[1] Chylinski K, Makarova KS, Charpentier E, et al. Classification and evolution of type II CRISPR-Cas systems[J]. Nucleic Acids Research, 2014, 42(10):6091-6105. [2] 朱金洁. CRISPR-Cas9介导的玉米基因组定点编辑研究[D]:北京:中国农业大学, 2015. [3] Jiang W, Bikard D, Cox D, et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems[J]. Nature Biotechnology, 2013, 31(3):233-239. [4] Nishimasu H, Ran FA, Hsu PD, et al. Crystal structure of Cas9 in complex with guide RNA and target DNA[J]. Cell, 2011, 156(5):935-949. [5] Chang N, Sun C, Gao L, et al. Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos[J]. Cell Research, 2013, 23(4):465-472. [6] Sturino JM, Joseph MS, Todd RK. Engineered bacteriophage-defence systems in bioprocessing[J]. Nature Reviews Microbiology, 2006, 4(5):395-404. [7] Abedon ST. Bacterial ‘immunity’ against bacteriophages[J]. Bacteriophage, 2012, 2(1):50-54. [8] 王立人. CRISPR/CAS系统介导的基因组大片段DNA编辑[D]:上海:华东师范大学, 2015. [9] Bondy-Denomy J, Davidson AR. To acquire or resist:the complex biological effects of CRISPR-Cas systems[J]. Trends in Microbiology, 2014, 22(4):218-225. [10] Kunin V, Sorek R, Hugenholtz P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats[J]. Genome Biology, 2007, 8(4):61. [11] van Embden JDA, van Gorkom T, Kremer K, et al. Genetic variation and evolutionary origin of the direct repeat locus of mycobacterium tuberculosis complex bacteria[J]. Journal of Bacteriology, 2000, 182(9):2393-2401. [12] Demay C, Liens B, Burguière T, et al. SITVITWEB-A publicly available international multimarker database for studying Mycobac-terium tuberculosis genetic diversity and molecular epidemiology[J]. Infection, Genetics and Evolution, 2012, 12(4):755-766. [13] Zanden AGMVD, Kremer K, Schouls LM, et al. Improvement of differentiation and interpretability of spoligotyping for mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides[J]. Journal of Clinical Microbiology, 2002, 40(12):4628-4639. [14] Lillestøl R, Redder P, Garrett RA, et al. A putative viral defence mechanism in archaeal cells[J]. Archaea, 2006, 2(1):59-72. [15] Choi KR, Sang YL. CRISPR technologies for bacterial systems:current achievements and future directions[J]. Biotechnology Advances, 2016, 34(7):1180-1209. [16] Li C, Cao W. Advances in CRISPR/Cas9-mediated gene editing[J]. Chinese Journal of Biotechnology, 2015, 31(11):7080-7081. [17] Makarova KS, Haft DH, Barrangou R, et al. Evolution and classification of the CRISPR-Cas systems[J]. Nature Reviews Microbiology, 2011, 9(6):467-477. [18] Makarova KS. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems[J]. Biology Direct, 2011, 6(1):38-38. [19] Chylinski K, Le RA, Charpentier E. The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems[J]. RNA Biology, 2013, 10(5):726-737. [20] Wei C, Liu J, Yu Z, et al. TALEN or Cas9 - rapid, efficient and specific choices for genome modifications[J]. Journal of Genetics and Genomics, 2013, 40(6):281-289. [21] Anantharaman V, Iyer LM, Aravind L. Presence of a classical RRM-fold palm domain in Thg1-type 3'-5' nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains[J]. Biology Direct, 2010, 5(1):43. [22] Nickel L, Weidenbach K, Jäger D, et al. Two CRISPR-Cas systems in Methanosarcina mazei strain Gö1 display common processing features despite belonging to different types I and III[J]. RNA Biology, 2013, 10(5):779-791. [23] Marraffini LA, Sontheimer EJ. CRISPR interference limits horizontal gene transfer in Staphylococci by targeting DNA[J]. Science, 2008, 322(322):1843-1845. [24] Hale CR, Majumdar S, Elmore J, et al. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs[J]. Molecular Cell, 2012, 45 (3):292-302. [25] Makarova KS, Koonin EV. Annotation and classification of CRISPR-Cas systems[J]. Methods in Molecular Biology(Clifton, NJ), 2015, 1311:47-75. [26] Fujii W, Kakuta S, Yoshioka S, et al. Zygote-mediated generation of genome-modified mice using Streptococcus thermophilus 1 -derived CRISPR/Cas system[J]. Biochemical & Biophysical Research Communications, 2016, 477(3):473-476. [27] Wu Q, Tun HM, Leung FC, et al. Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275[J]. Scientific Reports, 2014, 4(7500):4974. [28] Horvath P, Romero DA, Coûtémonvoisin AC, et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus[J]. Journal of Bacteriology, 2008, 190(4):1401-1412. [29] 邓凯波, 霍贵成. 嗜热链球菌中CRISPR序列的检测与同源性分析[J]. 食品科学, 2013, 34(3):153-157. [30] Bolotin A, Quinquis B, Sorokin A, et al. Clustered regularly interspaced short palindrome repeats(CRISPRs)have spacers of extrachromosomal origin[J]. Microbiology, 2005, 151(Pt 8):2551-2561. [31] Mojica FJ, Díezvillaseñor C, Garcíamartínez J, et al. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements[J]. Journal of Molecular Evolution, 2005, 60(2):174-182. [32] Goh YJ, Goin C, O’Flaherty S, et al. Specialized adaptation of a lactic acid bacterium to the milk environment:the comparative genomics of Streptococcus thermophilus LMD-9[J]. Microbial Cell Factories, 2011, 10 Suppl 1(1):S22. [33] Brouns SJ, Jore MM, Lundgren M, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes[J]. Science, 2008, 321(5891):960-964. [34] Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096):81. [35] Sapranauskas R, Gasiunas G, Fremaux C, et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli[J]. Nucleic Acids Research, 2011, 39(21):9275-9282. [36] Jinek M, Jiang F, Taylor DW, et al. Structures of Cas9 endonucle-ases reveal RNA-mediated conformational activation[J]. Science, 2014, 343(6176):124799. [37] Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression[J]. Cell, 2013, 152(5):1173-1183. [38] Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE, Church GM. 2013. RNA-guided human genome engineering via Cas9. Science 339:823-826. [39] Zhang L, Jia R, Palange NJ, et al. Large genomic fragment deletions and insertions in mouse using CRISPR/Cas9[J]. PLoS One, 2015, 10(3):e0120396. [40] Oh JH, van Pijkeren JP. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. [J]. Nucleic Acids Research, 2014, 42(17):e131. [41] Yosef I, Goren MG, Edgar R, et al. Using the CRISPR-Cas system to positively select mutants in genes essential for its function[J]. Methods in Molecular Biology, 2015, 1311:233-250. [42] Ding Q, Regan SN, Xia Y, et al. Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs[J]. Cell Stem Cell, 2013, 12(4):393-394. [43] Jinek M, East A, Cheng A, et al. RNA-programmed genome editing in human cells[J]. Elife, 2013, 2(2):e00471. [44] Pattanayak V, Lin S, Guilinger JP, et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity[J]. Nature Biotechnology, 2013, 31(9):839-843. [45] Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes[J]. Nature Biotechnology, 2014, 32(4):347-355. [46] Fu Y, Foden JA, Khayter C, et al. High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells[J]. NatureBiotechnology, 2013, 31(9):822-826. [47] Cho SW, Kim S, Kim Y, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases[J]. Genome Research, 2014, 24(1):377-389. [48] Semenova E, Severinov K. Interference by clustered regularly interspaced short palindromic repeat(CRISPR)RNA is governed by a seed sequence[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(25):10098-10103. [49] Cradick TJ, Fine EJ, Antico CJ, et al. CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity[J]. Nucleic Acids Research, 2013, 41(20):9584-9592. [50] Zhang F. CRISPR/Cas9 for genome editing:progress, implications and challenges[J]. Human Molecular Genetics, 2014, 24(R6):40-48. [51] Gupta RM, Musunuru K. Expanding the genetic editing tool kit:ZFNs, TALENs, and CRISPR-Cas9[J]. The Journal of Clinical Investigation, 2014, 124(10):4154-4161. [52] Shah SA, Shah SA, Erdmann S, et al. Protospacer recognition motifs:mixed identities and functional diversity[J]. RNA Biology, 2013, 10(5):891-899. [53] Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification[J]. Nature Biotechnology, 2014, 32(6):577-582. [54] Tsai SQ, Wyvekens N, Khayter C, et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing[J]. Nature Biotechnology, 2014, 32(6):569-576. [55] Chen S, Sanjana Neville E, Zheng K, et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis[J]. Cell, 2015, 160(6):1246-1260. [56] Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 339(6121):819-823. |