机器学习方法在CRISPR/Cas9系统中的应用

doi:10.16288/j.yczz.18-135

遗传 ›› 2018, Vol. 40 ›› Issue (9): 704-723.doi: 10.16288/j.yczz.18-135

机器学习方法在CRISPR/Cas9系统中的应用

张桂珊(),杨勇,张灵敏,戴宪华()

中山大学电子与信息工程学院,广州 510006

收稿日期:2018-05-15 修回日期:2018-07-19 出版日期:2018-09-20 发布日期:2018-07-30
作者简介:张桂珊,博士研究生,研究方向：生物信息学。E-mail: zhanggsh7@mail2.sysu.edu.cn
基金资助:
国家自然科学基金项目(61872396)

Application of machine learning in the CRISPR/Cas9 system

Zhang Guishan(),Yang Yong,Zhang Lingmin,Dai Xianhua()

School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou 510006, China

Received:2018-05-15 Revised:2018-07-19 Online:2018-09-20 Published:2018-07-30
Supported by:
Supported by National Natural Science Foundation of China(61872396)

摘要/Abstract

摘要：

基于CRISPR/Cas9系统介导的第三代基因组定点编辑技术,已被广泛应用于基因编辑和基因表达调控等研究领域。如何提高该技术对基因组编辑的效率与特异性、最大限度降低脱靶风险一直是该领域的难点。近年来,机器学习为解决CRISPR/Cas9系统所面临的问题提供了新思路,基于机器学习的CRISPR/Cas9系统已逐渐成为研究热点。本文阐述了CRISPR/Cas9的作用机理,总结了现阶段该技术面临的基因组编辑效率低、存在潜在的脱靶效应、前间区序列邻近基序(PAM)限制识别序列等问题,最后对机器学习应用于优化设计高效向导RNA (sgRNA)序列、预测sgRNA的活性、脱靶效应评估、基因敲除、高通量功能基因筛选等领域的研究现状与发展前景进行了展望,以期为基因组编辑领域的研究提供参考。

关键词: CRISPR/Cas9, 机器学习, sgRNA, 脱靶效应, 基因敲除

Abstract:

The third generation of the CRISPR/Cas9-mediated genome fixed-point editing technology has been widely used in the field of gene editing and gene expression regulation. How to improve the on-target efficiency and specificity of this system, as well as reduce its off-target effects are always the bottleneck in its development. Machine learning provides novel methods to the problems of the CRISPR/Cas9 system, and CRISPR/Cas9-based machine learning has recently become a very hot research topic. In this review, we firstly outline the mechanism of the CRISPR/Cas9 system. Subsequently, we elaborate the current issues of CRISPR/Cas9, including low efficiency and potential off-target effects, and sequence-recognizing limitation from protospacer adjacent motif (PAM). Finally, we summarize the applications of methods within the machine learning framework for optimizing the CRISPR/Cas9 system, such as optimized single-guide RNA (sgRNA) design, CRISPR/Cas9 cleavage efficiency prediction, off-target effects evaluation, gene knock-out as well as high-throughput functional genetic screening and prospects for development.

Key words: CRISPR/Cas9, machine learning, sgRNA, off-target effect, gene knock-out

张桂珊, 杨勇, 张灵敏, 戴宪华. 机器学习方法在CRISPR/Cas9系统中的应用[J]. 遗传, 2018, 40(9): 704-723.

Zhang Guishan, Yang Yong, Zhang Lingmin, Dai Xianhua. Application of machine learning in the CRISPR/Cas9 system[J]. Hereditas(Beijing), 2018, 40(9): 704-723.

参考文献

[1]	Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini L, Zhang F . Multiplex genome engineering using CRISPR/Cas systems. Science, 2013,339(6121):819-823.
[2]	Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA . RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol, 2013,31(3):233-239.
[3]	Hsu PD, Lander ES, Zhang F . Development and applications of CRISPR-Cas9 for genome engineering. Cell, 2014,157(6):1262-1278.
[4]	Fu Y, 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.
[5]	Pattanayak V, Lin S, Guilinger JP, Ma E, 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.
[6]	Wong N, Liu W, Wang X . WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol, 2015,16:218.
[7]	Hinz JM, Laughery MF, Wyrick JJ . Nucleosomes inhibit Cas9 endonuclease activity in vitro. Biochemistry, 2015,54(48):7063-7066.
[8]	Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS . Compact and highly active next- generation libraries for CRISPR-mediated gene repression and activation. Elife, 2016,5:e19760.
[9]	Lee CM, Davis TH, Bao G . Examination of CRISPR/ Cas9 design tools and the effect of target site accessibility on Cas9 activity. Exp Physiol, 2017,103(4):456-460.
[10]	Isaac RS, Jiang FG, Doudna JA, Lim WA, Narlikar GJ, Almeida R . Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Elife, 2016,5:e13450.
[11]	Kosicki M, Tomberg K, Bradley A . Repair of double- strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol, 2018,36(8):765-771.
[12]	Goldberg DE. Genetic Algorithms in Search, Optimization and Machine Learning. Boston, MA, USA: Addison-Wesley Longman Publishing Co., Inc., 1989.
[13]	Listgarten J, Weinstein M, Kleinstiver BP, Sousa AA, Joung JK, Crawford J, Gao K, Hoang L, Elibol M, Doench JG, Fusi N . Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs. Nat Biomed Eng, 2018,2(1):38-47.
[14]	Kim HK, Min S, Song M, Jung S, Choi JW, Kim Y, Lee S, Yoon S, Kim HH . Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity. Nat Biotechnol, 2018,36(3):239-241.
[15]	Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G . CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res, 2014,42(11):7473-7485.
[16]	Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG . Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol, 2017,36(2):179-189.
[17]	Kuscu C, Arslan S, Singh R, Thorpe J, Adli M . Genome-wide analysis reveals characteristics of off- target sites bound by the Cas9 endonuclease. Nat Biotechnol, 2014,32(7):677-683.
[18]	Hart T, Tong A, Chan K, van Leeuwen J, Seetharaman A, Aregger M, Chandrashekhar M, Hustedt N, Seth S, Noonan A , Habsid A, Sizova O, Nedyalkova L, Climie R, Lawson K, Sartori MA, Alibai S, Tieu D, Masud S, Mero P, Weiss A, Brown KR, U?aj M, Billmann M, Rahman M, Costanzo M, Myers CL, Andrews B, Boone C, Durocher D, Moffat J . Evaluation and design of genome-wide CRISPR/Cas9 knockout screens. bioRxiv. 2017,7(8):2719-2727.
[19]	Alkhnbashi OS, Costa F, Shah SA, Garrett RA, Saunders SJ, Backofen R . CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics, 2014,30(17):i489-i496.
[20]	Hart T, Moffat J . BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinformatics, 2016,17:164.
[21]	Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, Choi JW, Woo E, Koh HC, Nam JW, Kim H . In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat Methods, 2017,14(2):153-159.
[22]	Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE . Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology, 2016,34(2):184-191.
[23]	Kuan PF, Powers S, He S, Li K, Zhao X, Huang B . A systematic evaluation of nucleotide properties for CRISPR sgRNA design. BMC Bioinformatics, 2017,18(1):297.
[24]	Chen L, Wang SP, Zhang YH, Li JR, Xing ZH, Yang J, Huang T, Cai YD . Identify key sequence features to improve CRISPR sgRNA efficacy. IEEE Access, 2017,5:26582-26590.
[25]	Shah SA, Vestergaard G, Garrett RA . CRISPR/Cas and CRISPR/Cmr Immune Systems of Archaea. Springer Vienna, 2012: 163-181.
[26]	Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A . Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol, 1987,169(12):5429-5433.
[27]	Jansen R, Embden JD, Gaastra W, Schouls LM . Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol, 2002,43(6):1565-1575.
[28]	Garneau JE, Dupuis M-è, 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]	Horvath P, Barrangou R . CRISPR/Cas, the immune system of bacteria and archaea. Science, 2010,327(5962):167-170.
[30]	Mojica FJM, DíezVillase?or C, García-Martínez J, Almendros C . Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology, 2009,155(pt 3):733-740.
[31]	Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, 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.
[32]	Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O . Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell, 2014,156(5):935-949.
[33]	Lu XJ, Xue HY, Ke ZP, Chen JL, Ji LJ . CRISPR-Cas9: a new and promising player in gene therapy. J Med Genet, 2015,52(5):289-296.
[34]	Rouet P, Smih F, Jasin M . Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol, 1994,14(12):8096-8106.
[35]	Rouet P, Smih F, Jasin M . Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc Natl Acad Sci USA, 1994,91(13):6064-6068.
[36]	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.
[37]	Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA . DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 2014,507(7490):62-67.
[38]	Zhang Y, Ge X, Yang F, Zhang L, Zheng J, Tan X, Jin ZB, Qu J, Gu F . Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells. Sci Rep, 2014,4:5405.
[39]	Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F . DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol, 2013,31(9):827-832.
[40]	Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK . Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature, 2015,523(7561):481-485.
[41]	Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM . CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol, 2013,31(9):833-838.
[42]	O'Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ . A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res, 2015,43(6):3389-3404.
[43]	Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA . Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol, 2014,32(7):670-676.
[44]	Bae S, Kweon J, Kim HS, Kim JS . Microhomology- based choice of Cas9 nuclease target sites. Nat Methods, 2014,11(7):705-706.
[45]	Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE . Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol, 2014,32(12):1262-1267.
[46]	Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ . CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods, 2015,12(10):982-988.
[47]	Wang T, Wei JJ, Sabatini DM, Lander ES . Genetic screens in human cells using the CRISPR-Cas9 system. Science, 2014,343(6166):80-84.
[48]	Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim JS . Analysis of off-target effects of CRISPR/Cas- derived RNA-guided endonucleases and nickases. Genome Res, 2014,24(1):132-141.
[49]	Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK . Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol, 2014,32(3):279-284.
[50]	Koch B, Nijmeijer B, Kueblbeck M, Cai Y, Walther N, Ellenberg J . Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing. Nat Protoc, 2018,13(6):1465-1487.
[51]	Ran FA, Hsu Patrick D, Lin CY, Gootenberg Jonathan S, Konermann S, Trevino AE, Scott David A, Inoue A, Matoba S, Zhang Y . Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 2013,154(6):1380-1389.
[52]	Abadi S, Yan WX, Amar D, Mayrose I . A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLoS Comput Biol, 2017,13(10):e1005807.
[53]	Xie S, Shen B, Zhang C, Huang X, Zhang Y . sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PloS One, 2014,9(6):e100448.
[54]	MacPherson CR, Scherf A . Flexible guide-RNA design for CRISPR applications using Protospacer Workbench. Nat Biotechnol, 2015,33(8):805-806.
[55]	Ma M, Ye AY, Zheng W, Kong L . A guide RNA sequence design platform for the CRISPR/Cas9 system for model organism genomes. Biomed Res Int, 2013,2013:270805.
[56]	Guilinger JP, Thompson DB, Liu DR . Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol, 2014,32(6):577-582.
[57]	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.
[58]	Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK . High-fidelity CRISPR- Cas9 nucleases with no detectable genome-wide off- target effects. Nature, 2016,529(7587):490-495.
[59]	Frock RL, Hu J, Meyers RM, Ho Y-J, Kii E, Alt FW . Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol, 2015,33(2):179-186.
[60]	Rahman MK, Rahman MS . CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems. PLoS One, 2017,12(8):e0181943.
[61]	Erard N, Knott SRV, Hannon GJ . A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout. Mol Cell, 2017,67(6):1080.
[62]	Chari R, Yeo NC, Chavez A, Church GM . sgRNA Scorer 2.0: A species-independent model to predict CRISPR/Cas9 activity. ACS Synth Biol, 2017,6(5):902-904.
[63]	Ma J, Koster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS . CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics, 2016,32(21):3336-3338.
[64]	Prykhozhij SV, Rajan V, Gaston D, Berman JN . CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One, 2015,10(3):e0119372.
[65]	Xu H, Xiao T, Chen C-H, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS . Sequence determinants of improved CRISPR sgRNA design. Genome Res, 2015,25(8):1147-1157.
[66]	Chari R, Mali P, Moosburner M, Church GM . Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods, 2015,12(9):823-826.
[67]	Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M, Liu XS . Improved design and analysis of CRISPR knockout screens. Bioinformatics, 2018, doi: 10.1093/bioinformatics/bty450.
[68]	Box GEP, Cox DR . An Analysis of Transformations. J Roy Statist Soc Ser B, 1964,26(2):211-252.
[69]	Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu XB, Makarova KS, Makarova KS, Koonin E, Sharp PA, Zhang F . In vivo genome editing using Staphylococcus aureus Cas9. Nature, 2015,520(7546):186-191.
[70]	Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F . Rationally engineered Cas9 nucleases with improved specificity. Science, 2016,351(6268):84-88.
[71]	Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK . GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol, 2015,33(2):187-197.
[72]	Hilton IB, D'ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA . Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol, 2015,33(5):510-517.
[73]	Friedman JH . On bias, variance, 0/1—loss, and the curse-of-dimensionality. Data Min Knowl Disc, 1997,1(1):55-77.
[74]	Grabczewski K, Jankowski N . Mining for complex models comprising feature selection and classification. Feat Extrac, 2004,207:473-489.
[75]	Guyon I, Elisseeff A . An introduction to variable and feature selection. J Mach Learn Res, 2003,3:1157-1182.
[76]	Faraggi D, Reiser B . Estimation of the area under the ROC curve. Stat Med, 2002,21(20):3093-3106.
[77]	Robnik-?ikonja M . Improving Random Forests. Lect Not Comput Sci, 2004,3201:359-370.
[78]	Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F . A model-based background adjustment for oligonucleotide expression arrays. Publ Amer Stat Assoc, 2004,99(468):909-917.
[79]	Chen W, Lin H, Feng PM, Ding C, Zuo YC, Chou KC . iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties. PLoS One, 2012,7(10):e47843.
[80]	Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA . Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell, 2015,160(6):1246-1260.
[81]	Sander JD, Joung JK . CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol, 2014,32(4):347-355.
[82]	Graham DB, Root DE . Resources for the design of CRISPR gene editing experiments. Genome Biol, 2015,16:260.
[83]	Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS . CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell, 2013,154(2):442-451.
[84]	Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, Gersbach CA . RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods, 2013,10(10):973-976.
[85]	Chuai GH, Wang QL, Liu Q . In silico meets in vivo: towards computational CRISPR-Based sgRNA design. Trends Biotechnol, 2017,35(1):12-21.
[86]	Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC, Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey-Prevot B, Root DE, Sabatini DM, Taipale J, Perrimon N, Bernards R . Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods, 2006,3(10):777-779.
[87]	Hart T, Brown KR, Sircoulomb F, Rottapel R, Moffat J . Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol Syst Biol, 2014,10:733.
[88]	Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC . Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nat Commun, 2017,8:15178.
[89]	Yan JF, Chuai GH, Zhou C, Zhu CY, Yang J, Zhang C, Gu F, Xu H, Wei J, Liu Q . Benchmarking CRISPR on-target sgRNA design. Brief Bioinform, 2018,19(4):721-724.
[90]	Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS . MAGeCK enables robust identification of essential genes from genome- scale CRISPR/Cas9 knockout screens. Genome Biol, 2014,15(12):554.
[91]	Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R . Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science, 2015,350(6262):823-826.
[92]	Shi J, Wang E, Milazzo JP, Wang Z, Kinney JB, Vakoc CR . Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol, 2015,33(6):661-667.
[93]	Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, Mero P, Dirks P, Sidhu S, Roth FP, Rissland OS, Durocher D, Angers S, Moffat J . High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell, 2015,163(6):1515-1526.
[94]	Ong SH, Li Y, Koike-Yusa H, Yusa K . Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries. Sci Rep, 2017,7(1):7384.
[95]	Evers B, Jastrzebski K, Heijmans JP, Grernrum W, Beijersbergen RL, Bernards R . CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes. Nat Biotechnol, 2016,34(6):631-633.
[96]	Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B . Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell, 2013,155(7):1479-1491.
[97]	Liu H, Wei Z, Dominguez A, Li Y, Wang X, Qi LS . CRISPR-ERA: a comprehensive design tool for CRISPR- mediated gene editing, repression and activation. Bioinformatics, 2015,31(22):3676-3678.
[98]	Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS . Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife, 2016,5, e12677.
[99]	Vidigal JA, Ventura A . Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries. Nat Commun, 2015,6:8083.
[100]	Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, Degennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F . Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol, 2017,35(1):31-34.
[101]	Kim D, Bae S, Park J, Kim E, Kim S, Yu HR, Hwang J, Kim JI, Kim JS . Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods, 2015,12(3):237-243.
[102]	Kim D, Kim S, Kim S, Park J, Kim JS . Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq. Genome Res, 2016,26(3):406-415.
[103]	Haeussler M, Kai S, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneidermaunoury S, Shkumatava A, Teboul L, Kent J, Joly JS, Concordet JP . Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol, 2016,17(1):148.
[104]	Li C, Zong Y, Wang Y, Jin S, Zhang D, Song Q, Zhang R, Gao C . Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion. Genome Biol, 2018,19(1):59.
[105]	Wei Y, Zhang XH, Li DL . The “new favorite” of gene editing technology—single base editors. Hereditas (Beijing), 2017,39(12):1115-1121
[105]	魏瑜, 张晓辉, 李大力 . 基因编辑之“新宠”—单碱基基因组编辑系统. 遗传, 2017,39(12):1115-1121.
[106]	Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, Zeina CM, Gao X, Rees HA, Lin Z, Liu DR . Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature, 2018,556(7699):57-63.
[107]	Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F . RNA editing with CRISPR-Cas13. Science, 2017,358(6366):1019-1027.

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

机器学习方法在CRISPR/Cas9系统中的应用

Application of machine learning in the CRISPR/Cas9 system

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	郑晓飞,黄海燕,吴强. 染色质架构蛋白CTCF调控UGT1基因簇的表达[J]. 遗传, 2019, 41(6): 509-523.
[2]	王珏, 黄娟, 许蕊. 利用CRISPR/Cas9和piggyBac实现果蝇基因组无缝编辑[J]. 遗传, 2019, 41(5): 422-429.
[3]	张楷, 刘蔚, 刘小凤, 陈瑶生, 刘小红, 何祖勇. 利用CRISPR/Cas9系统构建人HPRT1基因定点突变细胞株[J]. 遗传, 2019, 41(10): 939-949.
[4]	刘恒, 李东明, 朱兰玉, 赖乐锦, 闫婉云, 陆玉双, 韦伊, 黄月琪, 方媚, 苏元港, 杨芳, 舒伟. 利用CRISPR/Cas9敲除人源细胞系中LMNA基因的研究[J]. 遗传, 2019, 41(1): 66-75.
[5]	任云晓, 肖茹丹, 娄晓敏, 方向东. 基因编辑技术及其在基因治疗中的应用[J]. 遗传, 2019, 41(1): 18-27.
[6]	赵学彤, 杨亚东, 渠鸿竹, 方向东. 组学时代下机器学习方法在临床决策支持中的应用[J]. 遗传, 2018, 40(9): 693-703.
[7]	刘海龙, 谌阳, 高杨, 周玲, 韩晓松, 赵长志, 杨高娟, 陈毅龙, 杨慧, 谢胜松. 靶向miRNA前体不同类型sgRNA的丰度及特异性评估[J]. 遗传, 2018, 40(7): 561-571.
[8]	唐浚博, 曹浩伟, 许蕊, 张丹丹, 黄娟. 果蝇睾丸基因敲除突变体的构建及表型分析[J]. 遗传, 2018, 40(6): 478-487.
[9]	李慧卿, 陈超, 陈冉冉, 宋雪薇, 李佶娜, 朱延明, 丁晓东. 利用CRISPR/Cas9双基因敲除系统初步解析大豆GmSnRK1.1和GmSnRK1.2对ABA及碱胁迫的响应[J]. 遗传, 2018, 40(6): 496-507.
[10]	童晓玲,方春燕,盖停停,石津,鲁成,代方银. CRISPR/Cas9系统在昆虫中的应用[J]. 遗传, 2018, 40(4): 266-278.
[11]	彭哲也,唐紫珺,谢民主. 机器学习方法在基因交互作用探测中的研究进展[J]. 遗传, 2018, 40(3): 218-226.
[12]	谢晶, 范辰, 张景龙, 张仕强. Ash2l-1/Ash2l-2在小鼠胚胎干细胞中的表达特异性及互补效应[J]. 遗传, 2018, 40(3): 237-249.
[13]	辛高伟, 胡熙璕, 王克剑, 王兴春. Cas9蛋白变体VQR高效识别水稻NGAC前间区序列邻近基序[J]. 遗传, 2018, 40(12): 1112-1119.
[14]	刘旭, 张平, 张晓枫, 李兴, 白宇, 贾克荣, 郭晓东, 张豪, 马晓燕, 仓明, 刘东军, 郭旭东. 利用CRISPR/Cas9系统构建FGF21基因敲除小鼠模型[J]. 遗传, 2018, 40(1): 66-74.
[15]	李红花,刘钢. CRISPR/Cas9在丝状真菌基因组编辑中的应用[J]. 遗传, 2017, 39(5): 355-367.