Cech, T. R. & Steitz, J. A. The noncoding RNA revolution—trashing old rules to forge new ones. Cell 157, 77–94 (2014).

Article  CAS  PubMed  Google Scholar 

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 

Wang, K. C. & Chang, H. Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904–914 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

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).

Article  CAS  PubMed  Google Scholar 

Pichon, X. et al. RNA binding protein/RNA element interactions and the control of translation. Curr. Protein Pept. Sci. 13, 294–304 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Abil, Z., Denard, C. A. & Zhao, H. Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNA. J. Biol. Eng. 8, 7 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Tischer, D. & Weiner, O. D. Illuminating cell signalling with optogenetic tools. Nat. Rev. Mol. Cell Biol.y 15, 551–558 (2014).

Article  CAS  Google Scholar 

Kawano, F., Shi, F. & Yazawa, M. Optogenetics: switching with red and blue. Nat. Chem. Biol. 13, 573–574 (2017).

Article  CAS  PubMed  Google Scholar 

Weber, A. M. et al. A blue light receptor that mediates RNA binding and translational regulation. Nat. Chem. Biol.y 15, 1085–1092 (2019).

Article  CAS  Google Scholar 

Pilsl, S., Morgan, C., Choukeife, M., Moglich, A. & Mayer, G. Optoribogenetic control of regulatory RNA molecules. Nat. Commun. 11, 4825 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Renzl, C., Kakoti, A. & Mayer, G. Aptamer-mediated reversible transactivation of gene expression by light. Angew. Chem. Int. Ed. Engl. 59, 22414–22418 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, R. et al. Optogenetic control of RNA function and metabolism using engineered light-switchable RNA-binding proteins. Nat. Biotechnol. 40, 779–786 (2022).

Article  PubMed  Google Scholar 

Ranzani, A. T. et al. Light-dependent control of bacterial expression at the mRNA Level. ACS Synth. Biol. 11, 3482–3492 (2022).

Article  CAS  PubMed  Google Scholar 

Bubeck, F. et al. Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9. Nat. Methods 15, 924–927 (2018).

Article  CAS  PubMed  Google Scholar 

Knott, G. J. & Doudna, J. A. CRISPR-Cas guides the future of genetic engineering. Science 361, 866–869 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, K. I. et al. A chemical-inducible CRISPR-Cas9 system for rapid control of genome editing. Nat. Chem. Biol. 12, 980–987 (2016).

Article  CAS  PubMed  Google Scholar 

Setten, R. L., Rossi, J. J. & Han, S. P. The current state and future directions of RNAi-based therapeutics. Nat. Rev. Drug Discov. 18, 421–446 (2019).

Article  CAS  PubMed  Google Scholar 

Chen, Y. & Varani, G. Engineering RNA-binding proteins for biology. FEBS J. 280, 3734–3754 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choudhury, R., Tsai, Y. S., Dominguez, D., Wang, Y. & Wang, Z. Engineering RNA endonucleases with customized sequence specificities. Nat. Commun. 3, 1147 (2012).

Article  PubMed  Google Scholar 

Cooke, A., Prigge, A., Opperman, L. & Wickens, M. Targeted translational regulation using the PUF protein family scaffold. Proc. Natl. Acad. Sci. USA 108, 15870–15875 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  PubMed  PubMed Central  Google Scholar 

Batra, R. et al. Elimination of toxic microsatellite repeat expansion RNA by RNA-targeting Cas9. Cell 170, 899–912.e10 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019–1027 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chaulk, S. G. & MacMillan, A. M. Caged RNA: photo-control of a ribozyme reaction. Nucleic Acids Res. 26, 3173–3178 (1998).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zetsche, B., Volz, S. E. & Zhang, F. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat. Biotechnol. 33, 139–142 (2015).

Article  CAS  PubMed  Google Scholar 

Nihongaki, Y., Otabe, T., Ueda, Y. & Sato, M. A split CRISPR-Cpf1 platform for inducible genome editing and gene activation. Nat. Chem. Biol. 15, 882–888 (2019).

Article  CAS  PubMed  Google Scholar 

Nihongaki, Y., Kawano, F., Nakajima, T. & Sato, M. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat. Biotechnol. 33, 755–760 (2015).

Article  CAS  PubMed  Google Scholar 

Nihongaki, Y. et al. CRISPR-Cas9-based photoactivatable transcription systems to induce neuronal differentiation. Nat. Methods 14, 963–966 (2017).

Article  CAS  PubMed  Google Scholar 

Richter, F. et al. Engineering of temperature- and light-switchable Cas9 variants. Nucleic Acids Res. 44, 10003–10014 (2016).

CAS  PubMed  PubMed Central  Google Scholar 

Zhou, X. X. et al. A single-chain photoswitchable CRISPR-Cas9 architecture for light-inducible gene editing and transcription. ACS Chem. Biol. 13, 443–448 (2018).

Article  CAS  PubMed  Google Scholar 

Ma, H. et al. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat. Methods 15, 928–931 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qin, P. et al. Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. Nat. Commun. 8, 14725 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583–588 (2015).

Article  CAS  PubMed  Google Scholar 

Shao, S. et al. Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system. Nucleic Acids Res. 44, e86 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Ma, H. et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat. Biotechnol. 34, 528–530 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

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 

Boersma, S. et al. Multi-color single-molecule imaging uncovers extensive heterogeneity in mRNA decoding. Cell 178, 458–472.e19 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nowak, C. M., Lawson, S., Zerez, M. & Bleris, L. Guide RNA engineering for versatile Cas9 functionality. Nucleic Acids Res. 44, 9555–9564 (2016).