References
- Smith HO and Wilcox KW (1992) A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. 1970. Biotechnology 24, 38-50
- Capecchi MR (1989) Altering the genome by homologous recombination. Science 244, 1288-1292 https://doi.org/10.1126/science.2660260
- Smithies O, Gregg RG, Boggs SS, Koralewski MA and Kucherlapati RS (1985) Insertion of DNA sequences into the human chromosomal beta-globin locus by homologous recombination. Nature 317, 230-234 https://doi.org/10.1038/317230a0
- Thomas KR, Folger KR and Capecchi MR (1986) High frequency targeting of genes to specific sites in the mammalian genome. Cell 44, 419-428 https://doi.org/10.1016/0092-8674(86)90463-0
- Watts G (2007) Nobel prize is awarded for work leading to "knockout mouse". BMJ 335, 740
- Lin FL, Sperle K and Sternberg N (1985) Recombination in mouse L cells between DNA introduced into cells and homologous chromosomal sequences. Proc Natl Acad Sci U S A 82, 1391-1395 https://doi.org/10.1073/pnas.82.5.1391
- Rouet P, Smih F and Jasin M (1994) Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 14, 8096-8106 https://doi.org/10.1128/MCB.14.12.8096
- Kim YG, Cha J and Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 93, 1156-1160 https://doi.org/10.1073/pnas.93.3.1156
- Boch J, Scholze H, Schornack S et al (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509-1512 https://doi.org/10.1126/science.1178811
- Zhang F, Cong L, Lodato S, Kosuri S, Church GM and Arlotta P (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 29, 149-153 https://doi.org/10.1038/nbt.1775
- Gupta RM and Musunuru K (2014) Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9. J Clin Invest 124, 4154-4161 https://doi.org/10.1172/JCI72992
- Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA and Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 https://doi.org/10.1126/science.1225829
- Mali P, Yang L, Esvelt KM et al (2013) RNA-guided human genome engineering via Cas 9. Science 339, 823-826 https://doi.org/10.1126/science.1232033
- Adli M (2018) The CRISPR tool kit for genome editing and beyond. Nat Commun 9, 1911 https://doi.org/10.1038/s41467-018-04252-2
- Rothkamm K, Kruger I, Thompson LH and Lobrich M (2003) Pathways of DNA double-strand break repair during the mammalian cell cycle. Mol Cell Biol 23, 5706-5715 https://doi.org/10.1128/MCB.23.16.5706-5715.2003
- Mao Z, Bozzella M, Seluanov A and Gorbunova V (2008) DNA repair by nonhomologous end joining and homologous recombination during cell cycle in human cells. Cell Cycle 7, 2902-2906 https://doi.org/10.4161/cc.7.18.6679
- Davis AJ and Chen DJ (2013) DNA double strand break repair via non-homologous end-joining. Transl Cancer Res 2, 130-143
- Chang HH and Lieber MR (2016) Structure-Specific nuclease activities of Artemis and the Artemis: DNA-PKcs complex. Nucleic Acids Res 44, 4991-4997 https://doi.org/10.1093/nar/gkw456
- Her J and Bunting SF (2018) How cells ensure correct repair of DNA double-strand breaks. J Biol Chem 293, 10502-10511 https://doi.org/10.1074/jbc.TM118.000371
- Bennardo N, Cheng A, Huang N and Stark JM (2008) Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair. PLoS Genet 4, e1000110 https://doi.org/10.1371/journal.pgen.1000110
- Chiruvella KK, Liang Z and Wilson TE (2013) Repair of double-strand breaks by end joining. Cold Spring Harb Perspect Biol 5, a012757
- Salsman J and Dellaire G (2017) Precision genome editing in the CRISPR era. Biochem Cell Biol 95, 187-201 https://doi.org/10.1139/bcb-2016-0137
- Branzei D and Foiani M (2008) Regulation of DNA repair throughout the cell cycle. Nat Rev Mol Cell Biol 9, 297-308 https://doi.org/10.1038/nrm2351
- Marechal A and Zou L (2013) DNA damage sensing by the ATM and ATR kinases. Cold Spring Harb Perspect Biol 5, 1-17
- Symington LS (2014) End resection at double-strand breaks: mechanism and regulation. Cold Spring Harb Perspect Biol 6, 1-18
- Buisson R, Niraj J, Pauty J et al (2014) Breast cancer proteins PALB2 and BRCA2 stimulate polymerase eta in recombination-associated DNA synthesis at blocked replication forks. Cell Rep 6, 553-564 https://doi.org/10.1016/j.celrep.2014.01.009
- Jasin M and Rothstein R (2013) Repair of strand breaks by homologous recombination. Cold Spring Harb Perspect Biol 5, a012740 https://doi.org/10.1101/cshperspect.a012740
- Hug N, Longman D and Caceres JF (2016) Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res 44, 1483-1495 https://doi.org/10.1093/nar/gkw010
- Carroll D (2016) Genome editing: progress and challenges for medical applications. Genome Med 8, 120 https://doi.org/10.1186/s13073-016-0378-9
- Port F, Chen HM, Lee T and Bullock SL (2014) Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc Natl Acad Sci U S A 111, E2967-2976 https://doi.org/10.1073/pnas.1405500111
- Sybenga J (1999) What makes homologous chromosomes find each other in meiosis? A review and an hypothesis. Chromosoma 108, 209-219 https://doi.org/10.1007/s004120050371
- Ma CJ, Gibb B, Kwon Y, Sung P and Greene EC (2017) Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament. Nucleic Acids Res 45, 749-761 https://doi.org/10.1093/nar/gkw1125
- Ruan J, Xu J, Chen-Tsai RY and Li K (2017) Genome editing in livestock: Are we ready for a revolution in animal breeding industry? Transgenic Res 26, 715-726 https://doi.org/10.1007/s11248-017-0049-7
- Taleei R and Nikjoo H (2013) Biochemical DSB-repair model for mammalian cells in G1 and early S phases of the cell cycle. Mutat Res 756, 206-212 https://doi.org/10.1016/j.mrgentox.2013.06.004
- Nami F, Basiri M, Satarian L, Curtiss C, Baharvand H and Verfaillie C (2018) Strategies for In Vivo Genome Editing in Nondividing Cells. Trends Biotechnol 36, 770-786 https://doi.org/10.1016/j.tibtech.2018.03.004
- Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR and Ploegh HL (2015) Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 33, 538-542 https://doi.org/10.1038/nbt.3190
- Chu VT, Weber T, Wefers B et al (2015) Increasing the efficiency of homology-directed repair for CRISPR -Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33, 543-548 https://doi.org/10.1038/nbt.3198
- Pinder J, Salsman J and Dellaire G (2015) Nuclear domain 'knock-in' screen for the evaluation and identification of small molecule enhancers of CRISPR-based genome editing. Nucleic Acids Res 43, 9379-9392 https://doi.org/10.1093/nar/gkv993
- Greco GE, Matsumoto Y, Brooks RC, Lu Z, Lieber MR and Tomkinson AE (2016) SCR7 is neither a selective nor a potent inhibitor of human DNA ligase IV. DNA Repair (Amst) 43, 18-23 https://doi.org/10.1016/j.dnarep.2016.04.004
- Leahy JJ, Golding BT, Griffin RJ et al (2004) Identification of a highly potent and selective DNA-dependent protein kinase (DNA-PK) inhibitor (NU7441) by screening of chromenone libraries. Bioorg Med Chem Lett 14, 6083-6087 https://doi.org/10.1016/j.bmcl.2004.09.060
- Munck JM, Batey MA, Zhao Y et al (2012) Chemosensitization of cancer cells by KU-0060648, a dual inhibitor of DNA-PK and PI-3K. Mol Cancer Ther 11, 1789-1798 https://doi.org/10.1158/1535-7163.MCT-11-0535
- Song J, Yang D, Xu J, Zhu T, Chen YE and Zhang J (2016) RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency. Nat Commun 7, 10548 https://doi.org/10.1038/ncomms10548
- Yu S, Song Z, Luo J, Dai Y nd Li N (2011) Over-expression of RAD51 or RAD54 but not RAD51/4 enhances extrachromosomal homologous recombination in the human sarcoma (HT-1080) cell line. J Biotechnol 154, 21-24 https://doi.org/10.1016/j.jbiotec.2011.03.023
- Charpentier M, Khedher AHY, Menoret S et al (2018) CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair. Nat Commun 9, 1133 https://doi.org/10.1038/s41467-018-03475-7
- Robert F, Barbeau M, Ethier S, Dostie J and Pelletier J (2015) Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing. Genome Med 7, 93 https://doi.org/10.1186/s13073-015-0215-6
- Haapaniemi E, Botla S, Persson J, Schmierer B and Taipale J (2018) CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nat Med 24, 927-930 https://doi.org/10.1038/s41591-018-0049-z
- Lin S, Staahl BT, Alla RK and Doudna JA (2014) Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife 3, e04766 https://doi.org/10.7554/eLife.04766
- Yang D, Scavuzzo MA, Chmielowiec J, Sharp R, Bajic A and Borowiak M (2016) Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases. Sci Rep 6, 21264 https://doi.org/10.1038/srep21264
- Song F and Stieger K (2017) Optimizing the DNA Donor Template for Homology-Directed Repair of Double-Strand Breaks. Mol Ther Nucleic Acids 7, 53-60 https://doi.org/10.1016/j.omtn.2017.02.006
- Richardson CD, Kazane KR, Feng SJ et al (2018) CRISPR-Cas9 genome editing in human cells works via the Fanconi Anemia pathway. Nat Genetics 50, 1132-1139 https://doi.org/10.1038/s41588-018-0174-0
- Gutschner T, Haemmerle M, Genovese G, Draetta GF and Chin L (2016) Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair. Cell Rep 14, 1555-1566 https://doi.org/10.1016/j.celrep.2016.01.019
- Orthwein A, Noordermeer SM, Wilson MD et al (2015) A mechanism for the suppression of homologous recombination in G1 cells. Nature 528, 422-426 https://doi.org/10.1038/nature16142
- Zaboikin M, Zaboikina T, Freter C and Srinivasakumar N (2017) Non-Homologous end joining and homology directed DNA repair frequency of double-stranded breaks introduced by genome editing reagents. PLoS One 12, e0169931 https://doi.org/10.1371/journal.pone.0169931
- Suzuki K, Tsunekawa Y, Hernandez-Benitez R et al (2016) In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144-149 https://doi.org/10.1038/nature20565
- Maresca M, Lin VG, Guo N and Yang Y (2013) Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res 23, 539-546 https://doi.org/10.1101/gr.145441.112
- Savic N, Ringnalda FC, Lindsay H et al (2018) Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology- directed repair. Elife 7, 1-18
- Ma M, Zhuang F, Hu X et al (2017) Efficient generation of mice carrying homozygous double-floxp alleles using the Cas9-Avidin/Biotin-donor DNA system. Cell Res 27, 578-581 https://doi.org/10.1038/cr.2017.29
- Gu B, Posfai E and Rossant J (2018) Efficient generation of targeted large insertions by microinjection into two-cellstage mouse embryos. Nat Biotechnol 36, 632-637 https://doi.org/10.1038/nbt.4166
- Oceguera-Yanez F, Kim SI, Matsumoto T et al (2016) Engineering the AAVS1 locus for consistent and scalable transgene expression in human iPSCs and their differentiated derivatives. Methods 101, 43-55 https://doi.org/10.1016/j.ymeth.2015.12.012
- Charlesworth CT, Deshpande PS, Dever DP et al (2018) Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans. bioRxiv https://doi.org/10.1101/243345
- Biehs R, Steinlage M, Barton O et al (2017) DNA Doublestrand break resection occurs during non-homologous end joining in G1 but Is distinct from resection during homologous recombination. Mol Cell 65, 671-684 e675 https://doi.org/10.1016/j.molcel.2016.12.016
- Kosicki M, Tomberg K and Bradley A (2018) Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol 36, 765-771