich C, Yoon YJ, Singer RH. 2016.. Translation dynamics of single mRNAs in live cells and neurons. . Science 352:(6292):1430–35
     [Crossref] [Google Scholar]
  137. 137.
    Wu B, Miskolci V, Sato H, Tutucci E, Kenworthy CA, et al. 2015.. Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences. . Genes Dev. 29:(8):876–86
     [Crossref] [Google Scholar]
  138. 138.
    Yan X, Hoek TA, Vale RD, Tanenbaum ME. 2016.. Dynamics of translation of single mRNA molecules in vivo. . Cell 165:(4):976–89
     [Crossref] [Google Scholar]
  139. 139.
    Zhao N, Kamijo K, Fox PD, Oda H, Morisaki T, et al. 2019.. A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo. . Nat. Commun. 10::2947
     [Crossref] [Google Scholar]
/content/journals/10.1146/annurev-biophys-030822-034116
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Translation Dynamics of Single mRNAs in Live Cells
Annual Review of Biophysics 53, 65 (2024); https://doi.org/10.1146/annurev-biophys-030822-034116
/content/journals/10.1146/annurev-biophys-030822-034116
/content/journals/10.1146/annurev-biophys-030822-034116
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