Highly efficient genome editing via CRISPR/Cas9 to create clock gene knockout cells

Journal of Biological Rhythms

Volumn 30, Issue 5, 2015, Pages 389-395

  Korge, Sandra ^a   Grudziecki, Astrid ^a   Kramer, Achim ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

Circadian rhythms; Clock genes; CRISPR Cas9; Fbxl3; Genome editing

Indexed keywords

ARNTL PROTEIN, HUMAN; CRY1 PROTEIN, HUMAN; CRYPTOCHROME; F BOX PROTEIN; FBXL3 PROTEIN, HUMAN; LUCIFERASE; TRANSCRIPTION FACTOR ARNTL;

BIOLOGICAL MODEL; CIRCADIAN RHYTHM; CRISPR CAS SYSTEM; GENE INACTIVATION; GENETICS; HEK293 CELL LINE; HUMAN; HUMAN GENOME; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROCEDURES; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TUMOR CELL LINE; WESTERN BLOTTING;

ARNTL TRANSCRIPTION FACTORS; BASE SEQUENCE; BLOTTING, WESTERN; CELL LINE, TUMOR; CIRCADIAN CLOCKS; CRISPR-CAS SYSTEMS; CRYPTOCHROMES; F-BOX PROTEINS; GENE KNOCKOUT TECHNIQUES; GENOME, HUMAN; HEK293 CELLS; HUMANS; LUCIFERASES; MODELS, GENETIC; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 84960385154     PISSN: 07487304     EISSN: 15524531     Source Type: Journal    
DOI: 10.1177/0748730415597519     Document Type: Article

References (31)

1. Agne M, Blank I, Emhardt AJ, Gäbelein CG, Gawlas F, Gillich N, Gonschorek P, Juretschke TJ, Krämer SD, Louis N, et al. (2014) Modularized CRISPR/dCas9 effector toolkit for target-specific gene regulation. ACS Synth Biol 3:986-989.
2. Bell CC, Magor GW, Gillinder KR, and Perkins AC (2014) A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing. BMC Genomics 15:1002.
3. Brown SA, Fleury-Olela F, Nagoshi E, Hauser C, Juge C, Meier CA, Chicheportiche R, Dayer JM, Albrecht U, and Schibler U (2005) The period length of fibroblast circadian gene expression varies widely among human individuals. PLoS Biol 3:e338.
4. Bunger MK, Wilsbacher LD, Moran SM, Clendenin C, Radcliffe LA, Hogenesch JB, Simon MC, Takahashi JS, and Bradfield CA (2000) Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 103:1009-1017.
5. Busino L, Bassermann F, Maiolica A, Lee C, Nolan PM, Godinho SI, Draetta GF, and Pagano M (2007) SCFFbxl3 controls the oscillation of the circadian clock by directing the degradation of cryptochrome proteins. Science 316:900-904.
6. Cho SW, Kim S, Kim JM, and Kim JS (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31:230-232.
7. Debruyne JP, Noton E, Lambert CM, Maywood ES, Weaver DR, and Reppert SM (2006) A clock shock: mouse CLOCK is not required for circadian oscillator function. Neuron 50:465-477.
8. Dibner C, Schibler U, and Albrecht U (2010) The mammalian circadian timing system: organization and coordination of central and peripheral clocks. Annu Rev Physiol 72:517-549.
9. Gaj T, Gersbach CA, and Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397-405.
10. Godinho SI, Maywood ES, Shaw L, Tucci V, Barnard AR, Busino L, Pagano M, Kendall R, Quwailid MM, et al. (2007) The after-hours mutant reveals a role for Fbxl3 in determining mammalian circadian period. Science 316:897-900.
11. Hirano A, Yumimoto K, Tsunematsu R, Matsumoto M, Oyama M, Kozuka-Hata H, Nakagawa T, Lanjakornsiripan D, Nakayama KI, et al. (2013) FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. Cell 152:1106-1118.
12. Koike-Yusa H, Li Y, Tan EP, Velasco-Herrera Mdel C, and Yusa K (2014) Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol 32:267-273.
13. Lamia KA, Sachdeva UM, Di Tacchio L, Williams EC, Alvarez JG, Egan DF, Vasquez DS, Juguilon H, Panda S, et al. (2009) AMPK regulates the circadian clock by cryptochrome phosphorylation and degradation. Science 326:437-440.
14. Maggio I and Gonçalves MA (2015) Genome editing at the crossroads of delivery, specificity, and fidelity. Trends Biotechnol 33:280-291.
15. Maier B, Wendt S, Vanselow JT, Wallach T, Reischl S, Oehmke S, Schlosser A, and Kramer A (2009) A large-scale functional RNAi screen reveals a role for CK2 in the mammalian circadian clock. Genes Dev 23:708-718.
16. Merlin C, Beaver LE, Taylor OR, Wolfe SA, and Reppert SM (2013) Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases. Genome Res 23:159-168.
17. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, and Zhang F (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8:2281-2308.
18. Sanjana NE, Shalem O, and Zhang F (2014) Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods 11:783-784.
19. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, et al. (2014) Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343:84-87.
20. Shi G, Xing L, Liu Z, Qu Z, Wu X, Dong Z, Wang X, Gao X, Huang M, Yan J, et al. (2013) Dual roles of FBXL3 in the mammalian circadian feedback loops are important for period determination and robustness of the clock. Proc Natl Acad Sci U S A 110:4750-4755.
21. Siepka SM, Yoo SH, Park J, Song W, Kumar V, Hu Y, Lee C, and Takahashi JS (2007) Circadian mutant Overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression. Cell 129:1011-1023.
22. Swiech L, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, Sur M, and Zhang F (2015) In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat Biotechnol 33:102-106.
23. Trevino AE and Zhang F (2014) Genome editing using Cas9 nickases. Methods Enzymol 546:161-174.
24. van der Horst GT, Muijtjens M, Kobayashi K, Takano R, Kanno S, Takao M, de Wit J, Verkerk A, Eker AP, van Leenen D, et al. (1999) Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature 398:627-630.
25. Wang T, Wei JJ, Sabatini DM, and Lander ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science 343:80-84.
26. Wang M, Zhong Z, Zhong Y, Zhang W, and Wang H (2015) The zebrafish period2 protein positively regulates the circadian clock through mediation of retinoic acid receptor (RAR)-related orphan receptor α (Rorα). J Biol Chem 290:4367-4382.
27. Wijshake T, Baker DJ, and van de Sluis B (2014) Endonucleases: new tools to edit the mouse genome. Biochim Biophys Acta 1842:1942-1950.
28. Yoo SH, Mohawk JA, Siepka SM, Shan Y, Huh SK, Hong HK, Kornblum I, Kumar V, Koike N, Xu M, et al. (2013) Competing E3 ubiquitin ligases govern circadian periodicity by degradation of CRY in nucleus and cytoplasm. Cell 152:1091-1105.
29. Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW 3RD, et al. (2009) A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell 139:199-210.
30. Zheng B, Albrecht U, Kaasik K, Sage M, Lu W, Vaishnav S, Li Q, Sun ZS, Eichele G, Bradley A, et al. (2001) Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock. Cell 105:683-694.
31. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, and Wei W (2014) High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509:487-491.