Table 3

Biochemical tools for identifying lncRNA targets

TechniqueCross-linking methodPull-downOligo designOligo modificationsElutionReference
CHARTWhole-cell fixation with 1% formaldehyde for 10′ and nuclei fixation with 3% formaldehyde for 30′25-mer DNA antisense capture oligosC-oligos designed to target RNase H sensitivity sitesBiotinylated at 3′ end with 18-carbon spacer armRNase HSimon et al., 2011 (62)
ChIRPWhole-cell fixation with 3% formaldehyde for 30′20-mer DNA antisense tiling oligosTiling entire RNA sequence, split into “even” and “odd” setsBiotinylated at 3′ end with 18-carbon spacer armRNase H or RNase AChu et al., 2011 (63)
RAPWhole-cell fixation with 2 mmol/L disuccinimidyl glutarate for 45′, followed by 3% formaldehyde for 10′120-nt RNA tiling oligosTiling every 15 nt across the entire RNA sequence, excluding repetitive regionsProbes transcribed in vitro in the presence of biotin–uridine triphosphateProteinase KEngreitz et al., 2013 (64)