Escaping from CRISPR–Cas-mediated knockout: the facts, mechanisms, and applications

Wang, Ying; Zhai, Yujing; Zhang, Mingzhe; Song, Chunlin; Zhang, Yuqing; Zhang, Gang

doi:10.1186/s11658-024-00565-x

Cellular & Molecular Biology Letters

Table 1 Reported cases with alternative splicing, exon skipping, and translation reinitiation in knockout models generated by CRISPR–Cas

From: Escaping from CRISPR–Cas-mediated knockout: the facts, mechanisms, and applications

Working model	Targeted gene	In-frame transcript	Truncated protein	Function analysis	Mechanisms proposed	Ref.
HCT116; RPE1	CDC14A	Detected	Not examined	Not examined	Exon skipping	[10]
HeLa; HEK293T	FLOT1; AGA	Detected	Detected	Not examined	Exon skipping	[11]
NIH3T3	Gli3	Not examined	Detected	Not examined	Translation reinitiation	[12]
zebrafish	chd7; hace1; pycr1a	Not detected	Predicted for hace1, pycr1a	Functional for hace1	Exon skipping; translation reinitiation	[13]
teloHAEC	PHACTR1	Detected	Detected	Not examined	Exon skipping	[14]
KP; NIH3T3; C2C12; HCT116	Kras; Ctnnb1; Dmd; LMNA; p65	Detected for Ctnnb1, Dmd, LMNA	Detected for Ctnnb1	Functional for Ctnnb1	Exon skipping	[15]
Zebrafish	smyd1a	Not detected	Not examined	Not examined	Alternative splicing	[16]
Rabbit	DMD; LMNA; GCK; ANO5; GHR	Not detected	Not examined	Not examined	Alternative splicing	[17]
Locust	LmigOr35	Detected	Not examined	Not examined	Exon skipping	[18]
RPE1	BUB1	Detected	Detected	Functional	Alternative splicing	[19]
Mouse	Ccnb3	Detected	Detected	May be functional	Alternative splicing	[20]
HeLa	BUB1	Not examined	Detected	Functional	Not proposed	[21]
HAP1; K562	136 genes	Examined and detected in BRD3, MTF2, PI4KB, DNMT1, NGLY1	Detected in ~ 30% knock out cell lines	Examined BRD4, DNMT1, NGLY1 and functional	Exon skipping; translation reinitiation	[22]
HAP1; RMS13; MIA	RICTOR; VPS35; TOP1; SIRT1; CTNNB1; AXIN1; LRP6; PTEN; TBK1; BAP1; TLE3; PPM1A; BCL2L2; LPR5; SUFU; LKB1	Detected in TOP1, LKB1, SUFU	Detected in TOP1, SIRT1, CTNNB1, LRP6, LKB1, LRP5	Examined TOP1, LRP5 and functional	Exon skipping; translation reinitiation	[23]
Rice	OsIAA23	Detected	Not examined	Functional	Alternative splicing	[24]
C2C12	CK2α; CK2α′; CK2β	Not annotated	Detected	Functional	Not proposed	[25, 26]
Mouse	Rhbdf1	Detected	Not examined	Functional	Translation reinitiation	[27]
BEAS-2B; A549; MDA-MB-231	MDIG	Detected	Detected	Not examined	Exon skipping	[28]
Mouse	Ets2	Detected	Detected	Functional	Exon skipping	[29]
HeLa	CDC20	Detected	Detected	Functional	Translation reinitiation	[30]
HT29	EpCAM	Detected	Detected	Functional	Exon skipping; translation reinitiation	[31]
Rice	WDA1; BC10 and another 71 genes	Detected in 39 knockouts	Examined in WDA1 and detected	Examined in WDA1, BC10 and functional	Exon skipping; alternative splicing	[32]
THP1	IFNAR2	Detected	Detected	Functional	Exon skipping	[33]
HL1	PKP2; DSG2; DSC2; DSP; JUP	Detected in DSP, JUP	Detected in DSP, JUP	May be functional for DSP	Translation reinitiation	[34]
A375	XPA	Detected	Detected	Functional	Alternative splicing; translation reinitiation	[35]
A549; H1703	NRF2	Detected	Detected	Functional	Exon skipping	[36]
Mice	Ctnnb1	Detected	Detected	Functional	Exon skipping	[37]

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ISSN: 1689-1392

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