Table 2.

Comparison of CRISPR/Cas9 system and MO in disease modeling with zebrafish

	CRISPR/Cas9 system	MO
Targeted loss of function	Cas9 induces indels and frame-shifts (KO); CRISPRi represses gene transcription	Translation of target genes are blocked (KD)
Targeted gain of function	Sequences are inserted with templates co-injected with Cas9 (KI); CRISPRa activates gene transcription	Unavailable
Timeframe	In KO and KI studies, phenotypes can be observed in F0 (0–5d), F1 (3 m) or F2 (>6 m), off-target effects need to be considered in early generations	Phenotypes can be observed in F0 (0–5d)
Cost and throughput	Relatively cheap and high-throughput, depending on the study design and individual institutes	Cheap and high-throughput
On-target efficacy	Highly variable depending on the design and target sequence
Gene dosage modulation	Complete KO is accomplished with a coding frameshift. Gene dosage modulation can be done with CRISPRi/a	Complete KO is generally not available
Conditional function	Conditional gene editing is accomplished with conditional Cas9 expression	Generally not available
Duration of the effect	KO or KI is permanent and can be transmitted through generations	Transient KD
Reversibility	Cas9 KO is irreversible, CRISPRi/a is reversible	Reversible
Toxicity	Highly variable among the different sgRNAs, not correlate with the on-target efficacy	Increase with the MO dose injected

KO knock-out, KD knock-down, KI knock-in, MO morpholino oligomers