Genome editing through large insertion leads to the skipping of targeted exon

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Uddin, Borhan ^a   Chen, Nan Peng ^a   Panic, Marko ^a   Schiebel, Elmar ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

CRISPR Cas9; Exon skipping; Genome engineering; HCDC14A; HCDC14B; Zinc finger nucleases

Indexed keywords

CELL CYCLE PROTEIN; CELL DIVISION CYCLE 14A PROTEIN; CELL DIVISION CYCLE 14B PROTEIN; CRISPR ASSOCIATED PROTEIN; CRISPR ASSOCIATED PROTEIN 9 NUCLEASE; NEOMYCIN; PUROMYCIN; UNCLASSIFIED DRUG; ZINC FINGER NUCLEASE; ENDONUCLEASE; ZINC FINGER PROTEIN;

ARTICLE; CDC14A GENE; CDC14B GENE; CONTROLLED STUDY; DNA END JOINING REPAIR; DNA SEQUENCE; DOUBLE STRANDED DNA BREAK; EXON SKIPPING; GENE; GENE DISRUPTION; GENE EXPRESSION; GENE INSERTION; GENE LOCUS; GENETIC PROCEDURES; GENOME EDITING; HOMOLOGOUS RECOMBINATION; HUMAN; HUMAN CELL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SOUTHERN BLOTTING; STOP CODON; CELL LINE; CHEMISTRY; CYTOLOGY; EXON; GENE EXPRESSION REGULATION; GENETIC ENGINEERING; HCT 116 CELL LINE; METABOLISM; PROCEDURES; RETINAL PIGMENT EPITHELIUM; RNA EDITING;

CELL LINE; CRISPR-ASSOCIATED PROTEINS; ENDONUCLEASES; EXONS; GENETIC ENGINEERING; HCT116 CELLS; HUMANS; MUTAGENESIS, INSERTIONAL; RETINAL PIGMENT EPITHELIUM; RNA EDITING; SEQUENCE ANALYSIS, DNA; ZINC FINGERS;

EID: 84953708487     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2284-8     Document Type: Article

References (31)

1. Morgan DO. Cyclin-dependent kinases: engines, clocks, and microprocessors. Annu Rev Cell Dev Biol. 1997;13:261-91.
2. Stegmeier F, Amon A. Closing mitosis: the functions of the Cdc14 phosphatase and its regulation. Annu Rev Genet. 2004;38:203-32.
3. Li L, Ljungman M, Dixon JE, Ljungmann M, Dixon JE. The Human Cdc14 Phosphatases Interact with and Dephosphorylate the Tumor Suppressor Protein p53. J Biol Chem. 2000;275:2410-4.
4. Rosso L, Marques AC, Weier M, Lambert N, Lambot M-AA, Vanderhaeghen P, et al. Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein. PLoS Biol. 2008;6:e140.
5. Gray CH, Good VM, Tonks NK, Barford D. The structure of the cell cycle protein Cdc14 reveals a proline-directed protein phosphatase. EMBO J. 2003;22:3524-35.
6. Cho HP, Liu Y, Gomez M, Dunlap J, Wang Y, Tyers M. The dual-specificity phosphatase CDC14B bundles and stabilizes microtubules the dual-specificity phosphatase CDC14B bundles and stabilizes microtubules . Mol Cell Biol. 2005;25:4541-51.
7. Mocciaro A, Schiebel E. Cdc14: a highly conserved family of phosphatases with non-conserved functions? J Cell Sci. 2010;123(Pt 17):2867-76.
8. Mailand N, Falck J, Lukas C, Syljuåsen RG, Welcker M, Bartek J, et al. Rapid destruction of human Cdc25A in response to DNA damage. Science. 2000;288:1425-9.
9. Tumurbaatar I, Cizmecioglu O, Hoffmann I, Grummt I, Voit R. Human Cdc14B promotes progression through mitosis by dephosphorylating Cdc25 and regulating Cdk1/Cyclin B activity. PLoS One. 2011;6:e14711.
10. Bassermann F, Frescas D, Guardavaccaro D, Busino L, Peschiaroli A, Pagano M. The Cdc14B-Cdh1-Plk1 axis controls the G2 DNA-damage-response checkpoint. Cell. 2008;134:256-67.
11. Berdougo E, Nachury MV, Jackson PK, Jallepalli PV. The nucleolar phosphatase Cdc14B is dispensable for chromosome segregation and mitotic exit in human cells. Cell Cycle. 2008;7:1184-90.
12. Mocciaro A, Berdougo E, Zeng K, Black E, Vagnarelli P, Earnshaw W, et al. Vertebrate cells genetically deficient for Cdc14A or Cdc14B retain DNA damage checkpoint proficiency but are impaired in DNA repair. J Cell Biol. 2010;189:631-9.
13. Ovejero S, Ayala P, Bueno A, Sacristán MP. Human Cdc14A regulates Wee1 stability by counteracting CDK-mediated phosphorylation. Mol Biol Cell. 2012;23:4515-25.
14. Guillamot M, Manchado E, Chiesa M, Gómez-López G, Pisano DG, Sacristán MP, et al. Cdc14b regulates mammalian RNA polymerase II and represses cell cycle transcription. Sci Rep. 2011;1:189.
15. Ran FA, Hsu PPD, Wright J, Agarwala V, Scott D a, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013;8:2281-308.
16. Sonoda E, Hochegger H, Saberi A, Taniguchi Y, Takeda S. Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst). 2006;5:1021-9.
17. Valentine CR. The association of nonsense codons with exon skipping. Mutat Res Rev Mutat Res. 1998;411:87-117.
18. Bremmer SC, Hall H, Martinez JS, Eissler CL, Hinrichsen TH, Rossie S, et al. Cdc14 phosphatases preferentially dephosphorylate a subset of cyclin-dependent kinase (Cdk) sites containing phosphoserine. J Biol Chem. 2012;287:1662-9.
19. Hall MC, Jeong DE, Henderson JT, Choi E, Bremmer SC, Iliuk AB, et al. Cdc28 and Cdc14 control stability of the anaphase-promoting complex inhibitor Acm1. J Biol Chem. 2008;283:10396-407.
20. Langeberg LK, Scott JD. Signalling scaffolds and local organization of cellular behaviour. Nat Rev Mol Cell Biol. 2015;16:232-44.
21. Zhu L, Zhang Y, Zhang W, Yang S, Chen J-Q, Tian D. Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics. 2009;10:47.
22. Sakharkar MK, Chow VTK, Kangueane P. Distributions of exons and introns in the human genome. In Silico Biol. 2004;4:387-93.
23. Panic M, Hata S, Neuner A, Schiebel E. The centrosomal linker and microtubules provide dual levels of spatial coordination of centrosomes. PLoS Genet. 2015;11:e1005243.
24. Doyon Y, Choi VM, Xia DF, Vo TD, Gregory PD, Holmes MC. Transient cold shock enhances zinc-finger nuclease-mediated gene disruption. Nat Methods. 2010;7:459-60.
25. Hsu PD, Scott D a, Weinstein J a, Ran FA, Konermann S, Agarwala V, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31:827-32.
26. Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339:823-6.
27. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014;343:80-4.
28. Southern E. Southern blotting. Nat Protoc. 2006;1:518-25.
29. Zhang Y, Ba Y, Liu C, Sun G, Ding L, Gao S, et al. PGC-1alpha induces apoptosis in human epithelial ovarian cancer cells through a PPARgamma-dependent pathway. Cell Res. 2007;17:363-73.
30. Carbery ID, Ji D, Harrington A, Brown V, Weinstein EJ, Liaw L, et al. Targeted genome modification in mice using zinc-finger nucleases. Genetics. 2010;186:451-9.
31. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970;227:680-5.