Das, S., Vera, M., Gandin, V., Singer, R. H. & Tutucci, E. Intracellular mRNA transport and localized translation. Nat. Rev. Mol. Cell Biol. 22, 483–504 (2021).
Leung, K. M. et al. Asymmetrical beta-actin mRNA translation in growth cones mediates attractive turning to netrin-1. Nat. Neurosci. 9, 1247–1256 (2006).
Moor, A. E. et al. Global mRNA polarization regulates translation efficiency in the intestinal epithelium. Science 357, 1299–1303 (2017).
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 (2019).
Buxbaum, A. R., Haimovich, G. & Singer, R. H. In the right place at the right time: visualizing and understanding mRNA localization. Nat. Rev. Mol. Cell Biol. 16, 95–109 (2015).
Jeffery, W. R., Tomlinson, C. R. & Brodeur, R. D. Localization of actin messenger RNA during early ascidian development. Dev. Biol. 99, 408–417 (1983).
Holt, C. E., Martin, K. C. & Schuman, E. M. Local translation in neurons: visualization and function. Nat. Struct. Mol. Biol. 26, 557–566 (2019).
Fazal, F. M. et al. Atlas of subcellular RNA localization revealed by APEX-seq. Cell 178, 473–490 (2019).
Alon, S. et al. Expansion sequencing: spatially precise in situ transcriptomics in intact biological systems. Science 371, eaax2656 (2021).
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).
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).
Terenzio, M. et al. Locally translated mTOR controls axonal local translation in nerve injury. Science 359, 1416–1421 (2018).
Zhao, W. et al. CRISPR-Cas9-mediated functional dissection of 3′-UTRs. Nucleic Acids Res. 45, 10800–10810 (2017).
Katz, Z. B. et al. β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration. Genes Dev. 26, 1885–1890 (2012).
Tsuboi, T. et al. Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis. eLife 9, e57814 (2020).
Abudayyeh, O. O. et al. RNA targeting with CRISPR-Cas13. Nature 550, 280–284 (2017).
Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019–1027 (2017).
Konermann, S. et al. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173, 665–676 (2018).
Tieu, V. et al. A versatile CRISPR-Cas13d platform for multiplexed transcriptomic regulation and metabolic engineering in primary human T cells. Cell 187, 1278–1295 (2024).
Wang, H. et al. CRISPR-mediated live imaging of genome editing and transcription. Science 365, 1301–1305 (2019).
Yang, L. Z. et al. Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems. Mol. Cell 76, 981–997 (2019).
Wilson, C., Chen, P. J., Miao, Z. & Liu, D. R. Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase. Nat. Biotechnol. 38, 1431–1440 (2020).
Liang, F. S., Ho, W. Q. & Crabtree, G. R. Engineering the ABA plant stress pathway for regulation of induced proximity. Sci. Signal. 4, rs2 (2011).
Liao, P. et al. The ameliorative effects and mechanisms of abscisic acid on learning and memory. Neuropharmacology 224, 109365 (2023).
Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877–879 (2008).
White, M. R. & Garcin, E. D. The sweet side of RNA regulation: glyceraldehyde-3-phosphate dehydrogenase as a noncanonical RNA-binding protein. Wiley Interdiscip. Rev. RNA 7, 53–70 (2016).
Vercellino, I. & Sazanov, L. A. The assembly, regulation and function of the mitochondrial respiratory chain. Nat. Rev. Mol. Cell Biol. 23, 141–161 (2022).
Yoon, Y. Sharpening the scissors: mitochondrial fission with aid. Cell Biochem. Biophys. 41, 193–206 (2004).
Kannan, S. et al. Compact RNA editors with small Cas13 proteins. Nat. Biotechnol. 40, 194–197 (2021).
Ozcan, A. et al. Programmable RNA targeting with the single-protein CRISPR effector Cas7-11. Nature 597, 720–725 (2021).
Hu, W. et al. Single-base tiled screen unveils design principles of PspCas13b for potent and off-target-free RNA silencing. Nat. Struct. Mol. Biol. 31, 1702–1716 (2024).
Park, H. Y., Trcek, T., Wells, A. L., Chao, J. A. & Singer, R. H. An unbiased analysis method to quantify mRNA localization reveals its correlation with cell motility. Cell Rep. 1, 179–184 (2012).
Yang, L. Z. et al. Multi-color RNA imaging with CRISPR-Cas13b systems in living cells. Cell Insight 1, 100044 (2022).
Luo, Y., Na, Z. & Slavoff, S. A. P-bodies: composition, properties, and functions. Biochemistry 57, 2424–2431 (2018).
Yang, P. et al. G3BP1 is a tunable switch that triggers phase separation to assemble stress granules. Cell 181, 325–345 (2020).
Hubstenberger, A. et al. P-body purification reveals the condensation of repressed mRNA regulons. Mol. Cell 68, 144–157 (2017).
Munoz, P. et al. TRF1 controls telomere length and mitotic fidelity in epithelial homeostasis. Mol. Cell. Biol. 29, 1608–1625 (2009).
Biamonti, G. & Vourc’h, C. Nuclear stress bodies. Cold Spring Harb. Perspect. Biol. 2, a000695 (2010).
Canale, P., Campolo, J., Borghini, A. & Andreassi, M. G. Long telomeric repeat-containing RNA (TERRA): biological functions and challenges in vascular aging and disease. Biomedicines 11, 3211 (2023).
Guardia, C. M. et al. Reversible association with motor proteins (RAMP): a streptavidin-based method to manipulate organelle positioning. PLoS Biol. 17, e3000279 (2019).
Janicki, S. M. et al. From silencing to gene expression: real-time analysis in single cells. Cell 116, 683–698 (2004).
Xu, H. et al. TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells. Nucleic Acids Res. 48, 13013–13014 (2020).
Safieddine, A. et al. A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport. Nat. Commun. 12, 1352 (2021).
Ning, L. et al. A bright, nontoxic, and non-aggregating red fluorescent protein for long-term labeling of fine structures in neurons. Front. Cell Dev. Biol. 10, 893468 (2022).
Afridi, R., Tsuda, M., Ryu, H. & Suk, K. The function of glial cells in the neuroinflammatory and neuroimmunological responses. Cells 11, 659 (2022).
Denny, J. B. Molecular mechanisms, biological actions, and neuropharmacology of the growth-associated protein GAP-43. Curr. Neuropharmacol. 4, 293–304 (2006).
Powell, J. E. et al. Targeted gene silencing in the nervous system with CRISPR-Cas13. Sci. Adv. 8, eabk2485 (2022).
Pilaz, L. J. et al. Subcellular mRNA localization and local translation of Arhgap11a in radial glial progenitors regulates cortical development. Neuron 111, 839–856 (2023).
Buxbaum, A. R., Wu, B. & Singer, R. H. Single β-actin mRNA detection in neurons reveals a mechanism for regulating its translatability. Science 343, 419–422 (2014).
Xu, K., Zhong, G. & Zhuang, X. Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339, 452–456 (2013).
David, A. et al. Nuclear translation visualized by ribosome-bound nascent chain puromycylation. J. Cell Biol. 197, 45–57 (2012).
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).
Eom, T., Antar, L. N., Singer, R. H. & Bassell, G. J. Localization of a β-actin messenger ribonucleoprotein complex with zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses. J. Neurosci. 23, 10433–10444 (2003).
Donnelly, C. J. et al. Axonally synthesized β-actin and GAP-43 proteins support distinct modes of axonal growth. J. Neurosci. 33, 3311–3322 (2013).
Gomez, T. M. & Letourneau, P. C. Actin dynamics in growth cone motility and navigation. J. Neurochem. 129, 221–234 (2014).
Wang, G. et al. Spatial organization of the transcriptome in individual neurons. Preprint at bioRxiv https://doi.org/10.1101/2020.12.07.414060 (2020).
Park, J. W., Vahidi, B., Taylor, A. M., Rhee, S. W. & Jeon, N. L. Microfluidic culture platform for neuroscience research. Nat. Protoc. 1, 2128–2136 (2006).
Thornburg-Suresh, E. J. C. & Summers, D. W. Microtubules, membranes, and movement: new roles for stathmin-2 in axon integrity. J. Neurosci. Res. 102, e25382 (2024).
Gumy, L. F. et al. Transcriptome analysis of embryonic and adult sensory axons reveals changes in mRNA repertoire localization. RNA 17, 85–98 (2011).
Zivraj, K. H. et al. Subcellular profiling reveals distinct and developmentally regulated repertoire of growth cone mRNAs. J. Neurosci. 30, 15464–15478 (2010).
Wessels, H. H. et al. Massively parallel Cas13 screens reveal principles for guide RNA design. Nat. Biotechnol. 38, 722–727 (2020).
Tsanov, N. et al. smiFISH and FISH-quant — a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res. 44, e165 (2016).
Andronov, L. et al. Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. Nat. Commun. 15, 4644 (2024).
Rust, M. J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–795 (2006).
Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Orengo, J. P., Bundman, D. & Cooper, T. A. A bichromatic fluorescent reporter for cell-based screens of alternative splicing. Nucleic Acids Res. 34, e148 (2006).
Vargas, D. Y., Raj, A., Marras, S. A., Kramer, F. R. & Tyagi, S. Mechanism of mRNA transport in the nucleus. Proc. Natl Acad. Sci. USA 102, 17008–17013 (2005).
Luo, B. et al. Endoplasmic reticulum stress eIF2α-ATF4 pathway-mediated cyclooxygenase-2 induction regulates cadmium-induced autophagy in kidney. Cell Death Dis. 7, e2251 (2016).
