Table 1 |.

Comparison of RNA-centric methods

Method	Application	Advantages	Disadvantages	References
Biotinylated RNA	SMN mRNA	Strong binding of biotin-end- labeled RNA with streptavidin beads	In vitro; potentially biased toward abundant proteins in cell extracts	16
S1 aptamer	ARE motif	Easy elution of RBP complex from streptavidin beads with biotin	In vitro; potentially biased toward abundant proteins	19
Cys4	Pre-miRNA	Elution of RBP complex with imidazole	In vitro; potentially biased toward abundant proteins	20
Protein microarray	TINCR, SNORD50	No cellular extract required; no MS required	In vitro; limited to direct interactions with proteins spotted on microarray	21,22
RAP	Xist, FIRRE noncoding RNA	In vivo; high specificity with UV cross-linking and long oligonucleotide probes (120 nt)	High input cell numbers	33
TRIP	p27 mRNA, CEP-1 mRNA	In vivo; high specificity with UV cross-linking	Two capture steps with poly(A) and biotinylated ASO capture decrease efficiency	37
PAIR	ANK mRNA	In vivo; high specificity with UV cross-linking	Cost and effort for production of peptide nucleic acid	35
MS2-BioTRAP	IRES	In vivo; high specificity with UV cross-linking	Requires MS2 conjugation to RNA, transfection/infection of RNA and labeler protein, and high input cell numbers	36
CHART	Xist, MALAT1, NEAT1	In vivo	Additional RNase H step to identify accessible sites for probes; high input cell numbers	31,52
ChIRP	TERC, Xist	In vivo; no prior knowledge of RNA accessibility required for probe design	Short probes may pull down similar sequence fragments; high input cell numbers	30,39
RaPID	ZIKV-host protein interactome; 3′ untranslated region motifs	In vivo; low number of cells required; direct labeling of protein	Requires BoxB link to RNA; short sequence limits; transfection/infection of RNA and labeler protein	44