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Illuminating RNA biology through imaging

Abstract

RNA processing plays a central role in accurately transmitting genetic information into functional RNA and protein regulators. To fully appreciate the RNA life-cycle, tools to observe RNA with high spatial and temporal resolution are critical. Here we review recent advances in RNA imaging and highlight how they will propel the field of RNA biology. We discuss current trends in RNA imaging and their potential to elucidate unanswered questions in RNA biology.

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Fig. 1: Timeline of subcellular RNA imaging technologies.
Fig. 2: Highlights of RNA biological insights gained through RNA imaging.
Fig. 3: The outlook towards a multidimensional approach to study RNA biology.

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References

  1. Singer, R. H. & Ward, D. C. Actin gene expression visualized in chicken muscle tissue culture by using in situ hybridization with a biotinated nucleotide analog. Proc. Natl Acad. Sci. USA 79, 7331–7335 (1982).

    PubMed Central  Google Scholar 

  2. Femino, A. M., Fay, F. S., Fogarty, K. & Singer, R. H. Visualization of single RNA transcripts in situ. Science 280, 585–590 (1998).

    Article  CAS  PubMed  Google Scholar 

  3. Raj, A., Bogaard, P., van den Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877–879 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Larsson, C. et al. In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat. Methods 1, 227–232 (2004).

    Article  CAS  PubMed  Google Scholar 

  5. Larsson, C., Grundberg, I., Söderberg, O. & Nilsson, M. In situ detection and genotyping of individual mRNA molecules. Nat. Methods 7, 395–397 (2010).

    Article  CAS  PubMed  Google Scholar 

  6. Wang, F. et al. RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. J. Mol. Diagnostics 14, 22–29 (2012).

    Article  CAS  Google Scholar 

  7. Rouhanifard, S. H. et al. ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Nat. Biotechnol. 37, 84–89 (2018).

    Article  CAS  Google Scholar 

  8. Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28, 1208–1212 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kishi, J. Y. et al. SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat. Methods 16, 533–544 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Tsanov, N. et al. smiFISH and FISH-quant—a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res. 44, e165 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Levesque, M. J., Ginart, P., Wei, Y. & Raj, A. Visualizing SNVs to quantify allele-specific expression in single cells. Nat. Methods 10, 865–867 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Mellis, I. A., Gupte, R., Raj, A. & Rouhanifard, S. H. Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Nat. Methods 14, 801–804 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Levsky, J. M., Shenoy, S. M., Pezo, R. C. & Singer, R. H. Single-cell gene expression profiling. Science 297, 836–840 (2002).

    Article  CAS  PubMed  Google Scholar 

  14. Lubeck, E., Coskun, A. F., Zhiyentayev, T., Ahmad, M. & Cai, L. Single-cell in situ RNA profiling by sequential hybridization. Nat. Methods 11, 360–361 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA 116, 19490–19499 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature 568, 235–239 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Wang, G., Moffitt, J. R. & Zhuang, X. Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. Sci. Rep. 8, 4847 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Ke, R. et al. In situ sequencing for RNA analysis in preserved tissue and cells. Nat. Methods 10, 857–860 (2013).

    Article  CAS  PubMed  Google Scholar 

  20. Gyllborg, D. et al. Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue. Nucleic Acids Res. 48, e112 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chen, X., Sun, Y.-C., Church, G. M., Lee, J. H. & Zador, A. M. Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res. 46, e22 (2018).

    Article  CAS  PubMed  Google Scholar 

  22. Wang, X. et al. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 361, eaat5691 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Lee, J. H. et al. Highly multiplexed subcellular RNA sequencing in situ. Science 343, 1360–1363 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Lee, J. H. et al. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat. Protoc. 10, 442–458 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Alon, S. et al. Expansion sequencing: spatially precise in situ transcriptomics in intact biological systems. Science 371, eaax2656 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Cho, C.-S. et al. Microscopic examination of spatial transcriptome using Seq-Scope. Cell 184, 3559–3572 (2021).

    Article  CAS  PubMed  Google Scholar 

  27. Glotzer, J. B., Saffrich, R., Glotzer, M. & Ephrussi, A. Cytoplasmic flows localize injected oskar RNA in Drosophila oocytes. Curr. Biol. 7, 326–337 (1997).

    Article  CAS  PubMed  Google Scholar 

  28. Wilkie, G. S. & Davis, I. Drosophila wingless and pair-rule transcripts localize apically by dynein-mediated transport of RNA particles. Cell 105, 209–219 (2001).

    Article  CAS  PubMed  Google Scholar 

  29. Cha, B. J., Koppetsch, B. S. & Theurkauf, W. E. In vivo analysis of drosophila bicoid mRNA localization reveals a novel microtubule-dependent axis specification pathway. Cell 106, 35–46 (2001).

    Article  CAS  PubMed  Google Scholar 

  30. Bao, G., Rhee, W. J. & Tsourkas, A. Fluorescent probes for live-cell RNA detection. Annu. Rev. Biomed. Eng. 11, 25–47 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Bertrand, E. et al. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2, 437–445 (1998).

    Article  CAS  PubMed  Google Scholar 

  32. Fusco, D. et al. Single mRNA molecules demonstrate probabilistic movement in living mammalian cells. Curr. Biol. 13, 161–167 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Wu, B. et al. Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences. Genes Dev. 29, 876–886 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Tutucci, E. et al. An improved MS2 system for accurate reporting of the mRNA life cycle. Nat. Methods 15, 81–89 (2018).

    Article  CAS  PubMed  Google Scholar 

  35. Park, S. Y., Moon, H. C. & Park, H. Y. Live-cell imaging of single mRNA dynamics using split superfolder green fluorescent proteins with minimal background. RNA 26, 101–109 (2020).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Wu, B., Chen, J. & Singer, R. H. Background free imaging of single mRNAs in live cells using split fluorescent proteins. Sci. Rep. 4, 3615 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Shao, S. et al. TagBiFC technique allows long-term single-molecule tracking of protein-protein interactions in living cells. Commun. Biol. 4, 378 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Chen, J. et al. High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis. Proc. Natl Acad. Sci. USA 106, 13535–13540 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Takizawa, P. A. & Vale, R. D. The myosin motor, Myo4p, binds Ash1 mRNA via the adapter protein, She3p. Proc. Natl Acad. Sci. USA 97, 5273–5278 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Wu, B., Buxbaum, A. R., Katz, Z. B., Yoon, Y. J. & Singer, R. H. Quantifying protein-mRNA interactions in single live cells. Cell 162, 211–220 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Brodsky, A. S. & Silver, P. A. Pre-mRNA processing factors are required for nuclear export. RNA 6, 1737–1749 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Daigle, N. & Ellenberg, J. λN-GFP: an RNA reporter system for live-cell imaging. Nat. Methods 4, 633–636 (2007).

    Article  CAS  PubMed  Google Scholar 

  43. Bos, T. J., Nussbacher, J. K., Aigner, S. & Yeo, G. W. in Advances in Experimental Medicine and Biology Vol. 907, 61–88 (Springer, 2016).

  44. Hocine, S., Raymond, P., Zenklusen, D., Chao, J. A. & Singer, R. H. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat. Methods 10, 119–121 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  45. Park, H. Y. et al. Visualization of dynamics of single endogenous mRNA labeled in live mouse. Science 343, 422–424 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Paige, J. S., Wu, K. Y. & Jaffrey, S. R. RNA mimics of green fluorescent protein. Science 333, 642–646 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Strack, R. L., Disney, M. D. & Jaffrey, S. R. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat. Methods 10, 1219–1224 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Wu, J. et al. Live imaging of mRNA using RNA-stabilized fluorogenic proteins. Nat. Methods 16, 862–865 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Filonov, G. S., Moon, J. D., Svensen, N. & Jaffrey, S. R. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 136, 16299–16308 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Dolgosheina, E. V. et al. RNA Mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem. Biol. 9, 2412–2420 (2014).

    Article  CAS  PubMed  Google Scholar 

  51. Kong, K. Y. S., Jeng, S. C. Y., Rayyan, B. & Unrau, P. J. RNA Peach and Mango: orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands. RNA 27, 604–615 (2021).

    Article  CAS  PubMed Central  Google Scholar 

  52. Cawte, A. D., Unrau, P. J. & Rueda, D. S. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays. Nat. Commun. 11, 1283 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Tyagi, S. & Kramer, F. R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303–308 (1996).

    Article  CAS  PubMed  Google Scholar 

  54. Bratu, D. P., Cha, B.-J., Mhlanga, M. M., Kramer, F. R. & Tyagi, S. Visualizing the distribution and transport of mRNAs in living cells. Proc. Natl Acad. Sci. USA 100, 13308–13313 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Tyagi, S. Imaging intracellular RNA distribution and dynamics in living cells. Nat. Methods 6, 331–338 (2009).

    Article  CAS  PubMed  Google Scholar 

  56. Turner-Bridger, B. et al. Single-molecule analysis of endogenous β-actin mRNA trafficking reveals a mechanism for compartmentalized mRNA localization in axons. Proc. Natl Acad. Sci. USA 115, E9697–E9706 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Cioni, J. M. et al. Late endosomes act as mRNA translation platforms and sustain mitochondria in axons. Cell 176, 56–72 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Wong, H. H. W. et al. RNA docking and local translation regulate site-specific axon remodeling in vivo. Neuron 95, 852–868 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Piper, M. et al. Differential requirement of F-actin and microtubule cytoskeleton in cue-induced local protein synthesis in axonal growth cones. Neural Dev. 10, 3 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  60. O’Connell, M. R. et al. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516, 263–266 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  61. Nelles, D. A. et al. Programmable RNA tracking in live cells with CRISPR/Cas9 resource programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165, 488–496 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Abudayyeh, O. O. et al. RNA targeting with CRISPR-Cas13. Nature 550, 280–284 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Yang, L. Z. et al. Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems. Mol. Cell 76, 981–997 (2019).

    Article  CAS  PubMed  Google Scholar 

  64. Chubb, J. R., Trcek, T., Shenoy, S. M. & Singer, R. H. Transcriptional pulsing of a developmental gene. Curr. Biol. 16, 1018–1025 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Golding, I., Paulsson, J., Zawilski, S. M. & Cox, E. C. Real-time kinetics of gene activity in individual bacteria. Cell 123, 1025–1036 (2005).

    Article  CAS  PubMed  Google Scholar 

  66. Darzacq, X. et al. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14, 796–806 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Tantale, K. et al. A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting. Nat. Commun. 7, 12248 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Larson, D. R., Zenklusen, D., Wu, B., Chao, J. A. & Singer, R. H. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332, 475–478 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Donovan, B. T. et al. Live-cell imaging reveals the interplay between transcription factors, nucleosomes and bursting. EMBO J. 38, e100809 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Sinha, D. K., Banerjee, B., Maharana, S. & Shivashankar, G. V. Probing the dynamic organization of transcription compartments and gene loci within the nucleus of living cells. Biophys. J. 95, 5432–5438 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Shah, S. et al. Dynamics and spatial genomics of the nascent transcriptome by intron seqFISH. Cell 174, 363–376 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Su, J. H., Zheng, P., Kinrot, S. S., Bintu, B. & Zhuang, X. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Cell 182, 1641–1659 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Feldman, D. et al. Optical pooled screens in human cells. Cell 179, 787–799 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Baurén, G. & Wieslander, L. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76, 183–192 (1994).

    Article  PubMed  Google Scholar 

  75. Vargas, D. Y. et al. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147, 1054–1065 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Brody, Y. et al. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol. 9, 1000573 (2011).

    Article  CAS  Google Scholar 

  77. Martin, R. M., Rino, J., Carvalho, C., Kirchhausen, T. & Carmo-Fonseca, M. Live-cell visualization of Pre-mRNA splicing with single-molecule sensitivity. Cell Rep. 4, 1144–1155 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Coulon, A. et al. Kinetic competition during the transcription cycle results in stochastic RNA processing. eLife 3, e03939 (2014).

    Article  PubMed Central  Google Scholar 

  79. Waks, Z., Klein, A. M. & Silver, P. A. Cell-to-cell variability of alternative RNA splicing. Mol. Syst. Biol. 7, 506 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  80. Wu, K. E., Parker, K. R., Fazal, F. M., Chang, H. Y. & Zou, J. RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing. RNA 26, 851–865 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Mattioli, C. C. et al. Alternative 3′UTRs direct localization of functionally diverse protein isoforms in neuronal compartments. Nucleic Acids Res. 47, 2560–2573 (2019).

    Article  CAS  Google Scholar 

  82. Fazal, F. M. et al. Atlas of subcellular RNA localization revealed by APEX-Seq. Cell 178, 473–490 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Dynes, J. L. & Steward, O. Dynamics of bidirectional transport of Arc mRNA in neuronal dendrites. J. Comp. Neurol. 500, 433–447 (2007).

    Article  CAS  PubMed  Google Scholar 

  84. Vargas, D. Y., Raj, A., Marras, S. A. E., Kramer, F. R. & Tyagi, S. Mechanism of mRNA transport in the nucleus. Proc. Natl Acad. Sci. USA 102, 17008–17013 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Mor, A. et al. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat. Cell Biol. 12, 543–552 (2010).

    Article  CAS  PubMed  Google Scholar 

  86. Grünwald, D. & Singer, R. H. In vivo imaging of labelled endogenous Β-actin mRNA during nucleocytoplasmic transport. Nature 467, 604–607 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  87. Carson, J. H. et al. Multiplexed RNA trafficking in oligodendrocytes and neurons. Biochim. Biophys. Acta 1779, 453–458 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Gao, Y., Tatavarty, V., Korza, G., Levin, M. K. & Carson, J. H. Multiplexed dendritic targeting of α calcium calmodulin-dependent protein kinase II, neurogranin, and activity-regulated cytoskeleton-associated protein RNAs by the A2 pathway. Mol. Biol. Cell 19, 2311–2327 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Tübing, F. et al. Dendritically localized transcripts are sorted into distinct ribonucleoprotein particles that display fast directional motility along dendrites of hippocampal neurons. J. Neurosci. 30, 4160–4170 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  90. Batish, M., Van Den Bogaard, P., Kramer, F. R. & Tyagi, S. Neuronal mRNAs travel singly into dendrites. Proc. Natl Acad. Sci. USA 109, 4645–4650 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Rodrigues, E. C., Grawenhoff, J., Baumann, S. J., Lorenzon, N. & Maurer, S. P. Mammalian neuronal mRNA transport complexes: the few knowns and the many unknowns. Front. Integr. Neurosci. 15, 692948 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Ya-Cheng Liao, A. et al. RNA granules hitchhike on lysosomes for long-distance transport, using annexin A11 as a molecular tether. Cell 179, 147–164 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  93. Medioni, C., Mowry, K. & Besse, F. Principles and roles of mRNA localization in animal development. Development 139, 3263–3276 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Kloc, M., Zearfoss, N. R. & Etkin, L. D. Mechanisms of subcellular mRNA localization. Cell 108, 533–544 (2002).

    Article  CAS  PubMed  Google Scholar 

  95. Engel, K. L., Arora, A., Goering, R., Lo, H.-Y. G. & Taliaferro, J. M. Mechanisms and consequences of subcellular RNA localization across diverse cell types. Traffic 21, 404–418 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Fernandopulle, M. S., Lippincott-Schwartz, J. & Ward, M. E. RNA transport and local translation in neurodevelopmental and neurodegenerative disease. Nat. Neurosci. 24, 622–632 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Thelen, M. P. & Kye, M. J. The role of RNA binding proteins for local mRNA translation: implications in neurological disorders. Front. Mol. Biosci. 6, 161 (2020).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  98. Lawrence, J. B. & Singer, R. H. Intracellular localization of messenger RNAs for cytoskeletal proteins. Cell 45, 407–415 (1986).

    Article  CAS  PubMed  Google Scholar 

  99. Stoeger, T., Battich, N., Herrmann, M. D., Yakimovich, Y. & Pelkmans, L. Computer vision for image-based transcriptomics. Methods 85, 44–53 (2015).

    Article  CAS  PubMed  Google Scholar 

  100. Samacoits, A. et al. A computational framework to study sub-cellular RNA localization. Nat. Commun. 9, 4584 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Petukhov, V. et al. Cell segmentation in imaging-based spatial transcriptomics. Nat. Biotechnol. 40, 345–354 (2021).

    Article  PubMed  CAS  Google Scholar 

  102. Battich, N., Stoeger, T. & Pelkmans, L. Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nat. Methods 10, 1127–1133 (2013).

    Article  CAS  PubMed  Google Scholar 

  103. Yoon, Y. J. et al. Glutamate-induced RNA localization and translation in neurons. Proc. Natl Acad. Sci. USA 113, E6877–E6886 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Moor, A. E. et al. Global mRNA polarization regulates translation efficiency in the intestinal epithelium. Science 357, 1299–1303 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Chouaib, R. et al. A dual protein-mRNA localization screen reveals compartmentalized translation and widespread co-translational RNA targeting. Dev. Cell 54, 773–791 (2020).

    Article  CAS  PubMed  Google Scholar 

  106. Turner-Bridger, B., Caterino, C. & Cioni, J. M. Molecular mechanisms behind mRNA localization in axons: axonal mRNA localisation. Open Biol. 10, 200177 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Halstead, J. M. et al. An RNA biosensor for imaging the first round of translation from single cells to living animals. Science 347, 1367–1671 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Wu, B., Eliscovich, C., Yoon, Y. J. & Singer, R. H. Translation dynamics of single mRNAs in live cells and neurons. Science 352, 1430–1435 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Morisaki, T. et al. Real-time quantification of single RNA translation dynamics in living cells. Science 352, 1425–1429 (2016).

    Article  CAS  PubMed  Google Scholar 

  110. Adivarahan, S. et al. Spatial organization of single mRNPs at different stages of the gene expression pathway. Mol. Cell 72, 727–738 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Wilbertz, J. H. et al. Single-molecule imaging of mRNA localization and regulation during the integrated stress response. Mol. Cell 73, 946–958 (2019).

    Article  CAS  PubMed  Google Scholar 

  112. Mateju, D. et al. Single-molecule imaging reveals translation of mRNAs localized to stress granules. Cell 183, 1801–1812 (2020).

    Article  CAS  PubMed  Google Scholar 

  113. Trcek, T., Larson, D. R., Moldón, A., Query, C. C. & Singer, R. H. Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell 147, 1484–1497 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Horvathova, I. et al. The dynamics of mRNA turnover revealed by single-molecule imaging in single cells. Mol. Cell 68, 615–625 (2017).

    Article  CAS  PubMed  Google Scholar 

  115. Sheth, U. & Parker, R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300, 805–808 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Tanenbaum, M. E., Gilbert, L. A., Qi, L. S., Weissman, J. S. & Vale, R. D. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635–646 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Hoek, T. A. et al. Single-molecule imaging uncovers rules governing nonsense-mediated mRNA decay. Mol. Cell 75, 324–339 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Parton, R. M., Davidson, A., Davis, I. & Weil, T. T. Subcellular mRNA localisation at a glance. J. Cell Sci. 127, 2127–2133 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Hangauer, M. J., Vaughn, I. W. & McManus, M. T. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet. 9, e1003569 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Carninci, P. Non-coding RNA transcription: turning on neighbours. Nat. Cell Biol. 109, 1023–1024 (2008).

    Article  CAS  Google Scholar 

  121. Pitchiaya, S., Androsavich, J. R. & Walter, N. G. Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly. EMBO Rep. 13, 709–715 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Pitchiaya, S., Krishnan, V., Custer, T. C. & Walter, N. G. Dissecting non-coding RNA mechanisms in cellulo by single-molecule high-resolution localization and counting. Methods 63, 188–199 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Pitchiaya, S., Heinicke, L. A., Park, J. I., Cameron, E. L. & Walter, N. G. Resolving subcellular miRNA trafficking and turnover at single-molecule resolution. Cell Rep. 19, 630–642 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Pitchiaya, S. et al. Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality. Mol. Cell 74, 521–533 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Cabili, M. N. et al. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol. 16, 20 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  126. Terranova, R. et al. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev. Cell 15, 668–679 (2008).

    Article  CAS  PubMed  Google Scholar 

  127. Nagano, T. et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322, 1717–1720 (2008).

    Article  CAS  PubMed  Google Scholar 

  128. Jouvenet, N., Simon, S. M. & Bieniasz, P. D. Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles. Proc. Natl Acad. Sci. USA 106, 19114–19119 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Chen, J. et al. Visualizing the translation and packaging of HIV-1 full-length RNA. Proc. Natl Acad. Sci. USA 117, 6145–6155 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Shaffer, S. M. et al. Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip. Lab Chip 15, 3170–3182 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Liu, F. et al. SARS-CoV-2 infects endothelial cells in vivo and in vitro. Front. Cell. Infect. Microbiol. 11, 701278 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Carossino, M. et al. Detection of SARS-CoV-2 by RNAscope® in situ hybridization and immunohistochemistry techniques. Arch. Virol. 165, 2373–2377 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Hepp, C. et al. Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridization of viral RNA. Sci. Rep. 11, 19579 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Burke, J. M., St Clair, L. A., Perera, R. & Parker, R. SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block. RNA 27, 1318–1329 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Wing, P. A. C., Keeley, T. P., Hodson, E. J., Bishop, T. & Mckeating, J. A. Hypoxic and pharmacological activation of HIF inhibits SARS-CoV-2 infection of lung epithelial cells. Cell Rep. 35, 109020 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Caicedo, J. C. et al. Data-analysis strategies for image-based cell profiling. Nat. Methods 14, 849–863 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Moen, E. et al. Deep learning for cellular image analysis. Nat. Methods 16, 1233–1246 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Ronneberger, O., Fischer, P. & Brox, T. U-Net: convolutional networks for biomedical image segmentation. Lect. Notes Comput. Sci. 9351, 234–241 (2015).

    Article  Google Scholar 

  139. Cao, Z., Pan, X., Yang, Y., Huang, Y. & Shen, H.-B. The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinformatics 34, 2185–2194 (2018).

    Article  CAS  PubMed  Google Scholar 

  140. Zhang, T. et al. RNALocate: a resource for RNA subcellular localizations. Nucleic Acids Res. 45, D135–D138 (2017).

    Article  CAS  PubMed  Google Scholar 

  141. Su, Z.-D. et al. iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC. Bioinformatics 34, 4196–4204 (2018).

    CAS  PubMed  Google Scholar 

  142. Nijssen, J., Aguila, J., Hoogstraaten, R., Kee, N. & Hedlund, E. Axon-seq decodes the motor axon transcriptome and its modulation in response to ALS. Stem Cell Rep. 11, 1565–1578 (2018).

    Article  CAS  Google Scholar 

  143. Bouvrette, L. P. B. et al. CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells. RNA 24, 98–113 (2018).

    Article  CAS  Google Scholar 

  144. Yan, Z., Lécuyer, E. & Blanchette, M. Prediction of mRNA subcellular localization using deep recurrent neural networks. Bioinformatics 35, i333–i342 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. McMahon, A. C. et al. TRIBE: hijacking an RNA-editing enzyme to identify cell-specific targets of RNA-binding proteins. Cell 165, 742–753 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Biswas, J., Rahman, R., Gupta, V., Rosbash, M. & Singer, R. H. MS2-TRIBE evaluates both protein-RNA interactions and nuclear organization of transcription by RNA editing. iScience 23, 101318 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Brannan, K. W. et al. Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. Nat. Methods 18, 507–519 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Wheeler, E. C. et al. Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors. Nat. Methods 17, 636–642 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Markmiller, S. et al. Context-dependent and disease-specific diversity in protein interactions within stress granules. Cell 172, 590–604 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Takei, Y. et al. Integrated spatial genomics reveals global architecture of single nuclei. Nature 590, 344–350 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

G.W.Y. is supported by NIH grants nos. AI132122, HG011864, NS103172, EY029166, HG004659 and HG009889. This research was partially supported by an Allen Distinguished Investigator Award to G.W.Y., a Paul G. Allen Frontiers Group advised grant of the Paul G. Allen Family Foundation. P.L. is supported by Schmidt Science Fellows. We thank M. Huang and C. Mah for their critical reading of the manuscript.

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Correspondence to Gene W. Yeo.

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G.W.Y. is a SAB member of Jumpcode Genomics and a co-founder, member of the Board of Directors, scientific advisor, equity holder and paid consultant for Locanabio and Eclipse BioInnovations. G.W.Y. is a visiting professor at the National University of Singapore. G.W.Y.’s interests have been reviewed and approved by the University of California San Diego, in accordance with its conflict-of-interest policies. The authors declare no other competing interests.

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Le, P., Ahmed, N. & Yeo, G.W. Illuminating RNA biology through imaging. Nat Cell Biol 24, 815–824 (2022). https://doi.org/10.1038/s41556-022-00933-9

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