TABLE 2.

RNA-content methods: common methods and methods based on Cas13.

Methods	Application	In vitro/In vivo	Advantages	Disadvantages	References
Biotinylated RNA	mRNA	In vitro	Strong combination between streptavidin beads and biotinylated RNA	Potentially biased toward abundant proteins	Zheng et al. (2016)
S1 aptamer	mRNA	In vitro	Simple purification without the need for recombinant protein production	Potentially biased toward abundant proteins; interference with native RBPs formation; unspecific interactions	Leppek and Stoecklin (2014)
RAP	lncRNA	In vivo	Strong combination between probe and RNA	High input cell numbers	McHugh et al. (2015)
TRIP	mRNA	In vivo	No need of genetic manipulation; UV cross-linking	Careful design and evaluation of ASO; differences in ASO binding sites may reduce efficiency	Matia-González et al. (2017)
PAIR	mRNA	In vivo	UV cross-linking	Difficult to product peptide nucleic acid	Zeng et al. (2006)
CHART	lncRNA	In vivo	Simple design; split pools of tiling oligonucleotide probes and glutaraldehyde crosslinking ensure the success	High input cell numbers	Chu et al. (2011)
RaPID	mRNA	In vivo	Low number of cells needed; interrogate motifs <50 nucleotides	Requires BoxB link to RNA; not all proteins can be detected due to biotinylation; it’s difficult to tell whether the protein is acting directly or indirectly	Ramanathan et al. (2018)
CARPID	lncRNA	In vivo	No need of genetic manipulation; Multiple gRNAs are designed to reduce background noise	Need a high abundance of targeted RNA; unstable binding; difficult to detect all the proteins due to the limitation of gRNA	Yi et al. (2020)
Cas13-based APEX targeting	hTR	In vivo	No need of genetic manipulation; introduce double-stranded RNA binding domain (dsRBD) to improve the stability of dCas13 complex	Need a high abundance of targeted RNA; unstable binding; difficult to detect all the proteins due to the limitation of gRNA	Han et al. (2020)
CRUIS	lncRNA, mRNA	In vivo	No need of genetic manipulation; no restriction on the type of RNA	Need a high abundance of targeted RNA; unstable binding; difficult to detect all the proteins due to the limitation of gRNA	Zhang et al. (2020)
CBRPP	lncRNA, mRNA	In vivo	No need of genetic manipulation; no restriction on the type of RNA	Need a high abundance of targeted RNA; unstable binding; difficult to detect all the proteins due to the limitation of gRNA	Li et al. (2021)
RPL	snRNA	In vivo	No need of genetic manipulation; no restriction on the type of RNA	Need a high abundance of targeted RNA; unstable binding; difficult to detect all the proteins due to the limitation of gRNA	Lin et al. (2021)
CBRIP	snRNA	In vivo	No restriction on the type of RNA; high stability and specificity	Need a high abundance of targeted RNA; difficult to detect all the proteins because of the limitation of gRNA	Chen et al. (2021)