Recent advances in developing molecular tools for targeted genome engineering of mammalian cells
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Various biological molecules naturally existing in diversifiedspecies including fungi, bacteria, and bacteriophage havefunctionalities for DNA binding and processing. The biologicalmolecules have been recently actively engineered for use incustomized genome editing of mammalian cells as themolecule-encoding DNA sequence information and theunderlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newlyconstructed artificial molecular tools have enabledmodifications of specific endogenous genetic elements in thegenome context at efficiencies that are much higher than thatof the conventional homologous recombination basedmethods. This minireview introduces the most recentlyspotlighted molecular genome engineering tools with their keyfeatures and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal ofthe inherent DNA sequence recognition rigidity from theoriginal molecular platforms, the addition of newly tailoredtargeting functions into the engineered molecules, and theenhancement of their targeting specificity. Effective targetedgenome engineering of mammalian cells will enable not onlysophisticated genetic studies in the context of the genome, butalso widely-applicable universal therapeutics based on thepinpointing and correction of the disease-causing geneticelements within the genome in the near future.
Abstract
Various biological molecules naturally existing in diversifiedspecies including fungi, bacteria, and bacteriophage havefunctionalities for DNA binding and processing. The biologicalmolecules have been recently actively engineered for use incustomized genome editing of mammalian cells as themolecule-encoding DNA sequence information and theunderlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newlyconstructed artificial molecular tools have enabledmodifications of specific endogenous genetic elements in thegenome context at efficiencies that are much higher than thatof the conventional homologous recombination basedmethods. This minireview introduces the most recentlyspotlighted molecular genome engineering tools with their keyfeatures and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal ofthe inherent DNA sequence recognition rigidity from theoriginal molecular platforms, the addition of newly tailoredtargeting functions into the engineered molecules, and theenhancement of their targeting specificity. Effective targetedgenome engineering of mammalian cells will enable not onlysophisticated genetic studies in the context of the genome, butalso widely-applicable universal therapeutics based on thepinpointing and correction of the disease-causing geneticelements within the genome in the near future.
참고문헌 (55)
- Gibson DG, "Creation of a bacterial cell controlled by a chemically synthesized genome", Science, 329, pp.52~56 (2010)
- Kim Y, "A library of TAL effector nucleases spanning the human genome", Nat Biotechnol, 31, pp.251~258 (2013)
- Pruett-Miller SM, "Comparison of zinc finger nucleases for use in gene targeting in mammalian cells", Mol Ther, 16, pp.707~717 (2008)
- Liang F, "Chromosomal double-strand break repair in Ku80-deficient cells", Proc Natl Acad Sci U S A, 93, pp.8929~8933 (1996)
- Ramalingam S, "A CRISPR way to engineer the human genome", Genome Biol, 14, pp.107~ (2013)
- Mao Z, "Comparison of nonhomologous end joining and homologous recombination in human cells", DNA Repair, 7, pp.1765~1771 (2008)
- Cornu TI, "DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases", Mol Ther, 16, pp.352~358 (2008)
- Lam KN, "Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays", Nucl Acids Res, 39, pp.4680~4690 (2011)
- Toscano MG, "Use of zinc-finger nucleases to knock out the WAS gene in K562cells: a human cellular model for Wiskott-Aldrich syndrome", Dis Models Mechanisms, 6, pp.544~554 (2013)
- Hockemeyer D, "Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases", Nat Biotechnol, 27, pp.851~857 (2009)
- Perez EE, "Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases", Nat Biotechnol, 26, pp.808~816 (2008)
- Cui X, "Targeted integration in rat and mouse embryos with zinc-finger nucleases", Nat Biotechnol, 29, pp.64~67 (2011)
- Pattanayak V, "Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection", Nat Methods, 8, pp.765~770 (2011)
- Dreier B, "Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains", J Molec Biol, 303, pp.489~502 (2000)
- Dreier B, "Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors", J Biol Chem, 276, pp.29466~29478 (2001)
- Dreier B, "Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors", J Biol Chem, 280, pp.35588~35597 (2005)
- Pruett-Miller SM, "Attenuation of zinc finger nuclease toxicity by small-molecule regulation of protein levels", PLoS Genet, 5, pp.e1000376~ (2009)
- Fu F, "Zinc Finger Database (ZiFDB)v2.0: a comprehensive database of C(2)H(2) zinc fingers and engineered zinc finger arrays", Nucl Acids Res, 41, pp.452~455 (2013)
- Sander JD, "Selection-free zinc-finger-nuclease engineering by context-dependent assembly(CoDA)", Nat Methods, 8, pp.67~69 (2011)
- Szczepek M, "Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases", Nat Biotechnol, 25, pp.786~793 (2007)
- Kim E, "Precision genome engineering with programmable DNA-nicking enzymes", Genome Res, 22, pp.1327~1333 (2012)
- Bogdanove AJ, "Principles and applications of TAL effectors for plant physiology and metabolism", Curr Opin Plant Biol, 19, pp.99~104 (2014)
- Boch J, "Breaking the code of DNA binding specificity of TAL-type III effectors", Science, 326, pp.1509~1512 (2009)
- Moscou MJ, "A simple cipher governs DNA recognition by TAL effectors", Science, 326, pp.1501~ (2009)
- Cermak T, "Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting", Nucleic Acids Res, 39, pp.82~ (2011)
- Mussolino C, "A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity", Nucleic Acids Res, 39, pp.9283~9293 (2011)
- Valton J, "Overcoming transcription activator-like effector(TALE)DNA binding domain sensitivity to cytosine methylation", J Biol Chem, 287, pp.38427~38432 (2012)
- Jones PA, "Functions of DNA methylation: islands, start sites, gene bodies and beyond", Nat Rev Genet, 13, pp.484~492 (2012)
- Weber E, "Assembly of designer TAL effectors by Golden Gate cloning", PLoS One, 6, pp.19722~ (2011)
- Zhang F, "Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription", Nat Biotechnol, 29, pp.149~153 (2011)
- Mali P, "Cas9 as a versatile tool for engineering biology", Nat Methods, 10, pp.957~963 (2013)
- Mali P, "RNA-guided human genome engineering via Cas9", Science, 339, pp.823~826 (2013)
- Cho SW, "Analysis of off-target effects of CRISPR", Cas-derived RNA-guided endonucleases and nickases, 2014, pp.24, 132~141
- Pattanayak V, "High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity", Nat Biotechnol, 31, pp.839~843 (2013)
- Hsu PD, "DNA targeting specificity of RNA-guided Cas9 nucleases", Nat Biotechnol, 31, pp.827~832 (2013)
- Cho SW, "Targeted genome engineering in human cells with the Cas9RNA-guided endonuclease", Nat Biotechnol, 31, pp.230~232 (2013)
- Fu Y, "High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells", Nat Biotechnol, 31, pp.822~826 (2013)
- Cradick TJ, "CRISPR", Cas9 systems targeting beta-globin and CCR5genes have substantial off-target activity, 2013, pp.41, 9584~9592
- Cong L, "Multiplex genome engineering using CRISPR", Cas systems, 2013, pp.339, 819~823
- Bae S, "Cas-OFFinder : a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases", Bioinformatics, 30, pp.1473~1475 (2014)
- Grizot S, "Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds", Nucleic Acids Res, 38, pp.2006~2018 (2010)
- Bolduc JM, "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor", Genes Dev, 17, pp.2875~2888 (2003)
- Moure CM, "The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity", J Molec Biol, 334, pp.685~695 (2003)
- Wang Y, "Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus", Nucleic Acids Res, 42, pp.6463~6475 (2014)
- Stoddard BL, "Homing endonuclease structure and function", Q Rev Biophys, 38, pp.49~95 (2005)
- Petek LM, "Frequent endonuclease cleavage at off-target locations in vivo", Mol Ther, 18, pp.983~986 (2010)
- Boissel S, "megaTALs : a rare-cleaving nuclease architecture for therapeutic genome engineering", Nucleic Acids Res, 42, pp.2591~2601 (2014)
- Gaj T, "A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells", Nucleic Acids Res, 41, pp.3937~3946 (2013)
- Gersbach CA, "Directed evolution of recombinase specificity by split gene reassembly", Nucleic Acids Res, 38, pp.4198~4206 (2010)
- Sarkar I, "HIV-1proviral DNA excision using an evolved recombinase", Science, 316, pp.1912~1915 (2007)
- Hacein-Bey-Abina S, "LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1", Science, 302, pp.415~419 (2003)
- Wu X, "Transcription start regions in the human genome are favored targets for MLV integration", Science, 300, pp.1749~1751 (2003)
- 임광일, "Retroviral integration profiles: their determinants and implications for gene therapy", BMB Reports, 45(4), pp.207~212 (2012), 생화학분자생물학회
- Schroder AR, "HIV-1 integration in the human genome favors active genes and local hotspots", Cell, 110, pp.521~529 (2002)
- Lim KI, "Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties", Proc Natl Acad Sci U S A, 107, pp.12475~12480 (2010)