TABLE 2

Comparison of CRISPRi to other repression methods

Repression methodMechanism of actionUsed in pooled genome-wide screensOff-target effectsAbility to target small RNAsAbility to target specific splice variantsLimitations in targetingNo. of components requiredReferences
CRISPRiTranscriptional elongation of mRNA is sterically blocked; the KRAB fusion recruits repressive chromatin marksYesMinimalYesOnly if different variants have different TSSsRequires an “NGG” PAM adjacent to a target sequence2 or 3 (dCas9, sgRNA, optional repression module); these may be collected on one vector in some cases3, 4, 20, 24, 26, 29, 30, 64
RNAiThe target mRNA is sequestered or degradedYesExtensiveNoYesNo16569
TALE or ZFTranscriptional elongation of mRNA is sterically blocked; the KRAB fusion recruits repressive chromatin marksNoMinimalYesOnly if different variants have different TSSsTALEs have no sequence limitations; ZFNs may require some engineering to target a given sequence139, 50, 51, 5456
miRNA sponges or antagomirsBoth miRNA sponges and antagomirs act as dominant negatives by binding to miRNAs and preventing them from acting on their target mRNAsNomiRNAs in a family sharing the same seed bind to sponges; antagomirs can distinguish between family membersYesNASponges are not ideal for selectively targeting 1 miRNA in a family sharing the same seed1; also, a single sponge can repress multiple miRNAs simultaneously7074