[1] | Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the human genome. Nat Rev Genet, 2015, 16(3): 172-183. | [2] | Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science, 2007, 315(5813): 848-853. | [3] | Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen WW, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang FT, Zhang JJ, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. Global variation in copy number in the human genome. Nature, 2006, 444(7118): 444-454. | [4] | Maillard AM, Ruef A, Pizzagalli F, Migliavacca E, Hippolyte L, Adaszewski S, Dukart J, Ferrari C, Conus P, M?nnik K, Zazhytska M, Siffredi V, Maeder P, Kutalik Z, Kherif F, Hadjikhani N, 16p11.2 European Consortium, Beckmann JS, Reymond A, Draganski B, Jacquemont S. The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity. Mol Psychiatry, 2015, 20(1): 140-147. | [5] | Horev G, Ellegood J, Lerch JP, Son YEE, Muthuswamy L, Vogel H, Krieger AM, Buja A, Henkelman RM, Wigler M, Mills AA. Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism. Proc Natl Acad Sci USA, 2011, 108(41): 17076-17081. | [6] | Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu T, Baker C, Williams C, Stalker H, Hamid R, Hannig V, Abdel-Hamid H, Bader P, McCracken E, Niyazov D, Leppig K, Thiese H, Hummel M, Alexander N, Gorski J, Kussmann J, Shashi V, Johnson K, Rehder C, Ballif B C, Shaffer L G, Eichler EE. A copy number variation morbidity map of developmental delay. Nat Genet, 2011, 43(9): 838-846. | [7] | de Koning APJ, Gu WJ, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet, 2011, 7(12): e1002384. | [8] | Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu YL, Lovci MT, Morell M, O'Shea KS, Moran JV, Gage FH. L1 retrotransposition in human neural progenitor cells. Nature, 2009, 460(7259): 1127-1131. | [9] | Gerstein MB, Bruce C, Rozowsky JS, Zheng DY, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Res, 2007, 17(6): 669-681. | [10] | Shapiro JA, Von Sternberg R. Why repetitive DNA is essential to genome function. Biol Rev Camb Philos Soc, 2005, 80(2): 227-250. | [11] | Cournac A, Koszul R, Mozziconacci J. The 3D folding of metazoan genomes correlates with the association of similar repetitive elements. Nucleic Acids Res, 2016, 44(1): 245-255. | [12] | Huang HY, Wu Q. CRISPR double cutting through the labyrinthine architecture of 3D genomes. J Genet Genomics, 2016, 43(5): 273-288. | [13] | Ong CT, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet, 2014, 15(4): 234-246. | [14] | Guo Y, Xu Q, Canzio D, Shou J, Li JH, Gorkin DU, Jung I, Wu HY, Zhai YN, Tang YX, Lu YC, Wu YH, Jia ZL, Li W, ZhangMQ, Ren B, Krainer AR, Maniatis T, Wu Q. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell, 2015, 162(4): 900-910. | [15] | Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell, 2007, 128(6): 1231-1245. | [16] | Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gon?alves ?, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell, 2012, 148(1-2): 335-348. | [17] | Monahan K, Rudnick ND, Kehayova PD, Pauli F, Newberry K M, Myers RM, Maniatis T. Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression. Proc Natl Acad Sci USA, 2012, 109(23): 9125-9130. | [18] | Guo Y, Monahan K, Wu HY, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc Natl Acad Sci USA, 2012, 109(51): 21081-21086. | [19] | Zhai YN, Xu Q, Guo Y, Wu Q. Characterization of a cluster of CTCF-binding sites in a protocadherin regulatory region. Hereditas (Beijing), 2016, 38(4): 323-336. | [19] | 翟亚男, 许泉, 郭亚, 吴强. 原钙粘蛋白基因簇调控区域中成簇的CTCF结合位点分析. 遗传, 2016, 38(4): 323-336. | [20] | Li JH, Shou J, Guo Y, Tang YX, Wu YH, Jia ZL, Zhai YN, Chen ZF, Xu Q, Wu Q. Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9. J Mol Cell Biol, 2015, 7(4): 284-298. | [21] | Li JH, Shou J, Wu Q. DNA fragment editing of genomes by CRISPR/Cas9. Hereditas (Beijing), 2015, 37(10): 992-1002. | [21] | 李金环, 寿佳, 吴强. CRISPR/Cas9系统在基因组DNA片段编辑中的应用. 遗传, 2015, 37(10): 992-1002. | [22] | Zhang T, Haws P, Wu Q. Multiple variable first exons: a mechanism for cell-and tissue-specific gene regulation. Genome Res, 2004, 14(1): 79-89. | [23] | Li C, Wu Q. Adaptive evolution of multiple-variable exons and structural diversity of drug-metabolizing enzymes. BMC Evol Biol, 2007, 7: 69. | [24] | Huang HY, Wu Q. Cloning and comparative analyses of the zebrafish UGT repertoire reveal its evolutionary diversity. PLoS One, 2010, 5(2): e9144. | [25] | Wang YM, Huang HY, Wu Q. Characterization of the zebrafish UGT repertoire reveals a new class of drug-metabolizing UDP glucuronosyltransferases. Mol Pharmacol, 2014, 86(1): 62-75. | [26] | Yang J, Cai L, Huang HY, Liu B, Wu Q. Genetic variations and haplotype diversity of the UGT1 gene cluster in the Chinese population. PLoS One, 2012, 7(4): e33988. | [27] | Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao YJ, Pirzada ZA, Eckert MR, Vogel J, Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature, 2011, 471(7340): 602-607. | [28] | Garneau JE, Dupuis Mè, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 2010, 468(7320): 67-71. | [29] | Li TM, Du B. CRISPR-Cas system and coevolution of bacteria and phages. Hereditas (Beijing), 2011, 33(3): 213-218. | [29] | 李铁民, 杜波. CRISPR-Cas系统与细菌和噬菌体的共进化. 遗传, 2011, 33(3): 213-218. | [30] | Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, Hsu PD, Wu XB, Jiang WY, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science, 2013, 339(6121): 819-823. | [31] | Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 2012, 337(6096): 816-821. | [32] | Mali P, Yang LH, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science, 2013, 339(6121): 823-826. | [33] | Wang GC, Ma M, Ye YZ, Xi JZ. High-throughput functional screening using CRISPR/Cas9 system. Hereditas (Beijing), 2016, 38(5): 391-401. | [33] | 王干诚, 马明, 叶延帧, 席建忠. 基于CRISPR/Cas9系统高通量筛选研究功能基因. 遗传, 2016, 38(5): 391-401. | [34] | Fu YF, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol, 2013, 31(9): 822-826. | [35] | Pattanayak V, Lin S, Guilinger JP, Ma EB, Doudna JA, Liu DR. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol, 2013, 31(9): 839-843. | [36] | Xie SS, Zhang Y, Zhang LS, Li GL, Zhao CZ, Ni P, Zhao SH. sgRNA design for the CRISPR/Cas9 system and evaluation of its off-target effects. Hereditas (Beijing), 2015, 37(11): 1125-1136. | [36] | 谢胜松, 张懿, 张利生, 李广磊, 赵长志, 倪攀, 赵书红. CRISPR/Cas9系统中sgRNA设计与脱靶效应评估. 遗传, 2015, 37(11): 1125-1136. | [37] | Tai DJC, Ragavendran A, Manavalan P, Stortchevoi A, Seabra CM, Erdin S, Collins RL, Blumenthal I, Chen XL, Shen YP, Sahin M, Zhang CS, Lee C, Gusella JF, Talkowski ME. Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR. Nat Neurosci, 2016, 19(3): 517-522. | [38] | Cho SW, Kim S, Kim JM, Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol, 2013, 31(3): 230-232. | [39] | Jinek M, East A, Cheng A, Lin S, Ma EB, Doudna J. RNA-programmed genome editing in human cells. eLife, 2013, 2: e00471. | [40] | Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc, 2013, 8(11): 2281-2308. | [41] | Wang HY, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell, 2013, 153(4): 910-918. | [42] | Wong N, Lai P, Pang E, Leung TWT, Lau JWY, Johnson PJ. A comprehensive karyotypic study on human hepatocellular carcinoma by spectral karyotyping. Hepatology, 2000, 32(5): 1060-1068. | [43] | Li YX, Park AI, Mou HW, Colpan C, Bizhanova A, Akama-Garren E, Joshi N, Hendrickson EA, Feldser D, Yin H, Anderson DG, Jacks T, Weng ZP, Xue W. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol, 2015, 16: 111. | [44] | Canver MC, Bauer DE, Dass A, Yien YY, Chung J, Masuda T, Maeda T, Paw BH, Orkin SH. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J Biol Chem, 2014, 289(31): 21312-21324. | [45] | Choi PS, Meyerson M. Targeted genomic rearrangements using CRISPR/Cas technology. Nat Commun, 2014, 5: 3728. | [46] | Kraft K, Geuer S, Will AJ, Chan WL, Paliou C, Borschiwer M, Harabula I, Wittler L, Franke M, Ibrahim DM, Kragesteen BK, Spielmann M, Mundlos S, Lupiá?ez DG, Andrey G. Deletions, inversions, duplications: engineering of structural variants using CRISPR/Cas in mice. Cell Rep, 2015, 10(5): 833-839 | [47] | Maddalo D, Manchado E, Concepcion CP, Bonetti C, Vidigal JA, Han YC, Ogrodowski P, Crippa A, Rekhtman N, de Stanchina E, Lowe SW, Ventura A. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system. Nature, 2014, 516(7531): 423-427. | [48] | Varshney GK, Carrington B, Pei WH, Bishop K, Chen ZL, Fan CX, Xu LS, Jones M, LaFave MC, Ledin J, Sood R, Burgess SM. A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish. Nat Protoc, 2016, 11(12): 2357-2375. | [49] | Fujii W, Kawasaki K, Sugiura K, Naito K. Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res, 2013, 41(20): e187. | [50] | Valenzuela DM, Murphy AJ, Frendewey D, Gale NW, Economides AN, Auerbach W, Poueymirou WT, Adams NC, Rojas J, Yasenchak J, Chernomorsky R, Boucher M, Elsasser AL, Esau L, Zheng J, Griffiths JA Wang, XR, Su H, Xue YZ, Dominguez MG, Noguera I, Torres R, Macdonald LE, Stewart AF, DeChiara1 TM, Yancopoulos GD. High-throughput engineering of the mouse genome coupled with high-resolution expression analysis. Nat Biotechnol, 2003, 21(6): 652-659. |
|