TABLE 1.

Classical RNA imaging methods and Cas13-mediated methods.

Methods	Application	In vitro/In vivo	Advantages	Disadvantages	References
RBP-FP system	mRNA	In vitro	High resolution	High background signals	Zimyanin et al. (2008), van Gemert et al. (2009), Lionnet et al. (2011), Muramoto et al. (2012), Yoshimura et al. (2012), Hocine et al. (2013), Hayashi et al. (2014), Rino et al. (2014)
BiFC system	mRNA	In vitro	Low background signals	Irreversibility; only suitable for visualizing long-lived RNAs; not suitable for visualizing real-time	Shyu and Hu (2008), Yamada et al. (2011)
RNA aptamer/fluorophore system	5S RNAs, 6S RNAs, mRNA	In vitro	Fast imaging; real-time imaging; suitable for long-time tracking of RNAs	High background signals	Paige et al. (2011), Dolgosheina et al. (2014), Shin et al. (2014)
Reporter gene system	miRNA	In vitro	Without affecting the properties of RNAs	Only suitable for the visualization of miRNA	Kim H. J. et al. (2009), Ko et al. (2009), Kang et al. (2012), Wang F. et al. (2013)
MBs	miRNA, mRNA	In vivo	Wide application	False-positive signals	Kang et al. (2011), Wang Z. et al. (2013), Lee et al. (2015b), Tay et al. (2015); Xia et al. (2017)
Nano-MBs	mRNA, miRNA	In vivo	Low background signals; excellent resistance to enzyme degradation; high cellular uptake; longer imaging fluorescence lifetime	RNA downregulation	Riahi et al. (2014), Lee et al. (2015a), Wang et al. (2015)
Quencher-free probes	mRNA, 28S rRNA, snoRNA, polyA RNA	In vivo	Robust; high sensitivity and specificity	Easily subject to self-dimerization	Kummer et al. (2011), Okamoto (2011), Oomoto et al. (2015)
dCas13a-NF	mRNA	In vivo	High efficiency; robust; low background noise; real-time imaging	Cumbersome design	Abudayyeh et al. (2017)
CRISPR-dPspCas13b-mediated imaging	lncRNA, mRNA	In vivo			Yang et al. (2019)
Imaging using dCas13 and dCas9	DNA, mRNA	In vivo			Wang et al. (2019), Yang et al. (2019)