1932

Abstract

RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred from DNA to proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution. We review current theoretical models for describing transcription and translation that were generated by single-molecule and single-cell studies. These methods provide a basis to study how single-molecule interactions generate phenotypes, fundamentally changing our understating of gene expression regulation.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biophys-070317-033037
2018-05-20
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/biophys/47/1/annurev-biophys-070317-033037.html?itemId=/content/journals/10.1146/annurev-biophys-070317-033037&mimeType=html&fmt=ahah

Literature Cited

  1. 1.  Albert FW, Muzzey D, Weissman JS, Kruglyak L 2014. Genetic influences on translation in yeast. PLOS Genet 10:e1004692
    [Google Scholar]
  2. 2.  Alpert T, Herzel L, Neugebauer KM 2017. Perfect timing: splicing and transcription rates in living cells. WIREs RNA 8:e1401
    [Google Scholar]
  3. 3.  Bahar Halpern K, Caspi I, Lemze D, Levy M, Landen S et al. 2015. Nuclear retention of mRNA in mammalian tissues. Cell Rep 13:2653–62
    [Google Scholar]
  4. 4.  Bahar Halpern K, Tanami S, Landen S, Chapal M, Szlak L et al. 2015. Bursty gene expression in the intact mammalian liver. Mol. Cell 58:147–56
    [Google Scholar]
  5. 5.  Battich N, Stoeger T, Pelkmans L 2013. Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nat. Methods 10:1127–33
    [Google Scholar]
  6. 6.  Battich N, Stoeger T, Pelkmans L 2015. Control of transcript variability in single mammalian cells. Cell 163:1596–610
    [Google Scholar]
  7. 7.  Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ et al. 2015. Genomic variation. Impact of regulatory variation from RNA to protein. Science 347:664–67
    [Google Scholar]
  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 2:437–45
    [Google Scholar]
  9. 9.  Blake WJ, KÆrn M, Cantor CR, Collins JJ 2003. Noise in eukaryotic gene expression. Nature 422:633–37
    [Google Scholar]
  10. 10.  Boiani M, Schöler HR 2005. Regulatory networks in embryo-derived pluripotent stem cells. Nat. Rev. Mol. Cell Biol. 6:872–84
    [Google Scholar]
  11. 11.  Bothma JP, Garcia HG, Esposito E, Schlissel G, Gregor T, Levine M 2014. Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. PNAS 111:10598–603
    [Google Scholar]
  12. 12.  Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine M 2015. Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo. eLife 4:e07956
    [Google Scholar]
  13. 13.  Bregman A, Avraham-Kelbert M, Barkai O, Duek L, Guterman A, Choder M 2011. Promoter elements regulate cytoplasmic mRNA decay. Cell 147:1473–83
    [Google Scholar]
  14. 14.  Brodsky AS, Silver PA 2002. Identifying proteins that affect mRNA localization in living cells. Methods 26:151–55
    [Google Scholar]
  15. 15.  Brody Y, Neufeld N, Bieberstein N, Causse SZ, Bohnlein EM et al. 2011. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLOS Biol 9:e1000573
    [Google Scholar]
  16. 16.  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. 16:95–109
    [Google Scholar]
  17. 17.  Cai L, Friedman N, Xie XS 2006. Stochastic protein expression in individual cells at the single molecule level. Nature 440:358–62
    [Google Scholar]
  18. 18.  Chambers I, Silva J, Colby D, Nichols J, Nijmeijer B et al. 2007. Nanog safeguards pluripotency and mediates germline development. Nature 450:1230–34
    [Google Scholar]
  19. 19.  Chao JA, Patskovsky Y, Almo SC, Singer RH 2008. Structural basis for the coevolution of a viral RNA–protein complex. Nat. Struct. Mol. Biol. 15:103–5
    [Google Scholar]
  20. 20.  Chen H, Larson DR 2016. What have single-molecule studies taught us about gene expression?. Genes Dev 30:1796–810
    [Google Scholar]
  21. 21.  Chen J, Nikolaitchik O, Singh J, Wright A, Bencsics CE et al. 2009. High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis. PNAS 106:13535–40
    [Google Scholar]
  22. 22.  Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X 2015. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:aaa6090
    [Google Scholar]
  23. 23.  Chong S, Chen C, Ge H, Xie XS 2014. Mechanism of transcriptional bursting in bacteria. Cell 158:314–26
    [Google Scholar]
  24. 24.  Chou T. 2003. Ribosome recycling, diffusion, and mRNA loop formation in translational regulation. Biophys. J. 85:755–73
    [Google Scholar]
  25. 25.  Chou T, Lakatos G 2004. Clustered bottlenecks in mRNA translation and protein synthesis. Phys. Rev. Lett. 93:198101
    [Google Scholar]
  26. 26.  Coulon A, Ferguson ML, de Turris V, Palangat M, Chow CC, Larson DR 2014. Kinetic competition during the transcription cycle results in stochastic RNA processing. eLife 3:e03939
    [Google Scholar]
  27. 27.  Dacheux E, Malys N, Meng X, Ramachandran V, Mendes P, McCarthy JEG 2017. Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Res 45:6981–92
    [Google Scholar]
  28. 28.  Dar RD, Razooky BS, Singh A, Trimeloni TV, McCollum JM et al. 2012. Transcriptional burst frequency and burst size are equally modulated across the human genome. PNAS 109:17454–59
    [Google Scholar]
  29. 29.  Dar RD, Razooky BS, Weinberger LS, Cox CD, Simpson ML 2015. The low noise limit in gene expression. PLOS ONE 10:e0140969
    [Google Scholar]
  30. 30.  Darmanis S, Gallant CJ, Marinescu VD, Niklasson M, Segerman A et al. 2016. Simultaneous multiplexed measurement of RNA and proteins in single cells. Cell Rep 14:380–89
    [Google Scholar]
  31. 31.  Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy SM et al. 2007. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14:796–806
    [Google Scholar]
  32. 32.  de Turris V, Nicholson P, Orozco RZ, Singer RH, Muhlemann O 2011. Cotranscriptional effect of a premature termination codon revealed by live-cell imaging. RNA 17:2094–107
    [Google Scholar]
  33. 33.  Derrida B. 1998. An exactly soluble non-equilibrium system: the asymmetric simple exclusion process. Phys. Rep. 301:65–83
    [Google Scholar]
  34. 34.  Derrida B, Domany E, Mukamel D 1992. An exact solution of a one-dimensional asymmetric exclusion model with open boundaries. J. Stat. Phys. 69:667–87
    [Google Scholar]
  35. 35.  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. 9:2412–20
    [Google Scholar]
  36. 36.  Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum LI et al. 2002. A kinetic framework for a mammalian RNA polymerase in vivo. Science 298:1623–26
    [Google Scholar]
  37. 37.  Eliscovich C, Shenoy SM, Singer RH 2017. Imaging mRNA and protein interactions within neurons. PNAS 114:E1875–84
    [Google Scholar]
  38. 38.  Elowitz MB, Levine AJ, Siggia ED, Swain PS 2002. Stochastic gene expression in a single cell. Science 297:1183–86
    [Google Scholar]
  39. 39.  Femino AM, Fay FS, Fogarty K, Singer RH 1998. Visualization of single RNA transcripts in situ. Science 280:585–90
    [Google Scholar]
  40. 40.  Femino AM, Fogarty K, Lifshitz LM, Carrington W, Singer RH 2003. Visualization of single molecules of mRNA in situ. Methods Enzymol 361:245–304
    [Google Scholar]
  41. 41.  Filipczyk A, Marr C, Hastreiter S, Feigelman J, Schwarzfischer M et al. 2015. Network plasticity of pluripotency transcription factors in embryonic stem cells. Nat. Cell Biol. 17:1235–46
    [Google Scholar]
  42. 42.  Filonov GS, Moon JD, Svensen N, Jaffrey SR 2014. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 136:16299–308
    [Google Scholar]
  43. 43.  Frieda KL, Linton JM, Hormoz S, Choi J Chow K-HK. et al. 2017. Synthetic recording and in situ readout of lineage information in single cells. Nature 541:107–11
    [Google Scholar]
  44. 44.  Fukaya T, Lim B, Levine M 2016. Enhancer control of transcriptional bursting. Cell 166:358–68
    [Google Scholar]
  45. 45.  Gandhi SJ, Zenklusen D, Lionnet T, Singer RH 2011. Transcription of functionally related constitutive genes is not coordinated. Nat. Struct. Mol. Biol. 18:27–34
    [Google Scholar]
  46. 46.  Garcia HG, Tikhonov M, Lin A, Gregor T 2013. Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning. Curr. Biol. 23:2140–45
    [Google Scholar]
  47. 47.  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 21:1393–95
    [Google Scholar]
  48. 48.  Golding I, Paulsson J, Zawilski SM, Cox EC 2005. Real-time kinetics of gene activity in individual bacteria. Cell 123:1025–36
    [Google Scholar]
  49. 49.  Grimm JB, English BP, Choi H, Muthusamy AK, Mehl BP et al. 2016. Bright photoactivatable fluorophores for single-molecule imaging. Nat. Methods 13:985–88
    [Google Scholar]
  50. 50.  Grunwald D, Singer RH 2010. In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Nature 467:604–7
    [Google Scholar]
  51. 51.  Haimovich G, Choder M, Singer RH, Trcek T 2013. The fate of the messenger is pre-determined: a new model for regulation of gene expression. Biochim. Biophys. Acta 1829:643–53
    [Google Scholar]
  52. 52.  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 22:660–66
    [Google Scholar]
  53. 53.  Halpern KB, Shenhav R, Matcovitch-Natan O, Toth B, Lemze D et al. 2017. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature 542:352–56
    [Google Scholar]
  54. 54.  Halstead JM, Lionnet T, Wilbertz JH, Wippich F, Ephrussi A et al. 2015. An RNA biosensor for imaging the first round of translation from single cells to living animals. Science 347:1367–671
    [Google Scholar]
  55. 55.  Hansen AS, O'Shea EK 2013. Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Mol. Syst. Biol. 9:704
    [Google Scholar]
  56. 56.  Hansen AS, O'Shea EK 2015. Limits on information transduction through amplitude and frequency regulation of transcription factor activity. eLife 4:e06559
    [Google Scholar]
  57. 57.  Hansen CH, van Oudenaarden A 2013. Allele-specific detection of single mRNA molecules in situ. Nat. Methods 10:869–71
    [Google Scholar]
  58. 58.  Hanson G, Coller J 2018. Codon optimality, bias and usage in translation and mRNA decay. Nat Rev Mol. Cell Biol. 19:20–30
    [Google Scholar]
  59. 59.  Heinrich S, Derrer CP, Lari A, Weis K, Montpetit B 2017. Temporal and spatial regulation of mRNA export: Single particle RNA-imaging provides new tools and insights. BioEssays 39:1600124
    [Google Scholar]
  60. 60.  Heinrich S, Sidler CL, Azzalin CM, Weis K 2017. Stem-loop RNA labeling can affect nuclear and cytoplasmic mRNA processing. RNA 23:134–41
    [Google Scholar]
  61. 61.  Hocine S, Raymond P, Zenklusen D, Chao JA, Singer RH 2013. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat. Methods 10:119–21
    [Google Scholar]
  62. 62.  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 68:615–25.e9
    [Google Scholar]
  63. 63.  Jansen A, Verstrepen KJ 2011. Nucleosome positioning in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 75:301–20
    [Google Scholar]
  64. 64.  Karousis ED, Nasif S, Mühlemann O 2016. Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact. WIREs RNA 7:661–82
    [Google Scholar]
  65. 65.  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
    [Google Scholar]
  66. 66.  Laissue PP, Alghamdi RA, Tomancak P, Reynaud EG, Shroff H 2017. Assessing phototoxicity in live fluorescence imaging. Nat. Methods 14:657–61
    [Google Scholar]
  67. 67.  Lange S, Katayama Y, Schmid M, Burkacky O, Brauchle C et al. 2008. Simultaneous transport of different localized mRNA species revealed by live-cell imaging. Traffic 9:1256–67
    [Google Scholar]
  68. 68.  Larson DR, Fritzsch C, Sun L, Meng X, Lawrence DS, Singer RH 2013. Direct observation of frequency modulated transcription in single cells using light activation. eLife 2:e00750
    [Google Scholar]
  69. 69.  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 332:475–78
    [Google Scholar]
  70. 70.  Lenstra TL, Coulon A, Chow CC, Larson DR 2015. Single-molecule imaging reveals a switch between spurious and functional ncRNA transcription. Mol. Cell 60:597–610
    [Google Scholar]
  71. 71.  Lenstra TL, Rodriguez J, Chen H, Larson DR 2016. Transcription dynamics in living cells. Annu. Rev. Biophys. 45:25–47
    [Google Scholar]
  72. 72.  Levsky JM, Shenoy SM, Pezo RC, Singer RH 2002. Single-cell gene expression profiling. Science 297:836–40
    [Google Scholar]
  73. 73.  Li JJ, Bickel PJ, Biggin MD 2014. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2:e270
    [Google Scholar]
  74. 74.  Lim F, Downey TP, Peabody DS 2001. Translational repression and specific RNA binding by the coat protein of the Pseudomonas phage PP7. J. Biol. Chem. 276:22507–13
    [Google Scholar]
  75. 75.  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 8:165–70
    [Google Scholar]
  76. 76.  Liu Y, Beyer A, Aebersold R 2016. On the dependency of cellular protein levels on mRNA abundance. Cell 165:535–50
    [Google Scholar]
  77. 77.  Liu Z, Lavis LD, Betzig E 2015. Imaging live-cell dynamics and structure at the single-molecule level. Mol. Cell 58:644–59
    [Google Scholar]
  78. 78.  Long X, Colonell J, Wong AM, Singer RH, Lionnet T 2017. Quantitative mRNA imaging throughout the entire Drosophila brain. Nat. Methods 14:703–6
    [Google Scholar]
  79. 79.  Los GV, Encell LP, McDougall MG, Hartzell DD, Karassina N et al. 2008. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 3:373–82
    [Google Scholar]
  80. 80.  Lubeck E, Cai L 2012. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat. Methods 9:743–48
    [Google Scholar]
  81. 81.  Lubeck E, Coskun AF, Zhiyentayev T, Ahmad M, Cai L 2014. Single-cell in situ RNA profiling by sequential hybridization. Nat. Methods 11:360–61
    [Google Scholar]
  82. 82.  Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bahler J 2012. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell 151:671–83
    [Google Scholar]
  83. 83.  Martin RM, Rino J, Carvalho C, Kirchhausen T, Carmo-Fonseca M 2013. Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep 4:1144–55
    [Google Scholar]
  84. 84.  Mellis IA, Gupte R, Raj A, Rouhanifard SH 2017. Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Nat. Methods 14:801–4
    [Google Scholar]
  85. 85.  Messier V, Zenklusen D, Michnick SW 2013. A nutrient-responsive pathway that determines M phase timing through control of B-cyclin mRNA stability. Cell 153:1080–93
    [Google Scholar]
  86. 86.  Moffitt JR, Hao J, Bambah-Mukku D, Lu T, Dulac C, Zhuang X 2016. High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing. PNAS 113:14456–61
    [Google Scholar]
  87. 87.  Moor AE, Golan M, Massasa EE, Lemze D, Weizman T et al. 2017. Global mRNA polarization regulates translation efficiency in the intestinal epithelium. Science 357:1299–303
    [Google Scholar]
  88. 88.  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. 12:543–52
    [Google Scholar]
  89. 89.  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 352:1425–29
    [Google Scholar]
  90. 90.  Morisaki T, Müller WG, Golob N, Mazza D, McNally JG 2014. Single-molecule analysis of transcription factor binding at transcription sites in live cells. Nat. Commun. 5:4456
    [Google Scholar]
  91. 91.  Mueller F, Senecal A, Tantale K, Marie-Nelly H, Ly N et al. 2013. FISH-quant: automatic counting of transcripts in 3D FISH images. Nat. Methods 10:277–78
    [Google Scholar]
  92. 92.  Mueller F, Stasevich TJ, Mazza D, McNally JG 2013. Quantifying transcription factor kinetics: at work or at play?. Crit. Rev. Biochem. Mol. Biol. 48:492–514
    [Google Scholar]
  93. 93.  Munsky B, Neuert G, van Oudenaarden A 2012. Using gene expression noise to understand gene regulation. Science 336:183–87
    [Google Scholar]
  94. 94.  Muzzey D, Sherlock G, Weissman JS 2014. Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans. Genome Res 24:963–73
    [Google Scholar]
  95. 95.  Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ et al. 2016. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165:488–96
    [Google Scholar]
  96. 96.  Paige JS, Wu KY, Jaffrey SR 2011. RNA mimics of green fluorescent protein. Science 333:642–46
    [Google Scholar]
  97. 97.  Park HY, Buxbaum AR, Singer RH 2010. Single mRNA tracking in live cells. Methods Enzymol 472:387–406
    [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 343:422–24
    [Google Scholar]
  99. 99.  Parker R. 2012. RNA degradation in Saccharomyces cerevisae. Genetics 191:671–702
    [Google Scholar]
  100. 100.  Paulsson J. 2004. Summing up the noise in gene networks. Nature 427:415–18
    [Google Scholar]
  101. 101.  Pelechano V, Wei W, Steinmetz LM 2015. Widespread co-translational RNA decay reveals ribosome dynamics. Cell 161:1400–12
    [Google Scholar]
  102. 102.  Pérez-Ortín JE, Alepuz P, Chávez S, Choder M 2013. Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression. J. Mol. Biol. 425:3750–75
    [Google Scholar]
  103. 103.  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. 214:769–81
    [Google Scholar]
  104. 104.  Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S 2006. Stochastic mRNA synthesis in mammalian cells. PLOS Biol 4:e309
    [Google Scholar]
  105. 105.  Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S 2008. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5:877–79
    [Google Scholar]
  106. 106.  Raj A, van Oudenaarden A 2008. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135:216–26
    [Google Scholar]
  107. 107.  Raser JM, O'Shea EK 2004. Control of stochasticity in eukaryotic gene expression. Science 304:1811–14
    [Google Scholar]
  108. 108.  Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A et al. 2017. The growing and glowing toolbox of fluorescent and photoactive proteins. Trends Biochem. Sci. 42:111–29
    [Google Scholar]
  109. 109.  Sanchez A, Golding I 2013. Genetic determinants and cellular constraints in noisy gene expression. Science 342:1188–93
    [Google Scholar]
  110. 110.  Saroufim MA, Bensidoun P, Raymond P, Rahman S, Krause MR et al. 2015. The nuclear basket mediates perinuclear mRNA scanning in budding yeast. J. Cell Biol. 211:1131–40
    [Google Scholar]
  111. 111.  Schmidt U, Basyuk E, Robert MC, Yoshida M, Villemin JP et al. 2011. Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation. J. Cell Biol. 193:819–29
    [Google Scholar]
  112. 112.  Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J et al. 2011. Global quantification of mammalian gene expression control. Nature 473:337–42
    [Google Scholar]
  113. 113.  Senecal A, Munsky B, Proux F, Ly N, Braye FE et al. 2014. Transcription factors modulate c-Fos transcriptional bursts. Cell Rep 8:75–83
    [Google Scholar]
  114. 114.  Sepulveda LA, Xu H, Zhang J, Wang M, Golding I 2016. Measurement of gene regulation in individual cells reveals rapid switching between promoter states. Science 351:1218–22
    [Google Scholar]
  115. 115.  Shaffer SM, Wu M-T, Levesque MJ, Raj A 2013. Turbo FISH: a method for rapid single molecule RNA FISH. PLOS ONE 8:e75120
    [Google Scholar]
  116. 116.  Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB 2013. Rate-limiting steps in yeast protein translation. Cell 153:1589–601
    [Google Scholar]
  117. 117.  Shaw LB, Sethna JP, Lee KH 2004. Mean-field approaches to the totally asymmetric exclusion process with quenched disorder and large particles. Phys. Rev. E 70:021901
    [Google Scholar]
  118. 118.  Shorter J. 2016. Membraneless organelles: phasing in and out. Nat. Chem. 8:528–30
    [Google Scholar]
  119. 119.  Siebrasse JP, Kaminski T, Kubitscheck U 2012. Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy. PNAS 109:9426–31
    [Google Scholar]
  120. 120.  Singh G, Pratt G, Yeo GW, Moore MJ 2015. The clothes make the mRNA: past and present trends in mRNP fashion. Annu. Rev. Biochem. 84:325–54
    [Google Scholar]
  121. 121.  Skinner SO, Sepulveda LA, Xu H, Golding I 2013. Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization. Nat. Protoc. 8:1100–13
    [Google Scholar]
  122. 122.  Smith CS, Lari A, Derrer CP, Ouwehand A, Rossouw A et al. 2015. In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J. Cell Biol. 211:1121–30
    [Google Scholar]
  123. 123.  Smith CS, Preibisch S, Joseph A, Abrahamsson S, Rieger B et al. 2015. Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking. J. Cell Biol. 209:609–19
    [Google Scholar]
  124. 124.  Speese SD, Ashley J, Jokhi V, Nunnari J, Barria R et al. 2012. Nuclear envelope budding enables large ribonucleoprotein particle export during synaptic Wnt signaling. Cell 149:832–46
    [Google Scholar]
  125. 125.  Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y et al. 2014. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516:272–75
    [Google Scholar]
  126. 126.  Strack RL, Disney MD, Jaffrey SR 2013. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat. Methods 10:1219–24
    [Google Scholar]
  127. 127.  Subramaniam AR, Zid BM, O'Shea EK 2014. An integrated approach reveals regulatory controls on bacterial translation elongation. Cell 159:1200–11
    [Google Scholar]
  128. 128.  Suter DM, Molina N, Gatfield D, Schneider K, Schibler U, Naef F 2011. Mammalian genes are transcribed with widely different bursting kinetics. Science 332:472–74
    [Google Scholar]
  129. 129.  Takahashi K, Yamanaka S 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–76
    [Google Scholar]
  130. 130.  Takizawa PA, Vale RD 2000. The myosin motor, Myo4p, binds Ash1 mRNA via the adapter protein, She3p. PNAS 97:5273–78
    [Google Scholar]
  131. 131.  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 159:635–46
    [Google Scholar]
  132. 132.  Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M et al. 2010. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329:533–38
    [Google Scholar]
  133. 133.  Tantale K, Mueller F, Kozulic-Pirher A, Lesne A, Victor JM et al. 2016. A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting. Nat. Commun. 7:12248
    [Google Scholar]
  134. 134.  Trcek T, Larson DR, Moldon A, Query CC, Singer RH 2011. Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell 147:1484–97
    [Google Scholar]
  135. 135.  Trcek T, Sato H, Singer RH, Maquat LE 2013. Temporal and spatial characterization of nonsense-mediated mRNA decay. Genes Dev 27:541–51
    [Google Scholar]
  136. 136.  Tsai A, Muthusamy AK, Alves MR, Lavis LD, Singer RH et al. 2017. Nuclear microenvironments modulate transcription from low-affinity enhancers. eLife 6:e28975
    [Google Scholar]
  137. 137.  Tutucci E, Stutz F 2011. Keeping mRNPs in check during assembly and nuclear export. Nat. Rev. Mol. Cell Biol. 12:377–84
    [Google Scholar]
  138. 138.  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 15:81–89
    [Google Scholar]
  139. 139.  Tyagi S, Kramer FR 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303–8
    [Google Scholar]
  140. 140.  Wang C, Han B, Zhou R, Zhuang X 2016. Real-time imaging of translation on single mRNA transcripts in live cells. Cell 165:990–1001
    [Google Scholar]
  141. 141.  Wu B, Buxbaum AR, Katz ZB, Yoon YJ, Singer RH 2015. Quantifying protein-mRNA interactions in single live cells. Cell 162:211–20
    [Google Scholar]
  142. 142.  Wu B, Chao JA, Singer RH 2012. Fluorescence fluctuation spectroscopy enables quantitative imaging of single mRNAs in living cells. Biophys. J. 102:2936–44
    [Google Scholar]
  143. 143.  Wu B, Eliscovich C, Yoon YJ, Singer RH 2016. Translation dynamics of single mRNAs in live cells and neurons. Science 352:1430–35
    [Google Scholar]
  144. 144.  Xu H, Sepulveda LA, Figard L, Sokac AM, Golding I 2015. Combining protein and mRNA quantification to decipher transcriptional regulation. Nat. Methods 12:739–42
    [Google Scholar]
  145. 145.  Xu H, Skinner SO, Sokac AM, Golding I 2016. Stochastic kinetics of nascent RNA. Phys. Rev. Lett. 117:128101
    [Google Scholar]
  146. 146.  Yan X, Hoek TA, Vale RD, Tanenbaum ME 2016. Dynamics of translation of single mRNA molecules in vivo. Cell 165:976–89
    [Google Scholar]
  147. 147.  Yang L, Titlow J, Ennis D, Smith C, Mitchell J et al. 2017. Single molecule fluorescence in situ hybridisation for quantitating post-transcriptional regulation in Drosophila brains. Methods 126:166–76
    [Google Scholar]
  148. 148.  Yoon YJ, Wu B, Buxbaum AR, Das S, Tsai A et al. 2016. Glutamate-induced RNA localization and translation in neurons. PNAS 113:E6877–86
    [Google Scholar]
  149. 149.  Yuan GC, Cai L, Elowitz M, Enver T, Fan G et al. 2017. Challenges and emerging directions in single-cell analysis. Genome Biol 18:84
    [Google Scholar]
  150. 150.  Zenklusen D, Larson DR, Singer RH 2008. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat. Struct. Mol. Biol. 15:1263–71
    [Google Scholar]
  151. 151.  Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T 2015. Tandem Spinach array for mRNA imaging in living bacterial cells. Sci. Rep. 5:17295
    [Google Scholar]
  152. 152.  Zhao R, Nakamura T, Fu Y, Lazar Z, Spector DL 2011. Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nat. Cell Biol. 13:1295–304
    [Google Scholar]
  153. 153.  Zia RKP, Dong JJ, Schmittmann B 2011. Modeling translation in protein synthesis with TASEP: a tutorial and recent developments. J. Stat. Phys. 144:405–28
    [Google Scholar]
/content/journals/10.1146/annurev-biophys-070317-033037
Loading
/content/journals/10.1146/annurev-biophys-070317-033037
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error