Genome editing a robust way of modifications, a brief introduction of its tools

Anders C, Niewoehner O, Duerst A, Jinek M. 2014. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569.

Abdelrahman M, Al-Sadi AM, Pour-Aboughadareh A, Burritt DJ, Tran LSP. 2018.  Genome editing using CRISPR/Cas9–targeted mutagenesis: An opportunity for yield improvements of crop plants grown under environmental stresses. Plant Physiology and Biochemistry 131, 31-36.

Andersson M, Turesson H, Nicolia A, Fält AS, Samuelsson M, Hofvander P. 2017. Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR Cas9 expression in protoplasts. Plant cell reports 36, 117-128.

Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551-2561.

Barrangou R, Fremaux C, Deveau H, Richards M, Patrick B, Sylvain M, Romero DA, Horvath P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712.

Bortesi L, Fischer R. 2015. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnology advances 33, 41-52.

Brouns SJJ, Jore MM, Lundgren M, Westra  ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, Van Der Oost J. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964.

Cantos C, Francisco P, Trijatmiko KR, Slamet-Loedin I, Chadha-Mohanty PK. 2014. Identification of “safe harbor” loci in indica rice genome by harnessing the property of zinc-finger nucleases to induce DNA damage and repair. Frontiers in plant science 5, 302.

Cermak T, Doyle EL,Christian M, Wang L, Yong Z, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas Daniel FV. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic acids research 39, e82- e82.

Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M, Sherman A, Arazi T, Gal‐On A. 2016.Development of broad virus resistance in non‐transgenic cucumber using CRISPR/Cas9 technology. Molecular plant pathology 17, 1140-1153.

Charpentier E, Doudna JA. 2013. Biotechnology: Rewriting a genome. Nature 495, 50.

Chen K, Gao C. 2014. Targeted genome modification technologies and their applicationsin cropimprovements. Plant cell reports 33, 575-583.

Chylinski K, Makarova KS, Charpentier E, Koonin EV. 2014. Classification and evolution of type II CRISPR-Cas systems. Nucleic acids research 42, 6091-6105.

Christian M, Qi Y, Zhang Y, Votays DF. 2013. Target mutagensis of Arbidopsis thaliana using engineered TAL effector nucleases (TALENs). G3- Genes Genomics      Genetics 3, 1697-170.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini  LA, Zhang F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823.

Cristobal AR, Guzman NM, Diez-vilasenor C, Gracia-Martinez J. 2014.Target motif affecting natural immunity by a constitutive CRISPER-Cas system in Escherichia coli.plos one 7, e50797.

Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Voge J, Charpentier E. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607.

Deng D, Yan C, Wu J, Pan X, Yan N. 2014. Revisiting the TALE repeat. Protein & cell 5, 297-306.

Gaj T, Gersbach CA, Barbas III CF. 2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in biotechnology 31, 397-405.

Gasperskaja E, Kučinskas V. 2017. The most common technologies and tools for functional genome analysis. Acta medica Lituanica 24, 1-11.

Ghimire B. 2017. Use of Crispr/Cas9 for Development of Disease Resistant Cultivars in Plant Breeding. International Journal of Applied Sciences and Biotechnology 5, 403-409.

Giovannetti E, Mey V, Nannizzi S, Pasqualetti G, Marini L, Del Tacca M, Danesi R. 2005. Cellular and pharmacogenetics foundation of synergistic interaction of pemetrexed and gemcitabine in human non–small-cell lung cancer cells. Molecular pharmacology 68, 110-118.

Golkar Z, Rochelle L, Bagasra O. 2016. Crisprs/Cas9 may provide new method for drug discovery and development. Journal of Molecular Biomarkers & Diagnosis 7(10), 4172.

Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPERdp databases and tools to display CRISPER and to generate dictionaries of spacers and repeats. BMC bioinformatics 8, 172.

Horvath P,Barrangou R. 2010. CRISPER/Cas, the immune system of bacteria and archea. science 327, 167-70.

Ishino Y, Shinagawa H, Makino K, Amemura, M, Nakata A. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of bacteriology 169, 5429-5433.

Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Toki S. 2015. CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochemical and biophysical research communications 467, 76-82.

Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of bacteriology 169, 5429-5433.

Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821.

Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S. 2014. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997.

Joung JK, Sander JD. 2013. TALENs: a widely applications technology for targeted genome editing. Nature Reviews Molecular Cell Biology 14, 49-55.

Kamburova VS, Nikitina EV, Shermatov SE, Buriev ZT, Kumpatla SP, Emani C, Abdurakhmonov IY. 2017. Genome editing in plants: an overview of tools and applications. International Journal of Agronomy 2017.

Kannan B, Jung JH, Moxley GW, Lee SM, Altpeter F. 2018. TALEN‐mediated targeted mutagenesis of more than 100 COMT copies/alleles in highly polyploid sugarcane improves saccharification efficiency without compromising biomass yield. Plant biotechnology journal 16, 856-866.

Knorre, DG, Vlasov VV. 1985. Reactive derivatives of nucleic-acids and their components as address reagents. Uspekhi khimii 54, 1420-1447.

Li T, Liu B, Spalding MH, Weeks DP, Yang B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology 30, 390.

Liu X, Wu S, Xu J, Sui C, Wei J. 2017. Application of CRISPR/Cas9 in plant biology. Acta pharmaceutica sinica B 7, 292-302.

Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf  YI, Yakunin AF. 2011. Evolution and classification of the CRISPR–Cas systems. Nature Reviews Microbiology 9, 467.

Mahfouz M, Li L, Piatek M, Fang X, Mansour H, Bangarusamy D, Zhu JK. 2012 Targeted transcriptional repression using a chimericTALE-SRDX repressor protein. Plant Molecular Biology 78, 311–321.

Mojica FJ, Díez-Villaseñor C, García-Martínez J, Almendros C. 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740.

Mojica FJ, Díez‐Villaseñor C, Soria E, Juez G. 2000. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Molecular microbiology 36, 244-246.

Mojica FJ, García-Martínez J, Soria E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of molecular evolution 60, 174-182.

Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949.

Osakabe K, Osakabe Y, Toki S. 2010. Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proceedings of the National Academy of Sciences 107, 12034-12039.

Palpant N, Dudzinski D. 2013. Zinc finger nucleases: looking toward translation. Gene therapy 20, 121.

Papaioannou I, Simons JP, Owen JS. 2012. Targeted in situ gene correction of dysfunctional APOE alleles to produce atheroprotective plasma ApoE3 protein.Cardiology research and practice 2012.

Piatek AA, Lenaghan SC, Stewart Jr CN. 2018. Advanced editing of the nuclear and plastid genomes in plants. Plant science 273, 42-49.

Rath D, Amlinger L, Rath A, Lundgren M4. 2015. The CRISPER-Cas immune system: biology, mechanisms and aplications. Biochem 117, 119-128.

Ren C, Liu X, Zhang Z, Wang Y, Duan W, Li S, Liang Z. 2016. CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.). Scientific reports 6, 32289.

Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK. 2012. FLASH assembly of TALENs for high-throughput genome editing. Nature Biotechnology 30, 460.

Shah T, Andleeb T, Lateef S, Noor MA. 2018. Genome editing in plants: Advancing crop transformation and overview of tools. Plant Physiology and Biochemistry 131, 12-21.

Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle E A, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X. 2009. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459, 437.

Soda N, Verma L, Giri J. 2018. CRISPR-Cas9 based plant genome editing: significance, opportunities and recent advances. Plant Physiology and Biochemistry 131, 2-11.

Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. 2014. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62.

Sun Q, Lin L, Liu D, Wu D, Fang Y, Wu J, Wang Y. 2018. CRISPR/Cas9-Mediated Multiplex Genome Editing of the BnWRKY11 and BnWRKY70 Genes in Brassica napus L. International journal of molecular sciences 19, 2716.

Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM. 2015. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant physiology 169, 931-945.

Townsend JA, Wright DA, Winfery RJ, Fu F, Maeder ML, Jhong JK, Joung K. 2009. High frequency modification of plant genes using engineered zinc finger nuclesases. Nature 442, 442-445. http://dx.doi.org/10.1038/nature 07845.

Upadhyay SK, Kumar J, Alok A, Tuli R. 2013. RNA-guided genome editing for target gene mutations in wheat. G3: Genes, Genomes, Genetics 3, 2233-2238.

Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Liu YG, Zhao K. 2016. Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PloS one 11, e0154027.

Wang P, Zhang J, Sun L, Ma Y, Xu J, Liang S, Deng J, Tan J, Zhang Q, Tu L. 2018a. High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system. Plant biotechnology journal 16, 137-150.

Wang X, Tu M, Wang D, Liu J, Li Y, Li Z, Wang Y, Wang X. 2018b. CRISPR/Cas9‐mediated efficient targeted mutagenesis in grape in the first generation. Plant biotechnology journal 16, 844-855.

Woo JW, Kim J, Kwon SI, Corvalán C, Cho SW, Kim H, Kim SG, Kim ST, Choe S, Kim JS. 2015. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature biotechnology 33, 1162.

Yin X, Biswal AK, Dionora J, Perdigon KM, Balahadia CP, Mazumdar S, Chater C, Lin HC, Coe RA, Kretzschmar T. 2017. CRISPR-Cas9 and CRISPR-Cpf1 mediated targeting of a stomatal developmental gene EPFL9 in rice. Plant cell reports 36, 745-757.

Zaidi SSA, Mukhtar MS, Mansoor S. 2018. Genome editing: targeting susceptibility genes for plant disease resistance. Trends in biotechnology.

Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, Li X, Pierick CJ, Dobbs D, Peterson T. 2010. High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proceedings of the National Academy of Sciences 107, 12028-12033.

Zhang H, Gou F, Zhang J, Liu W, Li Q, Mao Y, Botella JR, Zhu JK. 2016. TALEN‐mediated targeted mutagenesis produces a large variety of heritable mutations in rice. Plantbiotechnology journal 14, 186-194.

Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N. 2014. The CRISPR/C as9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant biotechnology journal 12, 797-807.

Zhang S, Zhang R, Song G, Gao J, Li, W, Han X, Chen M, LiY, Li G. 2018a. Targeted mutagenesis using the Agrobacterium tumefaciens-mediated CRISPR-Cas9 system in common wheat. BMC plant biology 18, 302.

Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, Chen K, Qiu JL, Gao C. 2016. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nature communications 7, 12617.

Zhang Y, Massel K, Godwin ID, Gao C. 2018b. Applications and potential of genome editing in crop improvement. Genome biology 19, 210.

Zhu B, Zhang W, Zhang T, Liu B, Jiang J. 2015. Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell 27, 2415–26.