基因组编辑技术及其在植物遗传改良上的应用
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摘要
以类转录激活因子效应物核酸酶(transcription activator-like effector nucleases,TALENs)和II型CRISPR(clustered regularly interspaced short palindromic repeats)为代表的基因组编辑技术,是植物基因功能研究和遗传改良的一种高效辅助工具。TALENs和CRISPR/Cas9能够精确地在植物基因组DNA序列上造成双链断裂(double strand break,DSB),激发细胞自身同源重组(homologous recombination,HR)和非同源末端接合(nonhomologous end-joining,NHEJ)的修复机制,从而完成对植物基因组的靶向修饰。本研究对这2种基因组编辑技术在结构特征、技术原理以及在植物靶向修饰上的应用展开了综述,并对TALENs和CRISPR/Cas9系统的应用前景进行了展望。
Technology of precise genome editing based on the transcription activator-like effector nucleases(TALENs)and the type II clustered regularly interpaced short palindromic repeats(CRISPR/Cas9)has been a powerful auxiliary tool for research on genetic functions and improvements of plants.TALENs and CRISPR/Cas9 can induce a double strand break(DSB)between the bound sequence resulting in cellular repairs on DSB through either the homologous recombination(HR)or non-homologous end joining(NHEJ)pathway prior to making modifications on the target genome.This article reviews the information relevant to TALENs and CRISPR/Cas9 based on the structure characteristics,action principle and applications of target modification on plants.Potential applications of the advanced technology were also discussed.
Technology of precise genome editing based on the transcription activator-like effector nucleases(TALENs)and the type II clustered regularly interpaced short palindromic repeats(CRISPR/Cas9)has been a powerful auxiliary tool for research on genetic functions and improvements of plants.TALENs and CRISPR/Cas9 can induce a double strand break(DSB)between the bound sequence resulting in cellular repairs on DSB through either the homologous recombination(HR)or non-homologous end joining(NHEJ)pathway prior to making modifications on the target genome.This article reviews the information relevant to TALENs and CRISPR/Cas9 based on the structure characteristics,action principle and applications of target modification on plants.Potential applications of the advanced technology were also discussed.
引文
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[7]WOOD A J,LO T W,ZEITLER B,et al.Targeted genome editing acrosss pecies using ZFNs and TALENs[J].Science,2011,333(6040):307.
[8]LIU J Y,LI C Q,YU Z S,et al.Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy[J].J Genet Genomics,2012,39(5):209-215.
[9]HOCKEMEYER D,WANG H Y,KIANI S,et al.Genetic engineering of human pluripotent cells using TALE nucleases[J].Nat Biotechnol,2011,29(8):731-734.
[10]MA S Y,ZHANG S L,WANG F,et al.Highly efficient and specific genome editing in silkworm using custom TALENs[J].PLoS One,2012,7(9):e45035.
[11]WATANABE T,OCHIAI H,SAKUMA T,et al.Nontransgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases[J].Nat Commun,2012,3(8):1017.
[12]CARLSON D F,TAN W,LILLICO S G,et al.Efficient TALEN-mediated gene knockout in livestock[J].Proc Natl Acad Sci USA,2012,109(43):17382-17387.
[13]TESSON L,USAL C,MNORET S,et al.Knockout rats generated by embryo microinjection of TALENs[J].Nat Biotechnol,2011,29(8):695-696.
[14]LI T,LIU B,SPALDING M H,et al.High-efficiency TALEN-based gene editing produces disease-resistant rice[J].Nat Biotechnol,2012,30(5):390-392.
[15]MAHFOUZ M M,LI L X,PIATEK M,et al.Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein[J].Plant Mol Biol,2012,78(3):311-321.
[16]LEI Y,GUO X,LIU Y,et al.Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases(TALENs)[J].Proc Natl Acad Sci USA,2012,109(43):17484-17489.
[17]SANDER J D,CADE L,KHAYTER C,et al.Targeted gene disruption in somatic zebrafish cells using engineered TALENs[J].Nat Biotechnol,2011,29(8):697-698.
[18]HUANG P,XIAO A,ZHOU M G,et al.Heritable gene targeting in zebrafish using customized TALENs[J].Nat Biotechnol,2011,29(8):699-700.
[19]BOCH J,SCHOLZE H,SCHORNACK S,et al.Breaking the code of DNA binding specificity of TAL-type III effectors[J].Science,2009,326,1509-1512.
[20]HERBERS K,CONRADA-STRAUCH J,BONAS U.Racespeci city of plant resistance to bacterial spot disease determined by repetitive motifs in a bacterial avirulence protein[J].Nature,1992,356(6365):172-174.
[21]DENG D,YAN C,PAN X,et al.Structural basis for sequence specific recognition of DNA by TAL effectors[J],Science,2012,335(6099):720-733.
[22]MAHFOUZ M M,LI L X,SHAMIMUZZAMAN M,et al.De novo-engineered transcription activator-like effector(TALE)hybrid nuclease with novel DNA binding specificity creates double-strand breaks[J].Proc Natl Acad Sci USA,2011,108(6):2623-2628.
[23]SOREK R,LAWRENCE C M,WIEDENHEFT B.CRISPRmediated adaptive immune systems in bacteria and archaea[J].Annu Rev Biochem,2013,82:237-266.
[24]CONG L,RAN F A,COX D,et al.Multiplex genome engineering using CRISPR/Cas systems[J].Science,2013,339:819-823.
[25]LI T,HUANG S,JIANG W Z,et al.TAL nucleases(TALNs):Hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain[J].Nucleic Acids Research,2011,39(1):359-372.
[26]CHRISTIAN M,CERMAK T,DOYLE E L,et al.Targeting DNA double-strand breaks with TAL effector nucleases[J].Genetics,2010,186:757-761.
[27]JINEK M,CHYLINSKI K,FONFARA I,et al.A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J].Science,2012,337:816-821.
[28]DELTCHEVA E,CHYLINSKI K,SHARMA C M,et al.CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III[J].Nature,2011,471(7340):602-607.
[29]HSU P D,LANDER E S,ZHANG F.Development and Applications of CRISPR-Cas9for Genome Engineering[J].Cell,2014,157:1262-1278.
[30]CERMAK T,DOYLE E L,CHRISTIAN M,et al.Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNAtargeting[J].Nucleic Acids Research,2011,39(17):7879-7890.
[31]LIANG Z,ZHANG K,CHEN K,Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system[J].J Genet Genom,2013,41:63-68.
[32]SHAN Q W,WANG Y P,CHEN K L,et al.Rapid and efficient gene modification in rice and Brachypodium using TALENs[J].Molecular Plant,2013,6(4):1365-1368.
[33]CHEN K L,SHAN Q W,GAO C X.An efficient TALEN mutagenesis system in rice[J].Methods,2014,69:2-8.
[34]WANG Y P,CHENG X,SHAN Q,et al.Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew[J].Nat Biotechnol,2014,32:947-951.
[35]SHAN Q,ZHANG Y,CHEN K,et al.Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology[J].Plant Biotechnol,2015,1-10.
[36]ZHANG H,ZHANG J S,WEI P L,et al.The CRISPR/Cas9system produces specific and homozygous targeted gene editing in rice in one generation[J].Plant Biotechnol,2014,(12):797-807.
[37]MIAO J,GUO D,ZHNAG J,et al.Targeted mutagenesis in rice using CRISPR-Cas system[J].Cell Res,2013,(23):1233-1236.
[38]FENG Z Y,MAO Y F,XU N F,et al.Multi-generation analysis reveals the inheritance,specificity and patterns of CRISPR/Cas induced gene modi cations in Arabidopsis[J].Proc Natl Acad Sci USA,2014,111:4632-4637.
[39]MAO Y,ZHANG H,ZHU J K,et al.Application of the CRISPR-Cas system for efficient genome engineering in plants[J].Mol Plant,2013,(6):2008-2011.
[40]SCHIML S,FAUSER F,PUCHTA H.The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny[J].Nat Biotechnol,2014,80:1139-1150.
[41]HSU P D,SCOTT D A,WEINSTEIN J A,et al.DNA targeting specificity of RNA-guided Cas9nucleases[J].Nat Biotechnol,2013,31:827-832.
[42]BEURDELEY M,BIETZ F,LI J,et al.Compact designer TALENs for efficient genome engineering[J].Nat communications,2013,(4):1762-1769.
[43]SUN N,ZHAO H M.A single-chain TALEN architecture for genome engineering[J].Molecular Bio Systems,2014,(10):446-453.
[44]TSAI S Q,WYVEKENS N,KHAYTER C,et al.Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing[J].Nat Biotechnol,2014,32:569-576.
[2]DURAI S,MANI M,KANDAVELOU K,et al.Zinc finger nucleases:custom-designed molecular scissors for genome engineering of plant and mammalian cells[J].Nucleic Acids Research,2005,33(18):5978-5990
[3]MILLER J C,TAN S,QIAO G,et al.A TALE nuclease architecture for efficient genome editing[J].Nat Biotechnol,2011,29:143-148.
[4]LILLESTOL P K,REDDER P,BARRETT R A,et al.A putative viral defence mechanism in archaeal cells[J].Archaea,2006,2(1):59-72.
[5]DING Q R,STEPHANIE N R,XIA Y L.Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs[J].Cell Stem Cell,2014,(12):393-394.
[6]LI T,HUANG S,ZHAO X F,et al.Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes[J].Nucleic Acids Res,2011,39(14):6315-6325.
[7]WOOD A J,LO T W,ZEITLER B,et al.Targeted genome editing acrosss pecies using ZFNs and TALENs[J].Science,2011,333(6040):307.
[8]LIU J Y,LI C Q,YU Z S,et al.Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy[J].J Genet Genomics,2012,39(5):209-215.
[9]HOCKEMEYER D,WANG H Y,KIANI S,et al.Genetic engineering of human pluripotent cells using TALE nucleases[J].Nat Biotechnol,2011,29(8):731-734.
[10]MA S Y,ZHANG S L,WANG F,et al.Highly efficient and specific genome editing in silkworm using custom TALENs[J].PLoS One,2012,7(9):e45035.
[11]WATANABE T,OCHIAI H,SAKUMA T,et al.Nontransgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases[J].Nat Commun,2012,3(8):1017.
[12]CARLSON D F,TAN W,LILLICO S G,et al.Efficient TALEN-mediated gene knockout in livestock[J].Proc Natl Acad Sci USA,2012,109(43):17382-17387.
[13]TESSON L,USAL C,MNORET S,et al.Knockout rats generated by embryo microinjection of TALENs[J].Nat Biotechnol,2011,29(8):695-696.
[14]LI T,LIU B,SPALDING M H,et al.High-efficiency TALEN-based gene editing produces disease-resistant rice[J].Nat Biotechnol,2012,30(5):390-392.
[15]MAHFOUZ M M,LI L X,PIATEK M,et al.Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein[J].Plant Mol Biol,2012,78(3):311-321.
[16]LEI Y,GUO X,LIU Y,et al.Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases(TALENs)[J].Proc Natl Acad Sci USA,2012,109(43):17484-17489.
[17]SANDER J D,CADE L,KHAYTER C,et al.Targeted gene disruption in somatic zebrafish cells using engineered TALENs[J].Nat Biotechnol,2011,29(8):697-698.
[18]HUANG P,XIAO A,ZHOU M G,et al.Heritable gene targeting in zebrafish using customized TALENs[J].Nat Biotechnol,2011,29(8):699-700.
[19]BOCH J,SCHOLZE H,SCHORNACK S,et al.Breaking the code of DNA binding specificity of TAL-type III effectors[J].Science,2009,326,1509-1512.
[20]HERBERS K,CONRADA-STRAUCH J,BONAS U.Racespeci city of plant resistance to bacterial spot disease determined by repetitive motifs in a bacterial avirulence protein[J].Nature,1992,356(6365):172-174.
[21]DENG D,YAN C,PAN X,et al.Structural basis for sequence specific recognition of DNA by TAL effectors[J],Science,2012,335(6099):720-733.
[22]MAHFOUZ M M,LI L X,SHAMIMUZZAMAN M,et al.De novo-engineered transcription activator-like effector(TALE)hybrid nuclease with novel DNA binding specificity creates double-strand breaks[J].Proc Natl Acad Sci USA,2011,108(6):2623-2628.
[23]SOREK R,LAWRENCE C M,WIEDENHEFT B.CRISPRmediated adaptive immune systems in bacteria and archaea[J].Annu Rev Biochem,2013,82:237-266.
[24]CONG L,RAN F A,COX D,et al.Multiplex genome engineering using CRISPR/Cas systems[J].Science,2013,339:819-823.
[25]LI T,HUANG S,JIANG W Z,et al.TAL nucleases(TALNs):Hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain[J].Nucleic Acids Research,2011,39(1):359-372.
[26]CHRISTIAN M,CERMAK T,DOYLE E L,et al.Targeting DNA double-strand breaks with TAL effector nucleases[J].Genetics,2010,186:757-761.
[27]JINEK M,CHYLINSKI K,FONFARA I,et al.A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J].Science,2012,337:816-821.
[28]DELTCHEVA E,CHYLINSKI K,SHARMA C M,et al.CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III[J].Nature,2011,471(7340):602-607.
[29]HSU P D,LANDER E S,ZHANG F.Development and Applications of CRISPR-Cas9for Genome Engineering[J].Cell,2014,157:1262-1278.
[30]CERMAK T,DOYLE E L,CHRISTIAN M,et al.Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNAtargeting[J].Nucleic Acids Research,2011,39(17):7879-7890.
[31]LIANG Z,ZHANG K,CHEN K,Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system[J].J Genet Genom,2013,41:63-68.
[32]SHAN Q W,WANG Y P,CHEN K L,et al.Rapid and efficient gene modification in rice and Brachypodium using TALENs[J].Molecular Plant,2013,6(4):1365-1368.
[33]CHEN K L,SHAN Q W,GAO C X.An efficient TALEN mutagenesis system in rice[J].Methods,2014,69:2-8.
[34]WANG Y P,CHENG X,SHAN Q,et al.Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew[J].Nat Biotechnol,2014,32:947-951.
[35]SHAN Q,ZHANG Y,CHEN K,et al.Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology[J].Plant Biotechnol,2015,1-10.
[36]ZHANG H,ZHANG J S,WEI P L,et al.The CRISPR/Cas9system produces specific and homozygous targeted gene editing in rice in one generation[J].Plant Biotechnol,2014,(12):797-807.
[37]MIAO J,GUO D,ZHNAG J,et al.Targeted mutagenesis in rice using CRISPR-Cas system[J].Cell Res,2013,(23):1233-1236.
[38]FENG Z Y,MAO Y F,XU N F,et al.Multi-generation analysis reveals the inheritance,specificity and patterns of CRISPR/Cas induced gene modi cations in Arabidopsis[J].Proc Natl Acad Sci USA,2014,111:4632-4637.
[39]MAO Y,ZHANG H,ZHU J K,et al.Application of the CRISPR-Cas system for efficient genome engineering in plants[J].Mol Plant,2013,(6):2008-2011.
[40]SCHIML S,FAUSER F,PUCHTA H.The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny[J].Nat Biotechnol,2014,80:1139-1150.
[41]HSU P D,SCOTT D A,WEINSTEIN J A,et al.DNA targeting specificity of RNA-guided Cas9nucleases[J].Nat Biotechnol,2013,31:827-832.
[42]BEURDELEY M,BIETZ F,LI J,et al.Compact designer TALENs for efficient genome engineering[J].Nat communications,2013,(4):1762-1769.
[43]SUN N,ZHAO H M.A single-chain TALEN architecture for genome engineering[J].Molecular Bio Systems,2014,(10):446-453.
[44]TSAI S Q,WYVEKENS N,KHAYTER C,et al.Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing[J].Nat Biotechnol,2014,32:569-576.