RNA transport from transcription to localized translation: a single molecule perspective

References

• Kim SH, Vieira M, Shim JY, et al. Recent progress in single-molecule studies of mRNA localization in vivo. RNA Biol. 2019;16(9):1108–1118.
   PubMed Web of Science ®Google Scholar
• Bovaird S, Patel D, Padilla J-CA, et al. Biological functions, regulatory mechanisms, and disease relevance of RNA localization pathways. FEBS Lett. 2018;592:2948–2972.
   PubMed Web of Science ®Google Scholar
• Moore S, Järvelin AI, Davis I, et al. Expanding horizons: new roles for non-canonical RNA-binding proteins in cancer. Curr Opin Genet Dev. 2018;48:112–120.
   PubMed Web of Science ®Google Scholar
• Biswas J, Liu Y, Singer RH, et al. Fluorescence imaging methods to investigate translation in single cells. Cold Spring Harb Perspect Biol. 2019;11:a032722.
   PubMed Web of Science ®Google Scholar
• Pichon X, Lagha M, Mueller F, et al. Toolbox to image gene expression in single cells: sensitive approaches for demanding challenges. Mol Cell. 2018;71:468–480.
   PubMed Web of Science ®Google Scholar
• Sato H, Das S, Singer RH, et al. Imaging of DNA and RNA in living eukaryotic cells to reveal spatiotemporal dynamics of gene expression. Annu Rev Biochem. 2020;159–187.
   PubMed Web of Science ®Google Scholar
• Tutucci E, Livingston NM, Singer RH, et al. Imaging mRNA in vivo, from birth to death. Annu Rev Biophys. 2018;47:85–106.
   PubMed Web of Science ®Google Scholar
• Femino AM, Fay FS, Fogarty K, et al. Visualization of single RNA transcripts in situ. Science. 1998;280:585–590.
   PubMed Web of Science ®Google Scholar
• Raj A, van den Bogaard P, Rifkin SA, et al. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008;5:877–879.
   PubMed Web of Science ®Google Scholar
• Femino AM, Fogarty K, Lifshitz LM, et al. Visualization of single molecules of mRNA in situ. Methods Enzymol. 2003;361:245–304.
   PubMed Web of Science ®Google Scholar
• Moffitt JR, Zhuang X. RNA imaging with multiplexed error-robust fluorescence in situ hybridization (MERFISH). Methods Enzymol. 2016;572:1–49.
   PubMed Web of Science ®Google Scholar
• Mueller F, Senecal A, Tantale K, et al. FISH-quant: automatic counting of transcripts in 3D FISH images. Nat Methods. 2013;10(4):277–278.
   PubMed Web of Science ®Google Scholar
• Tsanov N, Samacoits A, Chouaib R, et al. smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res. 2016;44:e165.
   PubMed Web of Science ®Google Scholar
• Stringer C, Michaelos M, Pachitariu M. Cellpose: a generalist algorithm for cellular segmentation. bioRxiv. 2020;2020(2):02.931238.
   Google Scholar
• Samacoits A, Chouaib R, Safieddine A, et al. A computational framework to study sub-cellular RNA localization. Nat Commun. 2018;9:4584.
   PubMed Web of Science ®Google Scholar
• Chen KH, Boettiger AN, Moffitt JR, et al. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science. 2015;348:aaa6090.
   PubMed Web of Science ®Google Scholar
• Eng C-HL, Lawson M, Zhu Q, et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature. 2019;568:235–239.
   PubMed Web of Science ®Google Scholar
• Lubeck E, Coskun AF, Zhiyentayev T, et al. Single-cell in situ RNA profiling by sequential hybridization. Nat Methods. 2014;11:360–361.
   PubMed Web of Science ®Google Scholar
• Xia C, Fan J, Emanuel G, et al. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc Natl Acad Sci U S A. 2019;116:19490–19499.
   PubMed Web of Science ®Google Scholar
• Battich N, Stoeger T, Pelkmans L. Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nat Methods. 2013;10:1127–1133.
   PubMed Web of Science ®Google Scholar
• Safieddine A, Coleno E, Traboulsi A-M, et al. A conserved choreography of mRNAs at centrosomes reveals a localization mechanism involving active polysome transport. bioRxiv. 2020;2020(9):04.282038.
   Google Scholar
• Adivarahan S, Livingston N, Nicholson B, et al. Spatial organization of single mRNPs at different stages of the gene expression pathway. Mol Cell. 2018;72(727–738):e5.
   Google Scholar
• Khong A, Parker R. mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction. J Cell Biol. 2018;217:4124–4140.
   PubMed Web of Science ®Google Scholar
• West JA, Mito M, Kurosaka S, et al. Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J Cell Biol. 2016;214:817–830.
   PubMed Web of Science ®Google Scholar
• Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods. 2012;9:743–748.
   PubMed Web of Science ®Google Scholar
• Fang M, Xie H, Dougan SK, et al. Stochastic cytokine expression induces mixed T helper cell states. PLoS Biol. 2013;11:e1001618.
   PubMed Web of Science ®Google Scholar
• Itzkovitz S, Lyubimova A, Blat IC, et al. Single-molecule transcript counting of stem-cell markers in the mouse intestine. Nat Cell Biol. 2011;14:106–114.
   PubMed Web of Science ®Google Scholar
• Raj A, Rifkin SA, Andersen E, et al. Variability in gene expression underlies incomplete penetrance. Nature. 2010;463:913–918.
   PubMed Web of Science ®Google Scholar
• Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol. 2008;15:1263–1271.
   PubMed Web of Science ®Google Scholar
• Lécuyer E, Yoshida H, Parthasarathy N, et al. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell. 2007;131:174–187.
   PubMed Web of Science ®Google Scholar
• Chouaib R, Safieddine A, Pichon X, et al. A dual protein-mRNA localization screen reveals compartmentalized translation and widespread co-translational RNA targeting. Dev Cell. 2020;54(773–791):e5.
   PubMedGoogle Scholar
• Xia C, Babcock HP, Moffitt JR, et al. Multiplexed detection of RNA using MERFISH and branched DNA amplification. Sci Rep. 2019;9:7721.
   PubMed Web of Science ®Google Scholar
• Ainger K, Avossa D, Morgan F, et al. Transport and localization of exogenous myelin basic protein mRNA microinjected into oligodendrocytes. J Cell Biol. 1993;123:431–441.
   PubMed Web of Science ®Google Scholar
• Pillai RS, Bhattacharyya SN, Artus CG, et al. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science. 2005;309:1573–1576.
   PubMed Web of Science ®Google Scholar
• Pitchiaya S, Androsavich JR, Walter NG. Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly. EMBO Rep. 2012;13:709–715.
   PubMed Web of Science ®Google Scholar
• Pitchiaya S, Mourao MDA, Jalihal AP, et al. Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality. Mol Cell. 2019;74(521–533):e6.
   Google Scholar
• Ghosh S, Marchand V, Gáspár I, et al. Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA. Nat Struct Mol Biol. 2012;19:441–449.
   PubMed Web of Science ®Google Scholar
• Shen Z, St-Denis A, Chartrand P. Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud. Genes Dev. 2010;24:1914–1926.
   PubMed Web of Science ®Google Scholar
• Vera M, Pani B, Griffiths LA, et al. The translation elongation factor eEF1A1 couples transcription to translation during heat shock response. eLife. 2014;3:e03164.
   PubMed Web of Science ®Google Scholar
• Zid BM, O’Shea EK. Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature. 2014;514:117–121.
   PubMed Web of Science ®Google Scholar
• Chen M, Yang Y, Krueger CJ, et al. Optimizing molecular beacons for intracellular analysis of RNA. Methods Mol Biol Clifton NJ. 2018;1649:243–257.
   PubMedGoogle Scholar
• Dolgosheina EV, Jeng SCY, Panchapakesan SSS, et al. RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem Biol. 2014;9:2412–2420.
   PubMed Web of Science ®Google Scholar
• Filonov GS, Moon JD, Svensen N, et al. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J Am Chem Soc. 2014;136:16299–16308.
   PubMed Web of Science ®Google Scholar
• Paige JS, Wu KY, Jaffrey SR. RNA mimics of green fluorescent protein. Science. 2011;333:642–646.
   PubMed Web of Science ®Google Scholar
• Song W, Filonov GS, Kim H, et al. Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. Nat Chem Biol. 2017;13:1187–1194.
   PubMed Web of Science ®Google Scholar
• Bouhedda F, Autour A, Ryckelynck M. Light-up RNA aptamers and their cognate fluorogens: from their development to their applications. Int J Mol Sci. 2018;19:44.
   Google Scholar
• Trachman RJ, Truong L, Ferré-D’Amaré AR. Structural principles of fluorescent RNA aptamers. Trends Pharmacol Sci. 2017;38:928–939.
   PubMed Web of Science ®Google Scholar
• Strack RL, Disney MD, Jaffrey SR. A superfolding spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat Methods. 2013;10:1219–1224.
   PubMed Web of Science ®Google Scholar
• Guet D, Burns LT, Maji S, et al. Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast. Nat Commun. 2015;6:8882.
   PubMed Web of Science ®Google Scholar
• Bouhedda F, Fam KT, Collot M, et al. A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells. Nat Chem Biol. 2020;16:69–76.
   PubMed Web of Science ®Google Scholar
• Cawte AD, Unrau PJ, Rueda DS. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays. Nat Commun. 2020;11:1283.
   PubMed Web of Science ®Google Scholar
• Chen X, Zhang D, Su N, et al. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat Biotechnol. 2019;37:1287–1293.
   PubMed Web of Science ®Google Scholar
• Li X, Kim H, Litke JL, et al. Fluorophore-promoted RNA folding and photostability enables imaging of single broccoli-tagged mRNAs in live mammalian cells. Angew Chem Int Ed Engl. 2020;59:4511–4518.
   PubMed Web of Science ®Google Scholar
• Wu J, Zaccara S, Khuperkar D, et al. Live imaging of mRNA using RNA-stabilized fluorogenic proteins. Nat Methods. 2019;16:862–865.
   PubMed Web of Science ®Google Scholar
• Bertrand E, Chartrand P, Schaefer M, et al. Localization of ASH1 mRNA particles in living yeast. Mol Cell. 1998;2:437–445.
   PubMed Web of Science ®Google Scholar
• Fusco D, Accornero N, Lavoie B, et al. Single mRNA molecules demonstrate probabilistic movement in living mammalian cells. Curr Biol CB. 2003;13:161–167.
   PubMed Web of Science ®Google Scholar
• Basyuk E, Galli T, Mougel M, et al. Retroviral genomic RNAs are transported to the plasma membrane by endosomal vesicles. Dev Cell. 2003;5:161–174.
   PubMed Web of Science ®Google Scholar
• Boireau S, Maiuri P, Basyuk E, et al. The transcriptional cycle of HIV-1 in real-time and live cells. J Cell Biol. 2007;179:291–304.
   PubMed Web of Science ®Google Scholar
• Chubb JR, Trcek T, Shenoy SM, et al. Transcriptional pulsing of a developmental gene. Curr Biol CB. 2006;16:1018–1025.
   PubMed Web of Science ®Google Scholar
• Darzacq X, Shav-Tal Y, de Turris V, et al. In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol. 2007;14:796–806.
   PubMed Web of Science ®Google Scholar
• Grünwald D, Singer RH. In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Nature. 2010;467:604–607.
   PubMed Web of Science ®Google Scholar
• Martin RM, Rino J, Carvalho C, et al. Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep. 2013;4:1144–1155.
   PubMed Web of Science ®Google Scholar
• Schmidt U, Basyuk E, Robert M-C, et al. Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation. J Cell Biol. 2011;193:819–829.
   PubMed Web of Science ®Google Scholar
• Shav-Tal Y, Darzacq X, Shenoy SM, et al. Dynamics of single mRNPs in nuclei of living cells. Science. 2004;304:1797–1800.
   PubMed Web of Science ®Google Scholar
• Janicki SM, Tsukamoto T, Salghetti SE, et al. From silencing to gene expression: real-time analysis in single cells. Cell. 2004;116:683–698.
   PubMed Web of Science ®Google Scholar
• Horvathova I, Voigt F, Kotrys AV, et al. The dynamics of mRNA turnover revealed by single-molecule imaging in single cells. Mol Cell. 2017;68(615–625):e9.
   Google Scholar
• Golding I, Paulsson J, Zawilski SM, et al. Real-time kinetics of gene activity in individual bacteria. Cell. 2005;123:1025–1036.
   PubMed Web of Science ®Google Scholar
• Yunger S, Rosenfeld L, Garini Y, et al. Single-allele analysis of transcription kinetics in living mammalian cells. Nat Methods. 2010;7:631–633.
   PubMed Web of Science ®Google Scholar
• Lionnet T, Czaplinski K, Darzacq X, et al. A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nat Methods. 2011;8:165–170.
   PubMed Web of Science ®Google Scholar
• Tantale K, Mueller F, Kozulic-Pirher A, et al. A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting. Nat Commun. 2016;7:12248.
   PubMed Web of Science ®Google Scholar
• Larson DR, Zenklusen D, Wu B, et al. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science. 2011;332:475–478.
   PubMed Web of Science ®Google Scholar
• Garcia HG, Tikhonov M, Lin A, et al. Quantitative imaging of transcription in living drosophila embryos links polymerase activity to patterning. Curr Biol CB. 2013;23:2140–2145.
   PubMed Web of Science ®Google Scholar
• Park HY, Lim H, Yoon YJ, et al. Visualization of dynamics of single endogenous mRNA labeled in live mouse. Science. 2014;343:422–424.
   PubMed Web of Science ®Google Scholar
• Bothma JP, Garcia HG, Esposito E, et al. Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living drosophila embryos. Proc Natl Acad Sci U S A. 2014;111:10598–10603.
   PubMed Web of Science ®Google Scholar
• Campbell PD, Chao JA, Singer RH, et al. Dynamic visualization of transcription and RNA subcellular localization in zebrafish. Dev Camb Engl. 2015;142:1368–1374.
   PubMed Web of Science ®Google Scholar
• Fernandez C, Lagha M. Lighting up gene activation in living drosophila embryos. Methods Mol Biol Clifton NJ. 2019;2038:63–74.
   PubMedGoogle Scholar
• Forrest KM, Gavis ER. Live imaging of endogenous RNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in drosophila. Curr Biol CB. 2003;13:1159–1168.
   PubMed Web of Science ®Google Scholar
• Lucas T, Ferraro T, Roelens B, et al. Live imaging of bicoid-dependent transcription in drosophila embryos. Curr Biol CB. 2013;23:2135–2139.
   PubMed Web of Science ®Google Scholar
• Weil TT, Forrest KM, Gavis ER. Localization of bicoid mRNA in late oocytes is maintained by continual active transport. Dev Cell. 2006;11:251–262.
   PubMed Web of Science ®Google Scholar
• Zimyanin VL, Belaya K, Pecreaux J, et al. In vivo imaging of oskar mRNA transport reveals the mechanism of posterior localization. Cell. 2008;134:843–853.
   PubMed Web of Science ®Google Scholar
• Ferraro T, Esposito E, Mancini L, et al. Transcriptional memory in the drosophila embryo. Curr Biol CB. 2016;26:212–218.
   PubMed Web of Science ®Google Scholar
• Bauer KE, Segura I, Gaspar I, et al. Live cell imaging reveals 3ʹ-UTR dependent mRNA sorting to synapses. Nat Commun. 2019;10:3178.
   PubMed Web of Science ®Google Scholar
• Garcia JF, Parker R. MS2 coat proteins bound to yeast mRNAs block 5ʹ to 3ʹ degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system. Rna N Y N. 2015;21:1393–1395.
   PubMed Web of Science ®Google Scholar
• Heinrich S, Sidler CL, Azzalin CM, et al. Stem-loop RNA labeling can affect nuclear and cytoplasmic mRNA processing. Rna N Y N. 2017;23:134–141.
   PubMed Web of Science ®Google Scholar
• Tutucci E, Vera M, Biswas J, et al. An improved MS2 system for accurate reporting of the mRNA life cycle. Nat Methods. 2018;15:81–89.
   PubMed Web of Science ®Google Scholar
• Chao JA, Patskovsky Y, Almo SC, et al. Structural basis for the coevolution of a viral RNA-protein complex. Nat Struct Mol Biol. 2008;15:103–105.
   PubMed Web of Science ®Google Scholar
• Coulon A, Ferguson ML, de Turris V, et al. Kinetic competition during the transcription cycle results in stochastic RNA processing. eLife. 2014;3:e03939.
   Web of Science ®Google Scholar
• Halstead JM, Lionnet T, Wilbertz JH, et al. Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals. Science. 2015;347:1367–1671.
   PubMed Web of Science ®Google Scholar
• Hocine S, Raymond P, Zenklusen D, et al. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat Methods. 2013;10:119–121.
   PubMed Web of Science ®Google Scholar
• Chen J, Nikolaitchik O, Singh J, et al. High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis. Proc Natl Acad Sci U S A. 2009;106:13535–13540.
   PubMed Web of Science ®Google Scholar
• Daigle N, Ellenberg J. LambdaN-GFP: an RNA reporter system for live-cell imaging. Nat Methods. 2007;4:633–636.
   PubMed Web of Science ®Google Scholar
• Takizawa PA, Vale RD. The myosin motor, Myo4p, binds Ash1 mRNA via the adapter protein, She3p. Proc Natl Acad Sci. 2000;97:5273–5278.
   PubMed Web of Science ®Google Scholar
• Chung S, Takizawa PA. In vivo visualization of RNA using the U1A-based tagged RNA system. Methods Mol Biol Clifton NJ. 2011;714:221–235.
   PubMedGoogle Scholar
• Takeuchi-Andoh T, Ohba S, Shinoda Y, et al. A simplified vector system for visualization of localized RNAs in Schizosaccharomyces pombe. Biosci Biotechnol Biochem. 2016;80:1362–1367.
   PubMed Web of Science ®Google Scholar
• Abudayyeh OO, Gootenberg JS, Essletzbichler P, et al. RNA targeting with CRISPR-Cas13. Nature. 2017;550:280–284.
   PubMed Web of Science ®Google Scholar
• Cox DBT, Gootenberg JS, Abudayyeh OO, et al. RNA editing with CRISPR-Cas13. Science. 2017;358:1019–1027.
   PubMed Web of Science ®Google Scholar
• Yang L-Z, Wang Y, Li S-Q, et al. Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems. Mol Cell. 2019;76(981–997):e7.
   Google Scholar
• Saldi T, Cortazar MA, Sheridan RM, et al. Coupling of RNA polymerase II transcription elongation with pre-mRNA Splicing. J Mol Biol. 2016;428:2623–2635.
   PubMed Web of Science ®Google Scholar
• Wende W, Friedhoff P, Sträßer K. Mechanism and regulation of co-transcriptional mRNP assembly and nuclear mRNA export [Internet]. In: Oeffinger M, Zenklusen D, editors. The biology of mRNA: structure and function. Cham: Springer International Publishing; 2019. p. 1–3. DOI:10.1007/978-3-030-31434-7_1
   Google Scholar
• Stewart M. Polyadenylation and nuclear export of mRNAs. J Biol Chem. 2019;294(9):2977–2987.
   PubMed Web of Science ®Google Scholar
• Mor A, Suliman S, Ben-Yishay R, et al. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat Cell Biol. 2010;12(6):543–552.
   PubMed Web of Science ®Google Scholar
• Smith CS, Preibisch S, Joseph A, et al. Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking. J Cell Biol. 2015;209(4):609–619.
   PubMed Web of Science ®Google Scholar
• Knockenhauer KE, Schwartz TU. The nuclear pore complex as a flexible and dynamic gate. Cell. 2016;164(6):1162–1171.
   PubMed Web of Science ®Google Scholar
• Ashkenazy-Titelman A, Shav-Tal Y, Kehlenbach RH. Into the basket and beyond: the journey of mRNA through the nuclear pore complex. Biochem J. 2020;477:23–44.
   PubMed Web of Science ®Google Scholar
• Lund MK, Guthrie C. The DEAD-box protein Dbp5p is required to dissociate Mex67p from exported mRNPs at the nuclear rim. Mol Cell. 2005;20(4):645–651.
   PubMed Web of Science ®Google Scholar
• Strässer K, Hurt E. Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p. Nature. 2001;413(6856):648–652.
   PubMed Web of Science ®Google Scholar
• Soheilypour M, Mofrad MRK. Quality control of mRNAs at the entry of the nuclear pore: cooperation in a complex molecular system. Nucl Austin Tex. 2018;9:202–211.
   PubMed Web of Science ®Google Scholar
• Ma J, Liu Z, Michelotti N, et al. High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat Commun. 2013;4(1):2414.
   PubMedGoogle Scholar
• Lin DH, Correia AR, Cai SW, et al. Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat Commun. 2018;9(1):2319.
   PubMedGoogle Scholar
• Saroufim M-A, Bensidoun P, Raymond P, et al. The nuclear basket mediates perinuclear mRNA scanning in budding yeast. J Cell Biol. 2015;211(6):1131–1140.
   PubMed Web of Science ®Google Scholar
• Fasken MB, Stewart M, Corbett AH. Functional significance of the interaction between the mRNA-binding protein, Nab2, and the nuclear pore-associated protein, Mlp1, in mRNA export. J Biol Chem. 2008;283(40):27130–27143.
   PubMed Web of Science ®Google Scholar
• Smith C, Lari A, Derrer CP, et al. In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol. 2015;211(6):1121–1130.
   PubMed Web of Science ®Google Scholar
• Derrer CP, Mancini R, Vallotton P, et al. The RNA export factor Mex67 functions as a mobile nucleoporin. J Cell Biol. 2019;218(12):3967–3976.
   PubMed Web of Science ®Google Scholar
• Ben-Yishay R, Mor A, Shraga A, et al. Imaging within single NPCs reveals NXF1’s role in mRNA export on the cytoplasmic side of the pore. J Cell Biol. 2019;218(9):2962–2981.
   PubMed Web of Science ®Google Scholar
• Visa N, Alzhanova-Ericsson AT, Sun X, et al. A pre-mRNA-binding protein accompanies the RNA from the gene through the nuclear pores and into polysomes. Cell. 1996;84(2):253–264.
   PubMed Web of Science ®Google Scholar
• Siebrasse JP, Veith R, Dobay A, et al. Discontinuous movement of mRNP particles in nucleoplasmic regions devoid of chromatin. Proc Natl Acad Sci U S A. 2008;105(51):20291–20296.
   PubMed Web of Science ®Google Scholar
• Siebrasse JP, Kaminski T, Kubitscheck U. Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy. Proc Natl Acad Sci U S A. 2012;109(24):9426–9431.
   PubMed Web of Science ®Google Scholar
• Khong A, Parker R. The landscape of eukaryotic mRNPs. Rna N Y N. 2020;26(3):229–239.
   PubMed Web of Science ®Google Scholar
• Katz ZB, Wells AL, Park HY, et al. β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration. Genes Dev. 2012;26(17):1885–1890.
   PubMed Web of Science ®Google Scholar
• Yamagishi M, Ishihama Y, Shirasaki Y, et al. Single-molecule imaging of β-actin mRNAs in the cytoplasm of a living cell. Exp Cell Res. 2009;315(7):1142–1147.
   PubMed Web of Science ®Google Scholar
• Doyle M, Kiebler MA. Mechanisms of dendritic mRNA transport and its role in synaptic tagging. Embo J. 2011;30(17):3540.
   PubMed Web of Science ®Google Scholar
• Das S, Moon HC, Singer RH, et al. A transgenic mouse for imaging activity-dependent dynamics of endogenous Arc mRNA in live neurons. Sci Adv. 2018;4(6):eaar3448.
   PubMed Web of Science ®Google Scholar
• Vallotton P, van Oijen AM, Whitchurch CB, et al. Diatrack particle tracking software: review of applications and performance evaluation. Traffic Cph Den. 2017;18:840–852.
   PubMed Web of Science ®Google Scholar
• Monnier N, Barry Z, Park HY, et al. Inferring transient particle transport dynamics in live cells. Nat Methods. 2015;12:838–840.
   PubMed Web of Science ®Google Scholar
• Chin A, Lécuyer E. RNA localization: making its way to the center stage. Biochim Biophys Acta Gen Subj. 2017;1861:2956–2970.
   PubMed Web of Science ®Google Scholar
• Mofatteh M, Bullock SL. SnapShot: subcellular mRNA localization. Cell. 2017;169(178–178):e1.
   PubMedGoogle Scholar
• Munro TP, Magee RJ, Kidd GJ, et al. Mutational analysis of a heterogeneous nuclear ribonucleoprotein A2 response element for RNA trafficking. J Biol Chem. 1999;274:34389–34395.
   PubMed Web of Science ®Google Scholar
• Chao JA, Patskovsky Y, Patel V, et al. ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev. 2010;24:148–158.
   PubMed Web of Science ®Google Scholar
• Patel VL, Mitra S, Harris R, et al. Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control. Genes Dev. 2012;26:43–53.
   PubMed Web of Science ®Google Scholar
• Pratt CA, Mowry KL. Taking a cellular road-trip: mRNA transport and anchoring. Curr Opin Cell Biol. 2013;25:99–106.
   PubMed Web of Science ®Google Scholar
• Beach DL, Salmon ED, Bloom K. Localization and anchoring of mRNA in budding yeast. Curr Biol CB. 1999;9:569–578.
   PubMed Web of Science ®Google Scholar
• Niessing D, Jansen R-P, Pohlmann T, et al. mRNA transport in fungal top models. Wiley Interdiscip Rev RNA. 2018;9(1).
   Web of Science ®Google Scholar
• Edelmann FT, Schlundt A, Heym RG, et al. Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex. Nat Struct Mol Biol. 2017;24:152–161.
   PubMed Web of Science ®Google Scholar
• Aronov S, Gelin-Licht R, Zipor G, et al. mRNAs encoding polarity and exocytosis factors are cotransported with the cortical endoplasmic reticulum to the incipient bud in Saccharomyces cerevisiae. Mol Cell Biol. 2007;27:3441–3455.
   PubMed Web of Science ®Google Scholar
• Fundakowski J, Hermesh O, Jansen R-P. Localization of a subset of yeast mRNAs depends on inheritance of endoplasmic reticulum. Traffic Cph Den. 2012;13:1642–1652.
   PubMed Web of Science ®Google Scholar
• Shepard KA, Gerber AP, Jambhekar A, et al. Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proc Natl Acad Sci U S A. 2003;100:11429–11434.
   PubMed Web of Science ®Google Scholar
• Heym RG, Zimmermann D, Edelmann FT, et al. In vitro reconstitution of an mRNA-transport complex reveals mechanisms of assembly and motor activation. J Cell Biol. 2013;203:971–984.
   PubMed Web of Science ®Google Scholar
• Lange S, Katayama Y, Schmid M, et al. Simultaneous Transport of Different Localized mRNA Species Revealed by Live-Cell Imaging. Traffic. 2008;9:1256–1267.
   PubMed Web of Science ®Google Scholar
• Neil CR, Jeschonek SP, Cabral SE, et al. L-bodies are novel RNA-protein condensates driving RNA transport in Xenopus oocytes [Internet]. Cell Biol. bioRxiv. 2020 [cited 2020 Oct 13]; Available from: http://biorxiv.org/lookup/doi/10.1101/2020.05.08.084814
   Google Scholar
• Batish M, van den Bogaard P, Kramer FR, et al. Neuronal mRNAs travel singly into dendrites. Proc Natl Acad Sci U S A. 2012;109:4645–4650.
   PubMed Web of Science ®Google Scholar
• Little SC, Sinsimer KS, Lee JJ, et al. Independent and coordinate trafficking of single Drosophila germ plasm mRNAs. Nat Cell Biol. 2015;17:558–568.
   PubMed Web of Science ®Google Scholar
• Dienstbier M, Boehl F, Li X, et al. Egalitarian is a selective RNA-binding protein linking mRNA localization signals to the dynein motor. Genes Dev. 2009;23:1546–1558.
   PubMed Web of Science ®Google Scholar
• Liu Y, Salter HK, Holding AN, et al. Bicaudal-D uses a parallel, homodimeric coiled coil with heterotypic registry to coordinate recruitment of cargos to dynein. Genes Dev. 2013;27:1233–1246.
   PubMed Web of Science ®Google Scholar
• McClintock MA, Dix CI, Johnson CM, et al. RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs. eLife. 2018;7:e36312.
   PubMed Web of Science ®Google Scholar
• Martin KC, Ephrussi A. mRNA localization: gene expression in the spatial dimension. Cell. 2009;136:719–730.
   PubMed Web of Science ®Google Scholar
• Wu B, Buxbaum AR, Katz ZB, et al. Quantifying protein-mRNA interactions in single live cells. Cell. 2015;162:211–220.
   PubMed Web of Science ®Google Scholar
• Katz ZB, English BP, Lionnet T, et al. Mapping translation “hot-spots” in live cells by tracking single molecules of mRNA and ribosomes. eLife. 2016;5:e10415.
   Web of Science ®Google Scholar
• Morisaki T, Lyon K, DeLuca KF, et al. Real-time quantification of single RNA translation dynamics in living cells. Science. 2016;352:1425–1429.
   PubMed Web of Science ®Google Scholar
• Tanenbaum ME, Gilbert LA, Qi LS, et al. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell. 2014;159:635–646.
   PubMed Web of Science ®Google Scholar
• Zhao N, Kamijo K, Fox PD, et al. A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo. Nat Commun. 2019;10:2947.
   PubMed Web of Science ®Google Scholar
• Pichon X, Bastide A, Safieddine A, et al. Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells. J Cell Biol. 2016;214:769–781.
   PubMed Web of Science ®Google Scholar
• Wang C, Han B, Zhou R, et al. Real-time imaging of translation on single mRNA transcripts in live cells. Cell. 2016;165:990–1001.
   PubMed Web of Science ®Google Scholar
• Wu B, Eliscovich C, Yoon YJ, et al. Translation dynamics of single mRNAs in live cells and neurons. Science. 2016;352:1430–1435.
   PubMed Web of Science ®Google Scholar
• Yan X, Hoek TA, Vale RD, et al. Dynamics of translation of single mRNA molecules in vivo. Cell. 2016;165:976–989.
   PubMed Web of Science ®Google Scholar
• Boersma S, Khuperkar D, Verhagen BMP, et al. Multi-color single-molecule imaging uncovers extensive heterogeneity in mRNA decoding. Cell. 2019;178(458–472):e19.
   Google Scholar
• Sepulveda G, Antkowiak M, Brust-Mascher I, et al. Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation in vertebrates. eLife. 2018;7:e34959.
   PubMed Web of Science ®Google Scholar
• Bergalet J, Patel D, Legendre F, et al. Inter-dependent centrosomal co-localization of the cen and ik2 cis-natural antisense mRNAs in drosophila. Cell Rep. 2020;30(3339–3352):e6.
   Google Scholar
• Kwon OS, Mishra RK, Safieddine A, Alasseur Q, Faucourt M, Coleno E, Barbosa I, Bertrand E, Spassky N, Hir HL. Exon Junction Complex dependent mRNA localization is linked to centrosome organization during ciliogenesis. bioRxiv 2020;358960.
   Google Scholar
• Palacios IM, Gatfield D, St Johnston D, et al. An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature. 2004;427:753–757.
   PubMed Web of Science ®Google Scholar
• Deglincerti A, Liu Y, Colak D, et al. Coupled local translation and degradation regulate growth cone collapse. Nat Commun. 2015;6:6888.
   PubMed Web of Science ®Google Scholar
• Kamenova I, Mukherjee P, Conic S, et al. Co-translational assembly of mammalian nuclear multisubunit complexes. Nat Commun. 2019;10:1740.
   PubMed Web of Science ®Google Scholar
• Shiber A, Döring K, Friedrich U, et al. Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling. Nature. 2018;561:268–272.
   PubMed Web of Science ®Google Scholar
• Moor AE, Golan M, Massasa EE, et al. Global mRNA polarization regulates translation efficiency in the intestinal epithelium. Science. 2017;357:1299–1303.
   PubMed Web of Science ®Google Scholar
• Cui XA, Palazzo AF. Localization of mRNAs to the endoplasmic reticulum. Wiley Interdiscip Rev RNA. 2014;5:481–492.
   PubMed Web of Science ®Google Scholar
• Reid DW, Nicchitta CV. Diversity and selectivity in mRNA translation on the endoplasmic reticulum. Nat Rev Mol Cell Biol. 2015;16:221–231.
   PubMed Web of Science ®Google Scholar
• Voigt F, Zhang H, Cui XA, et al. Single-molecule quantification of translation-dependent association of mRNAs with the endoplasmic reticulum. Cell Rep. 2017;21:3740–3753.
   PubMed Web of Science ®Google Scholar
• Pyhtila B, Zheng T, Lager PJ, et al. Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum. Rna N Y N. 2008;14:445–453.
   PubMed Web of Science ®Google Scholar
• Deshler JO, Highett MI, Schnapp BJ. Localization of Xenopus Vg1 mRNA by Vera protein and the endoplasmic reticulum. Science. 1997;276:1128–1131.
   PubMed Web of Science ®Google Scholar
• Schmid M, Jaedicke A, Du T-G, et al. Coordination of endoplasmic reticulum and mRNA localization to the yeast bud. Curr Biol CB. 2006;16:1538–1543.
   PubMed Web of Science ®Google Scholar
• Miorin L, Maiuri P, Hoenninger VM, et al. Spatial and temporal organization of tick-borne encephalitis flavivirus replicated RNA in living cells. Virology. 2008;379:64–77.
   PubMed Web of Science ®Google Scholar
• Miorin L, Romero-Brey I, Maiuri P, et al. Three-dimensional architecture of tick-borne encephalitis virus replication sites and trafficking of the replicated RNA. J Virol. 2013;87:6469–6481.
   PubMed Web of Science ®Google Scholar
• Knoops K, Kikkert M, SHE van den W, et al. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum. PLoS Biol. 2008;6:e226.
   PubMed Web of Science ®Google Scholar
• Neuman BW, Angelini MM, Buchmeier MJ. Does form meet function in the coronavirus replicative organelle? Trends Microbiol. 2014;22:642–647.
   PubMed Web of Science ®Google Scholar
• Lehmann M, Milev MP, Abrahamyan L, et al. Intracellular transport of human immunodeficiency virus type 1 genomic RNA and viral production are dependent on dynein motor function and late endosome positioning. J Biol Chem. 2009;284:14572–14585.
   PubMed Web of Science ®Google Scholar
• Molle D, Segura-Morales C, Camus G, et al. Endosomal trafficking of HIV-1 gag and genomic RNAs regulates viral egress. J Biol Chem. 2009;284:19727–19743.
   PubMed Web of Science ®Google Scholar
• Jolly C, Welsch S, Michor S, et al. The regulated secretory pathway in CD4(+) T cells contributes to human immunodeficiency virus type-1 cell-to-cell spread at the virological synapse. PLoS Pathog. 2011;7:e1002226.
   PubMed Web of Science ®Google Scholar
• Gaudin R, Berre S, Cunha de Alencar B, et al. Dynamics of HIV-containing compartments in macrophages reveal sequestration of virions and transient surface connections. PloS One. 2013;8:e69450.
   PubMed Web of Science ®Google Scholar
• Jouve M, Sol-Foulon N, Watson S, et al. HIV-1 buds and accumulates in “nonacidic” endosomes of macrophages. Cell Host Microbe. 2007;2:85–95.
   PubMed Web of Science ®Google Scholar
• Raposo G, Moore M, Innes D, et al. Human macrophages accumulate HIV-1 particles in MHC II compartments. Traffic Cph Den. 2002;3:718–729.
   PubMed Web of Science ®Google Scholar
• Mariani C, Desdouits M, Favard C, et al. Role of Gag and lipids during HIV-1 assembly in CD4(+) T cells and macrophages. Front Microbiol. 2014;5:312.
   PubMed Web of Science ®Google Scholar
• Eisfeld AJ, Kawakami E, Watanabe T, et al. RAB11A is essential for transport of the influenza virus genome to the plasma membrane. J Virol. 2011;85:6117–6126.
   PubMed Web of Science ®Google Scholar
• Ramos-Nascimento A, Kellen B, Ferreira F, et al. KIF13A mediates trafficking of influenza A virus ribonucleoproteins. J Cell Sci. 2017;130:4038–4050.
   PubMed Web of Science ®Google Scholar
• Vale-Costa S, Amorim MJ. Recycling endosomes and viral infection. Viruses. 2016;8:64.
   PubMed Web of Science ®Google Scholar
• Higuchi Y, Ashwin P, Roger Y, et al. Early endosome motility spatially organizes polysome distribution. J Cell Biol. 2014;204:343–357.
   PubMed Web of Science ®Google Scholar
• Olgeiser L, Haag C, Boerner S, et al. The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Rep. 2019;20:e46588.
   PubMed Web of Science ®Google Scholar
• Zander S, Baumann S, Weidtkamp-Peters S, et al. Endosomal assembly and transport of heteromeric septin complexes promote septin cytoskeleton formation. J Cell Sci. 2016;129:2778–2792.
   PubMed Web of Science ®Google Scholar
• Baumann S, König J, Koepke J, et al. Endosomal transport of septin mRNA and protein indicates local translation on endosomes and is required for correct septin filamentation. EMBO Rep. 2014;15:94–102.
   PubMed Web of Science ®Google Scholar
• König J, Baumann S, Koepke J, et al. The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs. Embo J. 2009;28:1855–1866.
   PubMed Web of Science ®Google Scholar
• Liao Y-C, Fernandopulle MS, Wang G, et al. RNA granules hitchhike on lysosomes for long-distance transport, using annexin A11 as a molecular tether. Cell. 2019;179(147–164):e20.
   Google Scholar
• Cioni J-M, Lin JQ, Holtermann AV, et al. Late endosomes act as mRNA translation platforms and sustain mitochondria in axons. Cell. 2019;176(56–72):e15.
   Google Scholar
• Popovic D, Nijenhuis W, Kapitein LC, et al. Co-translational targeting of transcripts to endosomes. bioRxiv. 2020;2020(7):17.208652.
   Google Scholar
• Chin A, Lécuyer E. Translating messages in different neighborhoods. Dev Cell. 2020;54:691–693.
   PubMed Web of Science ®Google Scholar