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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]