Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression

Literature Cited

1. 1. 

   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]
2. 2. 

   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]
3. 3. 

   Shav-Tal Y, Darzacq X, Singer RH 2006. Gene expression within a dynamic nuclear landscape. EMBO J 25:3469–79
   [Google Scholar]
4. 4. 

   Fukaya T, Lim B, Levine M 2016. Enhancer control of transcriptional bursting. Cell 166:358–68
   [Google Scholar]
5. 5. 

   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]
6. 6. 

   McSwiggen DT, Mir M, Darzacq X, Tjian R 2019. Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev 33:1619–34
   [Google Scholar]
7. 7. 

   Snead WT, Gladfelter AS. 2019. The control centers of biomolecular phase separation: how membrane surfaces, PTMs, and active processes regulate condensation. Mol. Cell 76:295–305
   [Google Scholar]
8. 8. 

   Mir M, Stadler MR, Ortiz SA, Hannon CE, Harrison MM et al. 2018. Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos. eLife 7:e40497
   [Google Scholar]
9. 9. 

   Tsai A, Alves MR, Crocker J 2019. Multi-enhancer transcriptional hubs confer phenotypic robustness. eLife 8:e45325
   [Google Scholar]
10. 10. 

    Guzikowski AR, Chen YS, Zid BM 2019. Stress-induced mRNP granules: form and function of processing bodies and stress granules. Wiley Interdiscip. Rev. RNA 10:e1524
    [Google Scholar]
11. 11. 

    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. 21:162–68
    [Google Scholar]
12. 12. 

    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 73:946–58.e7
    [Google Scholar]
13. 13. 

    Jalihal AP, Lund PE, Walter NG 2019. Coming together: RNAs and proteins assemble under the single-molecule fluorescence microscope. Cold Spring Harb. Perspect. Biol. 11:a032441
    [Google Scholar]
14. 14. 

    Daetwyler S, Huisken J. 2016. Fast fluorescence microscopy with light sheets. Biol. Bull. 231:14–25
    [Google Scholar]
15. 15. 

    Chen BC, Legant WR, Wang K, Shao L, Milkie DE et al. 2014. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346:1257998
    [Google Scholar]
16. 16. 

    Robinett CC, Straight A, Li G, Willhelm C, Sudlow G et al. 1996. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J. Cell Biol. 135:1685–700
    [Google Scholar]
17. 17. 

    Ding DQ, Hiraoka Y. 2017. Visualization of a specific genome locus by the lacO/LacI-GFP system. Cold Spring Harb. Protoc. 2017.pdb.prot091934
    [Google Scholar]
18. 18. 

    Belmont AS. 2001. Visualizing chromosome dynamics with GFP. Trends Cell Biol 11:250–57
    [Google Scholar]
19. 19. 

    Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M et al. 2018. CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Nucleic Acids Res 46:e100
    [Google Scholar]
20. 20. 

    Fu Y, Rocha PP, Luo VM, Raviram R, Deng Y et al. 2016. CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci. Nat. Commun. 7:11707
    [Google Scholar]
21. 21. 

    Ma H, Reyes-Gutierrez P, Pederson T 2013. Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. PNAS 110:21048–53
    [Google Scholar]
22. 22. 

    Ma Y, Wang M, Li W, Zhang Z, Zhang X et al. 2017. Live cell imaging of single genomic loci with quantum dot-labeled TALEs. Nat. Commun. 8:15318
    [Google Scholar]
23. 23. 

    Lindhout BI, Fransz P, Tessadori F, Meckel T, Hooykaas PJ, van der Zaal BJ 2007. Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins. Nucleic Acids Res 35:e107
    [Google Scholar]
24. 24. 

    Lane AB, Strzelecka M, Ettinger A, Grenfell AW, Wittmann T, Heald R 2015. Enzymatically generated CRISPR libraries for genome labeling and screening. Dev. Cell 34:373–78
    [Google Scholar]
25. 25. 

    Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W et al. 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–91
    [Google Scholar]
26. 26. 

    Chen B, Guan J, Huang B 2016. Imaging specific genomic DNA in living cells. Annu. Rev. Biophys. 45:1–23
    [Google Scholar]
27. 27. 

    Qin P, Parlak M, Kuscu C, Bandaria J, Mir M et al. 2017. Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. Nat. Commun. 8:14725
    [Google Scholar]
28. 28. 

    Ma H, Naseri A, Reyes-Gutierrez P, Wolfe SA, Zhang S, Pederson T 2015. Multicolor CRISPR labeling of chromosomal loci in human cells. PNAS 112:3002–7
    [Google Scholar]
29. 29. 

    Ma H, Tu LC, Naseri A, Huisman M, Zhang S et al. 2016. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat. Biotechnol. 34:528–30
    [Google Scholar]
30. 30. 

    Ma H, Tu LC, Naseri A, Chung YC, Grunwald D et al. 2018. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat. Methods 15:928–31
    [Google Scholar]
31. 31. 

    Wu X, Mao S, Yang Y, Rushdi MN, Krueger CJ, Chen AK 2018. A CRISPR/molecular beacon hybrid system for live-cell genomic imaging. Nucleic Acids Res 46:e80
    [Google Scholar]
32. 32. 

    Mao S, Ying Y, Wu X, Krueger CJ, Chen AK 2019. CRISPR/dual-FRET molecular beacon for sensitive live-cell imaging of non-repetitive genomic loci. Nucleic Acids Res 47:e131
    [Google Scholar]
33. 33. 

    Wang H, Nakamura M, Abbott TR, Zhao D, Luo K et al. 2019. CRISPR-mediated live imaging of genome editing and transcription. Science 365:1301–5
    [Google Scholar]
34. 34. 

    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]
35. 35. 

    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]
36. 36. 

    Pichon X, Lagha M, Mueller F, Bertrand E 2018. A growing toolbox to image gene expression in single cells: sensitive approaches for demanding challenges. Mol. Cell 71:468–80
    [Google Scholar]
37. 37. 

    Tutucci E, Livingston NM, Singer RH, Wu B 2018. Imaging mRNA in vivo, from birth to death. Annu. Rev. Biophys. 47:85–106
    [Google Scholar]
38. 38. 

    Vera M, Biswas J, Senecal A, Singer RH, Park HY 2016. Single-cell and single-molecule analysis of gene expression regulation. Annu. Rev. Genet. 50:267–91
    [Google Scholar]
39. 39. 

    Buxbaum AR, Wu B, Singer RH 2014. Single β-actin mRNA detection in neurons reveals a mechanism for regulating its translatability. Science 343:419–22
    [Google Scholar]
40. 40. 

    Grunwald D, Singer RH. 2010. In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Nature 467:604–7
    [Google Scholar]
41. 41. 

    Hoek TA, Khuperkar D, Lindeboom RGH, Sonneveld S, Verhagen BMP et al. 2019. Single-molecule imaging uncovers rules governing nonsense-mediated mRNA decay. Mol. Cell 75:324–39.e11
    [Google Scholar]
42. 42. 

    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]
43. 43. 

    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]
44. 44. 

    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 347:1367–71
    [Google Scholar]
45. 45. 

    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]
46. 46. 

    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]
47. 47. 

    Garcia JF, Parker R. 2016. Ubiquitous accumulation of 3′ mRNA decay fragments in Saccharomyces cerevisiae mRNAs with chromosomally integrated MS2 arrays. RNA 22:657–59
    [Google Scholar]
48. 48. 

    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]
49. 49. 

    Das S, Moon HC, Singer RH, Park HY 2018. A transgenic mouse for imaging activity-dependent dynamics of endogenous Arc mRNA in live neurons. Sci. Adv. 4:eaar3448
    [Google Scholar]
50. 50. 

    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]
51. 51. 

    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]
52. 52. 

    Paige JS, Wu KY, Jaffrey SR 2011. RNA mimics of green fluorescent protein. Science 333:642–46
    [Google Scholar]
53. 53. 

    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]
54. 54. 

    Autour A, Jeng SCY, Cawte AD, Abdolahzadeh A, Galli A et al. 2018. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Nat. Commun. 9:656
    [Google Scholar]
55. 55. 

    Braselmann E, Wierzba AJ, Polaski JT, Chrominski M, Holmes ZE et al. 2018. A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells. Nat. Chem. Biol. 14:964–71
    [Google Scholar]
56. 56. 

    Chen X, Zhang D, Su N, Bao B, Xie X et al. 2019. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat. Biotechnol. 37:1287–93
    [Google Scholar]
57. 57. 

    Wu J, Zaccara S, Khuperkar D, Kim H, Tanenbaum ME, Jaffrey SR 2019. Live imaging of mRNA using RNA-stabilized fluorogenic proteins. Nat. Methods 16:862–65
    [Google Scholar]
58. 58. 

    Tyagi S, Kramer FR. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303–8
    [Google Scholar]
59. 59. 

    Chen AK, Davydenko O, Behlke MA, Tsourkas A 2010. Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells. Nucleic Acids Res 38:e148
    [Google Scholar]
60. 60. 

    Yang Y, Chen M, Krueger CJ, Tsourkas A, Chen AK 2018. Quantifying gene expression in living cells with ratiometric bimolecular beacons. Methods Mol. Biol. 1649:231–42
    [Google Scholar]
61. 61. 

    Zhang X, Zajac AL, Huang L, Behlke MA, Tsourkas A 2014. Imaging the directed transport of single engineered RNA transcripts in real-time using ratiometric bimolecular beacons. PLOS ONE 9:e85813
    [Google Scholar]
62. 62. 

    Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG 2013. Fluorescent probes for nucleic acid visualization in fixed and live cells. Molecules 18:15357–97
    [Google Scholar]
63. 63. 

    Oomoto I, Suzuki-Hirano A, Umeshima H, Han YW, Yanagisawa H et al. 2015. ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues. Nucleic Acids Res 43:e126
    [Google Scholar]
64. 64. 

    Yoshimura H. 2018. Live cell imaging of endogenous RNAs using Pumilio homology domain mutants: principles and applications. Biochemistry 57:200–8
    [Google Scholar]
65. 65. 

    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]
66. 66. 

    Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J et al. 2017. RNA targeting with CRISPR-Cas13. Nature 550:280–84
    [Google Scholar]
67. 67. 

    Yuan K, Shermoen AW, O'Farrell PH 2014. Illuminating DNA replication during Drosophila development using TALE-lights. Curr. Biol. 24:R144–45
    [Google Scholar]
68. 68. 

    Duriez B, Chilaka S, Bercher JF, Hercul E, Prioleau MN 2019. Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase. Nucleic Acids Res 47:5155–69
    [Google Scholar]
69. 69. 

    Dovrat D, Dahan D, Sherman S, Tsirkas I, Elia N, Aharoni A 2018. A live-cell imaging approach for measuring DNA replication rates. Cell Rep 24:252–58
    [Google Scholar]
70. 70. 

    Gallardo F, Laterreur N, Cusanelli E, Ouenzar F, Querido E et al. 2011. Live cell imaging of telomerase RNA dynamics reveals cell cycle-dependent clustering of telomerase at elongating telomeres. Mol. Cell 44:819–27
    [Google Scholar]
71. 71. 

    Yamada T, Yoshimura H, Shimada R, Hattori M, Eguchi M et al. 2016. Spatiotemporal analysis with a genetically encoded fluorescent RNA probe reveals TERRA function around telomeres. Sci. Rep. 6:38910
    [Google Scholar]
72. 72. 

    Avogaro L, Querido E, Dalachi M, Jantsch MF, Chartrand P, Cusanelli E 2018. Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells. RNA Biol 15:787–96
    [Google Scholar]
73. 73. 

    Cusanelli E, Romero CA, Chartrand P 2013. Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres. Mol. Cell 51:780–91
    [Google Scholar]
74. 74. 

    Laprade H, Lalonde M, Guerit D, Chartrand P 2017. Live-cell imaging of budding yeast telomerase RNA and TERRA. Methods 114:46–53
    [Google Scholar]
75. 75. 

    Gilbert N. 2019. Biophysical regulation of local chromatin structure. Curr. Opin. Genet. Dev. 55:66–75
    [Google Scholar]
76. 76. 

    Robson MI, Ringel AR, Mundlos S 2019. Regulatory landscaping: how enhancer-promoter communication is sculpted in 3D. Mol. Cell 74:1110–22
    [Google Scholar]
77. 77. 

    Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–93
    [Google Scholar]
78. 78. 

    Szabo Q, Bantignies F, Cavalli G 2019. Principles of genome folding into topologically associating domains. Sci. Adv. 5:eaaw1668
    [Google Scholar]
79. 79. 

    Fabre PJ, Benke A, Manley S, Duboule D 2015. Visualizing the HoxD gene cluster at the nanoscale level. Cold Spring Harb. Symp. Quant. Biol. 80:9–16
    [Google Scholar]
80. 80. 

    Bintu B, Mateo LJ, Su JH, Sinnott-Armstrong NA, Parker M et al. 2018. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362:eaau1783
    [Google Scholar]
81. 81. 

    Hansen AS, Pustova I, Cattoglio C, Tjian R, Darzacq X 2017. CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife 6:e25776
    [Google Scholar]
82. 82. 

    Hansen AS, Hsieh TS, Cattoglio C, Pustova I, Saldana-Meyer R et al. 2019. Distinct classes of chromatin loops revealed by deletion of an RNA-binding region in CTCF. Mol. Cell 76:395–411.e13
    [Google Scholar]
83. 83. 

    Nagashima R, Hibino K, Ashwin SS, Babokhov M, Fujishiro S et al. 2019. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J. Cell Biol. 218:1511–30
    [Google Scholar]
84. 84. 

    Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R et al. 2004. From silencing to gene expression: real-time analysis in single cells. Cell 116:683–98
    [Google Scholar]
85. 85. 

    Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH 2017. Phase separation drives heterochromatin domain formation. Nature 547:241–45
    [Google Scholar]
86. 86. 

    Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB et al. 2017. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547:236–40
    [Google Scholar]
87. 87. 

    Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z et al. 2013. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503:290–94
    [Google Scholar]
88. 88. 

    Lim B, Heist T, Levine M, Fukaya T 2018. Visualization of transvection in living Drosophila embryos. Mol. Cell 70:287–96.e6
    [Google Scholar]
89. 89. 

    Tsai A, Singer RH, Crocker J 2018. Transvection goes live—visualizing enhancer-promoter communication between chromosomes. Mol. Cell 70:195–96
    [Google Scholar]
90. 90. 

    Wang H, Xu X, Nguyen CM, Liu Y, Gao Y et al. 2018. CRISPR-mediated programmable 3D genome positioning and nuclear organization. Cell 175:1405–17.e14
    [Google Scholar]
91. 91. 

    Dultz E, Mancini R, Polles G, Vallotton P, Alber F, Weis K 2018. Quantitative imaging of chromatin decompaction in living cells. Mol. Biol. Cell 29:1763–77
    [Google Scholar]
92. 92. 

    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]
93. 93. 

    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]
94. 94. 

    Canzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL et al. 2019. Antisense lncRNA transcription mediates DNA demethylation to drive stochastic protocadherin α promoter choice. Cell 177:639–53.e15
    [Google Scholar]
95. 95. 

    Masui O, Bonnet I, Le Baccon P, Brito I, Pollex T et al. 2011. Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell 145:447–58
    [Google Scholar]
96. 96. 

    Chen CK, Blanco M, Jackson C, Aznauryan E, Ollikainen N et al. 2016. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science 354:468–72
    [Google Scholar]
97. 97. 

    Pollex T, Heard E. 2019. Nuclear positioning and pairing of X-chromosome inactivation centers are not primary determinants during initiation of random X-inactivation. Nat. Genet. 51:285–95
    [Google Scholar]
98. 98. 

    Ng K, Daigle N, Bancaud A, Ohhata T, Humphreys P et al. 2011. A system for imaging the regulatory noncoding Xist RNA in living mouse embryonic stem cells. Mol. Biol. Cell 22:2634–45
    [Google Scholar]
99. 99. 

    Ha N, Lai LT, Chelliah R, Zhen Y, Yi Vanessa SP et al. 2018. Live-cell imaging and functional dissection of Xist RNA reveal mechanisms of X chromosome inactivation and reactivation. iScience 8:1–14
    [Google Scholar]
100. 100. 

     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 14:987–94
     [Google Scholar]
101. 101. 

     Liu Z, Legant WR, Chen BC, Li L, Grimm JB et al. 2014. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. eLife 3:e04236
     [Google Scholar]
102. 102. 

     Presman DM, Ball DA, Paakinaho V, Grimm JB, Lavis LD et al. 2017. Quantifying transcription factor binding dynamics at the single-molecule level in live cells. Methods 123:76–88
     [Google Scholar]
103. 103. 

     Bothma JP, Norstad MR, Alamos S, Garcia HG 2018. LlamaTags: a versatile tool to image transcription factor dynamics in live embryos. Cell 173:1810–22.e16
     [Google Scholar]
104. 104. 

     Cho WK, Spille JH, Hecht M, Lee C, Li C et al. 2018. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 361:412–15
     [Google Scholar]
105. 105. 

     Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA 2017. A phase separation model for transcriptional control. Cell 169:13–23
     [Google Scholar]
106. 106. 

     Lu H, Yu D, Hansen AS, Ganguly S, Liu R et al. 2018. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Nature 558:318–23
     [Google Scholar]
107. 107. 

     Plys AJ, Kingston RE. 2018. Dynamic condensates activate transcription. Science 361:329–30
     [Google Scholar]
108. 108. 

     Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM et al. 2018. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 361:eaar2555
     [Google Scholar]
109. 109. 

     Chowdhary S, Kainth AS, Gross DS 2017. Heat shock protein genes undergo dynamic alteration in their three-dimensional structure and genome organization in response to thermal stress. Mol. Cell. Biol 37:e00292-17 Erratum. 2018 Mol. Cell. Biol 38:e00069–18
     [Google Scholar]
110. 110. 

     Vera M, Pani B, Griffiths LA, Muchardt C, Abbott CM et al. 2014. The translation elongation factor eEF1A1 couples transcription to translation during heat shock response. eLife 3:e03164
     [Google Scholar]
111. 111. 

     Khanna N, Hu Y, Belmont AS 2014. HSP70 transgene directed motion to nuclear speckles facilitates heat shock activation. Curr. Biol. 24:1138–44
     [Google Scholar]
112. 112. 

     Vitor AC, Sridhara SC, Sabino JC, Afonso AI, Grosso AR et al. 2019. Single-molecule imaging of transcription at damaged chromatin. Sci. Adv. 5:eaau1249
     [Google Scholar]
113. 113. 

     Lionnet T, Singer RH. 2012. Transcription goes digital. EMBO Rep 13:313–21
     [Google Scholar]
114. 114. 

     Nicolas D, Zoller B, Suter DM, Naef F 2018. Modulation of transcriptional burst frequency by histone acetylation. PNAS 115:7153–58
     [Google Scholar]
115. 115. 

     Chen LF, Lin YT, Gallegos DA, Hazlett MF, Gomez-Schiavon M et al. 2019. Enhancer histone acetylation modulates transcriptional bursting dynamics of neuronal activity-inducible genes. Cell Rep 26:1174–88.e5
     [Google Scholar]
116. 116. 

     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]
117. 117. 

     Hocine S, Vera M, Zenklusen D, Singer RH 2015. Promoter-autonomous functioning in a controlled environment using single molecule FISH. Sci. Rep. 5:9934
     [Google Scholar]
118. 118. 

     Das S, Singer RH, Yoon YJ 2019. The travels of mRNAs in neurons: Do they know where they are going?. Curr. Opin. Neurobiol. 57:110–16
     [Google Scholar]
119. 119. 

     Eliscovich C, Singer RH. 2017. RNP transport in cell biology: the long and winding road. Curr. Opin. Cell Biol. 45:38–46
     [Google Scholar]
120. 120. 

     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]
121. 121. 

     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]
122. 122. 

     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]
123. 123. 

     Vargas DY, Shah K, Batish M, Levandoski M, Sinha S et al. 2011. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147:1054–65
     [Google Scholar]
124. 124. 

     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]
125. 125. 

     Ma J, Liu Z, Michelotti N, Pitchiaya S, Veerapaneni R et al. 2013. High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat. Commun. 4:2414
     [Google Scholar]
126. 126. 

     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]
127. 127. 

     Ben-Yishay R, Mor A, Shraga A, Ashkenazy-Titelman A, Kinor N et al. 2019. Imaging within single NPCs reveals NXF1’s role in mRNA export on the cytoplasmic side of the pore. J. Cell Biol. 218:2962–81
     [Google Scholar]
128. 128. 

     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]
129. 129. 

     Sambandan S, Akbalik G, Kochen L, Rinne J, Kahlstatt J et al. 2017. Activity-dependent spatially localized miRNA maturation in neuronal dendrites. Science 355:634–37
     [Google Scholar]
130. 130. 

     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]
131. 131. 

     Eliscovich C, Shenoy SM, Singer RH 2017. Imaging mRNA and protein interactions within neurons. PNAS 114:E1875–84
     [Google Scholar]
132. 132. 

     Biswas J, Liu Y, Singer RH, Wu B 2019. Fluorescence imaging methods to investigate translation in single cells. Cold Spring Harb. Perspect. Biol. 11:a032722
     [Google Scholar]
133. 133. 

     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]
134. 134. 

     Liao YC, 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 179:147–64.e20
     [Google Scholar]
135. 135. 

     Bauer KE, Segura I, Gaspar I, Scheuss V, Illig C et al. 2019. Live cell imaging reveals 3′-UTR dependent mRNA sorting to synapses. Nat. Commun. 10:3178
     [Google Scholar]
136. 136. 

     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]
137. 137. 

     Moissoglu K, Yasuda K, Wang T, Chrisafis G, Mili S 2019. Translational regulation of protrusion-localized RNAs involves silencing and clustering after transport. eLife 8:e44752
     [Google Scholar]
138. 138. 

     Pizzinga M, Bates C, Lui J, Forte G, Morales-Polanco F et al. 2019. Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth. J. Cell Biol. 218:1564–81
     [Google Scholar]
139. 139. 

     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]
140. 140. 

     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]
141. 141. 

     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]
142. 142. 

     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]
143. 143. 

     Yan X, Hoek TA, Vale RD, Tanenbaum ME 2016. Dynamics of translation of single mRNA molecules in vivo. Cell 165:976–89
     [Google Scholar]
144. 144. 

     Boersma S, Khuperkar D, Verhagen BMP, Sonneveld S, Grimm JB et al. 2019. Multi-color single-molecule imaging uncovers extensive heterogeneity in mRNA decoding. Cell 178:458–72.e19
     [Google Scholar]
145. 145. 

     Lyon K, Aguilera LU, Morisaki T, Munsky B, Stasevich TJ 2019. Live-cell single RNA imaging reveals bursts of translational frameshifting. Mol. Cell 75:172–83.e9
     [Google Scholar]
146. 146. 

     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
     [Google Scholar]
147. 147. 

     Pitchiaya S, Mourao MDA, Jalihal AP, Xiao L, Jiang X et al. 2019. Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality. Mol. Cell 74:521–33.e6
     [Google Scholar]
148. 148. 

     Heyer EE, Moore MJ. 2016. Redefining the translational status of 80S monosomes. Cell 164:757–69
     [Google Scholar]
149. 149. 

     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]
150. 150. 

     El-Brolosy MA, Kontarakis Z, Rossi A, Kuenne C, Gunther S et al. 2019. Genetic compensation triggered by mutant mRNA degradation. Nature 568:193–97
     [Google Scholar]
151. 151. 

     Ma Z, Zhu P, Shi H, Guo L, Zhang Q et al. 2019. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature 568:259–63
     [Google Scholar]
152. 152. 

     Zheng Q, Ayala AX, Chung I, Weigel AV, Ranjan A et al. 2019. Rational design of fluorogenic and spontaneously blinking labels for super-resolution imaging. ACS Cent. Sci. 5:1602–13
     [Google Scholar]
153. 153. 

     Jradi FM, Lavis LD. 2019. Chemistry of photosensitive fluorophores for single-molecule localization microscopy. ACS Chem. Biol. 14:1077–90
     [Google Scholar]
154. 154. 

     Greer CJ, Holy TE. 2019. Fast objective coupled planar illumination microscopy. Nat. Commun. 10:4483
     [Google Scholar]
155. 155. 

     Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC 2018. Recent progress in light sheet microscopy for biological applications. Appl. Spectrosc. 72:1137–69
     [Google Scholar]
156. 156. 

     Hansen AS, Woringer M, Grimm JB, Lavis LD, Tjian R, Darzacq X 2018. Robust model-based analysis of single-particle tracking experiments with Spot-On. eLife 7:e33125
     [Google Scholar]
157. 157. 

     Chen M, Ma Z, Wu X, Mao S, Yang Y et al. 2017. A molecular beacon-based approach for live-cell imaging of RNA transcripts with minimal target engineering at the single-molecule level. Sci. Rep. 7:1550
     [Google Scholar]
158. 158. 

     Baker MB, Bao G, Searles CD 2013. The use of molecular beacons to detect and quantify microRNA. Methods Mol Biol 1039:279–87
     [Google Scholar]
159. 159. 

     Ozawa T, Natori Y, Sato M, Umezawa Y 2007. Imaging dynamics of endogenous mitochondrial RNA in single living cells. Nat. Methods 4:413–19
     [Google Scholar]
160. 160. 

     Zinskie JA, Roig M, Janetopoulos C, Myers KA, Bruist MF 2018. Live-cell imaging of small nucleolar RNA tagged with the Broccoli aptamer in yeast. FEMS Yeast Res 18:foy093
     [Google Scholar]
161. 160a. 

     Ye H, Rong Z, Lin Y 2017. Live cell imaging of genomic loci using dCas9-SunTag system and a bright fluorescent protein. Protein Cell 8(11):853–55
     [Google Scholar]
162. 161. 

     Xue Y, Acar M. 2018. Live-cell imaging of chromatin condensation dynamics by CRISPR. iScience 4:216–35
     [Google Scholar]