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Part I - Biology of Endonucleases (Zinc-Finger Nuclease, TALENs and CRISPRs) and Regulatory Networks

Published online by Cambridge University Press:  30 July 2018

Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
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Summary

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Chapter
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Genome Editing and Engineering
From TALENs, ZFNs and CRISPRs to Molecular Surgery
, pp. 1 - 68
Publisher: Cambridge University Press
Print publication year: 2018

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References

References

Anders, C, Niewoehner, O, Duerst, A, Jinek, M. 2014. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513: 569573.CrossRefGoogle ScholarPubMed
Arribere, JA, Bell, RT, Fu, BXH, et al. 2014. Efficient marker-free recovery of custom genetic modifications with CRISPR/Cas9 in Caenorhabditis elegans. Genetics 198: 837846.CrossRefGoogle ScholarPubMed
Bell, RT, Fu, BXH, Fire, AZ. 2016. Cas9 variants expand the target repertoire in Caenorhabditis elegans. Genetics 202: 381388.CrossRefGoogle ScholarPubMed
Boch, J, Scholze, H, Schornack, S, et al. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326: 15091512.CrossRefGoogle ScholarPubMed
Bogdanove, AJ, Schornack, S, Lahaye, T. 2010. TAL effectors: finding plant genes for disease and defense. Curr Opin Plant Biol 13: 394401.CrossRefGoogle ScholarPubMed
Boulin, T, Bessereau, J-L. 2007. Mos1-mediated insertional mutagenesis in Caenorhabditis elegans. Nat Protoc 2: 12761287.CrossRefGoogle ScholarPubMed
Brenner, S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 7194.CrossRefGoogle ScholarPubMed
Carroll, D. 2014. Genome engineering with targetable nucleases. Annu Rev Biochem 83: 409439.CrossRefGoogle ScholarPubMed
Cencic, R, Miura, H, Malina, A, et al. 2014. Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage. PLoS One 9: e109213.CrossRefGoogle ScholarPubMed
Chen, B, Gilbert, LA, Cimini, BA, et al. 2013a. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155: 14791491.CrossRefGoogle ScholarPubMed
Chen, C, Fenk, LA, de Bono, M. 2013b. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res 41: e193.CrossRefGoogle ScholarPubMed
Chen, X, Li, M, Feng, X, Guang, S. 2015. Targeted chromosomal translocations and essential gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans. Genetics 201: 12951306.CrossRefGoogle ScholarPubMed
Cheng, AW, Wang, H, Yang, H, et al. 2013. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 23: 11631171.CrossRefGoogle ScholarPubMed
Chiu, H, Schwartz, HT, Antoshechkin, I, Sternberg, PW. 2013. Transgene-free genome editing in Caenorhabditis elegans using CRISPR-Cas. Genetics 195: 11671171.CrossRefGoogle ScholarPubMed
Cho, SW, Lee, J, Carroll, D, Kim, J-S, Lee, J. 2013. Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9–sgRNA ribonucleoproteins. Genetics 195: 11771180.CrossRefGoogle ScholarPubMed
Cong, L, Ran, FA, Cox, D, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819823.CrossRefGoogle ScholarPubMed
Conradt, B, Xue, D. 2005. Programmed cell death. Wormbook www.wormbook.org/chapters/www_programcelldeath/programcelldeath.html 113. (Accessed September 30, 2016).CrossRefGoogle Scholar
C. elegans Sequencing Consortium 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 20122018.CrossRefGoogle Scholar
Dickinson, DJ, Pani, AM, Heppert, JK, Higgins, CD, Goldstein, B. 2015. Streamlined genome engineering with a self-excising drug selection cassette. Genetics 200: 10351049.CrossRefGoogle ScholarPubMed
Dickinson, DJ, Ward, JD, Reiner, DJ, Goldstein, B. 2013. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods 10: 10281034.CrossRefGoogle ScholarPubMed
Doench, JG, Fusi, N, Sullender, M, et al. 2016. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 34: 184191.CrossRefGoogle ScholarPubMed
Doench, JG, Hartenian, E, Graham, DB, et al. 2014. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 32: 12621267.CrossRefGoogle ScholarPubMed
Dorman, JB, Albinder, B, Shroyer, T, Kenyon, C. 1995. The age-1 and daf-2 genes function in a common pathway to control the lifespan of Caenorhabditis elegans. Genetics 141: 13991406.CrossRefGoogle Scholar
Doudna, JA, Charpentier, E. 2014. Genome editing: the new frontier of genome engineering with CRISPR-Cas9. Science 346: 1258096.CrossRefGoogle ScholarPubMed
Edgley, M, D’Souza, A, Moulder, G, et al. 2002. Improved detection of small deletions in complex pools of DNA. Nucleic Acids Res 30: e52e52.CrossRefGoogle ScholarPubMed
Ellis, HM, Horvitz, HR. 1986. Genetic control of programmed cell death in the nematode C. elegans. Cell 44: 817829.CrossRefGoogle ScholarPubMed
Ellis, RE, Jacobson, DM, Horvitz, HR. 1991. Genes required for the engulfment of cell corpses during programmed cell death in Caenorhabditis elegans. Genetics 129: 7994.CrossRefGoogle ScholarPubMed
Farboud, B, Meyer, BJ. 2015. Dramatic enhancement of genome editing by CRISPR/Cas9 through improved guide RNA design. Genetics 199: 959971.CrossRefGoogle ScholarPubMed
Félix, M-A, Braendle, C, Cutter, AD. 2014. A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species. PLoS One 9: e94723.CrossRefGoogle ScholarPubMed
Fire, A, Xu, S, Montgomery, MK, et al. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806811.CrossRefGoogle ScholarPubMed
Friedland, AE, Tzur, YB, Esvelt, KM, et al. 2013. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10: 741743.CrossRefGoogle Scholar
Frøkjær-Jensen, C, Davis, MW, Ailion, M, Jorgensen, EM. 2012. Improved Mos1-mediated transgenesis in C. elegans. Nat Methods 9: 117118.CrossRefGoogle ScholarPubMed
Frøkjær-Jensen, C, Davis, MW, Hollopeter, G, et al. 2010. Targeted gene deletions in C. elegans using transposon excision. Nat Methods 7: 451453.CrossRefGoogle Scholar
Frøkjær-Jensen, C, Davis, WM, Hopkins, CE, et al. 2008. Single-copy insertion of transgenes in Caenorhabditis elegans. Nat Genet 40: 13751383.CrossRefGoogle ScholarPubMed
Frøkjaer-Jensen, C, Davis, MW, Sarov, M, et al. 2014. Random and targeted transgene insertion in C. elegans using a modified Mosl transposon. Nat Methods 11: 529534.CrossRefGoogle Scholar
Fruscoloni, P, Zamboni, M, Panetta, G, De Paolis, A, Tocchini-Valentini, GP. 1995. Mutational analysis of the transcription start site of the yeast tRNA(Leu3) gene. Nucleic Acids Res 23: 29142918.CrossRefGoogle ScholarPubMed
Fu, BXH, Hansen, LL, Artiles, KL, Nonet, ML, Fire, AZ. 2014. Landscape of target: guide homology effects on Cas9-mediated cleavage. Nucleic Acids Res 42: 1377813787.CrossRefGoogle ScholarPubMed
Gagnon, JA, Valen, E, Thyme, SB, et al. 2014. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9: e98186.CrossRefGoogle ScholarPubMed
Garneau, JE, Dupuis, M-È, Villion, M, et al. 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468: 6771.CrossRefGoogle ScholarPubMed
Gilbert, LA, Horlbeck, MA, Adamson, B, et al. 2014. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159: 647661.CrossRefGoogle ScholarPubMed
Gilbert, LA, Larson, MH, Morsut, L, et al. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154: 442451.CrossRefGoogle ScholarPubMed
Hengartner, MO, Ellis, R, Horvitz, R. 1992. Caenorhabditis elegans gene ced-9 protects cells from programmed cell death. Nature 356: 494499.CrossRefGoogle ScholarPubMed
Hinz, JM, Laughery, MF, Wyrick, JJ. 2015. Nucleosomes inhibit cas9 endonuclease activity in vitro. Biochemistry (Mosc) 54: 70637066.CrossRefGoogle ScholarPubMed
Horlbeck, MA, Witkowsky, LB, Guglielmi, B, et al. 2016. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife 5.CrossRefGoogle ScholarPubMed
Hsu, PD, Lander, ES, Zhang, F. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157: 12621278.CrossRefGoogle Scholar
Hwang, WY, Fu, Y, Reyon, D, et al. 2013a. Heritable and precise zebrafish genome editing using a CRISPR-Cas system. PLoS One 8: e68708.CrossRefGoogle ScholarPubMed
Hwang, WY, Fu, Y, Reyon, D, et al. 2013b. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31: 227229.CrossRefGoogle ScholarPubMed
Isaac, RS, Jiang, F, Doudna, JA, et al. 2016. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. eLife 5.CrossRefGoogle ScholarPubMed
Iwata, S, Yoshina, S, Suehiro, Y, Hori, S, Mitani, S. 2016. Engineering new balancer chromosomes in C. elegans via CRISPR/Cas9. Sci Rep 6: 33840.CrossRefGoogle Scholar
Jansen, G, Hazendonk, E, Thijssen, KL, Plasterk, RHA. 1997. Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat Genet 17: 119121.CrossRefGoogle ScholarPubMed
Jinek, M, Chylinski, K, Fonfara, I, et al. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816821.CrossRefGoogle ScholarPubMed
Katic, I, Großhans, H. 2013. Targeted heritable mutation and gene conversion by Cas9-CRISPR in Caenorhabditis elegans. Genetics 195: 11731176.CrossRefGoogle ScholarPubMed
Katic, I, Xu, L, Ciosk, R. 2015. CRISPR/Cas9 genome editing in Caenorhabditis elegans: evaluation of templates for homology-mediated repair and knock-ins by homology-independent DNA repair. G3 Genes, Genomes, Genetics 5: 16491656.CrossRefGoogle ScholarPubMed
Kent, T, Mateos-Gomez, PA, Sfeir, A, Pomerantz, RT. 2016. Polymerase θ is a robust terminal transferase that oscillates between three different mechanisms during end-joining. eLife 5.CrossRefGoogle ScholarPubMed
Kenyon, C, Chang, J, Gensch, E, Rudner, A, Tabtiang, R. 1993. A C. elegans mutant that lives twice as long as wild type. Nature 366: 461464.CrossRefGoogle Scholar
Kim, H, Ishidate, T, Ghanta, KS, Seth, M, et al. 2014. A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans. Genetics 197: 10691080.CrossRefGoogle ScholarPubMed
Kimura, KD, Tissenbaum, HA, Liu, Y, Ruvkun, G. 1997. daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Science 277: 942946.CrossRefGoogle ScholarPubMed
Kiontke, KC, Félix, M-A, Ailion, M, et al. 2011. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol Biol 11: 339.CrossRefGoogle ScholarPubMed
Kleinstiver, BP, Prew, MS, Tsai, SQ, et al. 2015. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523: 481485.CrossRefGoogle ScholarPubMed
Komor, AC, Kim, YB, Packer, MS, Zuris, JA, Liu, DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533: 420424.CrossRefGoogle ScholarPubMed
Konermann, S, Brigham, MD, Trevino, AE, et al. 2013. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500: 472476.CrossRefGoogle ScholarPubMed
Lee, RC, Feinbaum, RL, Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843854.CrossRefGoogle Scholar
Li, W, Yi, P, Ou, G. 2015. Somatic CRISPR-Cas9-induced mutations reveal roles of embryonically essential dynein chains in Caenorhabditis elegans cilia. J Cell Biol 208: 683692.CrossRefGoogle ScholarPubMed
Lin, K, Dorman, JB, Rodan, A, Kenyon, C. 1997. daf-16: an HNF-3/forkhead family member that can function to double the life-span of Caenorhabditis elegans. Science 278: 13191322.CrossRefGoogle ScholarPubMed
Liu, H, Wei, Z, Dominguez, A, et al. 2015. CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinforma Oxf Engl 31: 36763678.CrossRefGoogle ScholarPubMed
Lo, T-W, Pickle, CS, Lin, S, et al. 2013. Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics 195: 331348.CrossRefGoogle ScholarPubMed
Maeder, ML, Linder, SJ, Cascio, VM, et al. 2013. CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10: 977979.CrossRefGoogle ScholarPubMed
Mali, P, Aach, J, Stranges, PB, et al. 2013a. Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31: 833838.CrossRefGoogle ScholarPubMed
Mali, P, Esvelt, KM, Church, GM. 2013b. Cas9 as a versatile tool for engineering biology. Nat Methods 10: 957963.CrossRefGoogle ScholarPubMed
Markov, GV, Meyer, JM, Panda, O, et al. 2016. Functional conservation and divergence of daf-22 paralogs in Pristionchus pacificus dauer development. Mol Biol Evol 33: 25062514.CrossRefGoogle ScholarPubMed
McKenna, A, Findlay, GM, Gagnon, JA, et al. 2016. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353: aaf7907.CrossRefGoogle ScholarPubMed
Mello, CC, Kramer, JM, Stinchcomb, D, Ambros, V. 1991. Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J 10: 39593970.CrossRefGoogle Scholar
Mitani, S. 1995. Genetic regulation of mec-3 gene expression implicated in the specification of the mechanosensory neuron cell types in Caenorhabditis elegans. Dev Growth Differ 37: 551557.CrossRefGoogle ScholarPubMed
Mojica, FJM, Díez-Villaseñor, C, García-Martínez, J, Almendros, C. 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiol Read Engl 155: 733740.CrossRefGoogle ScholarPubMed
Montague, TG, Cruz, JM, Gagnon, JA, Church, GM, Valen, E. 2014. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42: W401W407.CrossRefGoogle ScholarPubMed
Moreno-Mateos, MA, Vejnar, CE, Beaudoin, J-D, et al. 2015. CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo. Nat Methods 12: 982988.CrossRefGoogle ScholarPubMed
Morris, JZ, Tissenbaum, HA, Ruvkun, G. 1996. A phosphatidylinositol-3-OH kinase family member regulating longevity and diapause in Caenorhabditis elegans. Nature 382: 536539.CrossRefGoogle ScholarPubMed
Morton, J, Davis, MW, Jorgensen, EM, Carroll, D. 2006. Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proc Natl Acad Sci USA 103: 1637016375.CrossRefGoogle ScholarPubMed
Moscou, MJ, Bogdanove, AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326: 1501.CrossRefGoogle ScholarPubMed
Nelles, DA, Fang, MY, O’Connell, MR, et al. 2016. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165: 488496.CrossRefGoogle ScholarPubMed
Nishida, K, Arazoe, T, Yachie, N, et al. 2016. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353: aaf8729.CrossRefGoogle ScholarPubMed
O’Connell, MR, Oakes, BL, Sternberg, SH, et al. 2014. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516: 263266.CrossRefGoogle ScholarPubMed
Ogg, S, Paradis, S, Gottlieb, S, et al. 1997. The Fork head transcription factor DAF-16 transduces insulin-like metabolic and longevity signals in C. elegans. Nature 389: 994999.CrossRefGoogle ScholarPubMed
Pabo, CO, Peisach, E, Grant, RA. 2001. Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 70: 313340.CrossRefGoogle ScholarPubMed
Paix, A, Folkmann, A, Rasoloson, D, Seydoux, G. 2015. High efficiency, homology-directed genome editing in Caenorhabditis elegans using CRISPR-Cas9 ribonucleoprotein complexes. Genetics 201: 4754.CrossRefGoogle ScholarPubMed
Paix, A, Wang, Y, Smith, HE, et al. 2014. Scalable and versatile genome editing using linear DNAs with microhomology to Cas9 sites in Caenorhabditis elegans. Genetics 198: 13471356.CrossRefGoogle ScholarPubMed
Pattanayak, V, Lin, S, Guilinger, JP, et al. 2013. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31: 839843.CrossRefGoogle ScholarPubMed
Pavletich, NP, Pabo, CO. 1991. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252: 809817.CrossRefGoogle Scholar
Perez-Pinera, P, Kocak, DD, Vockley, CM, et al. 2013. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 10: 973976.CrossRefGoogle ScholarPubMed
Praitis, V, Casey, E, Collar, D, Austin, J. 2001. Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics 157: 12171226.CrossRefGoogle ScholarPubMed
Qi, LS, Larson, MH, Gilbert, LA, et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152: 11731183.CrossRefGoogle ScholarPubMed
Reinhart, BJ, Slack, FJ, Basson, M, et al. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901906.CrossRefGoogle ScholarPubMed
Ren, X, Yang, Z, Xu, J, et al. 2014. Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep 9: 11511162.CrossRefGoogle ScholarPubMed
Richardson, CD, Ray, GJ, DeWitt, MA, Curie, GL, Corn, JE. 2016. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol 34: 339344.CrossRefGoogle ScholarPubMed
Sapranauskas, R, Gasiunas, G, Fremaux, C, et al. 2011. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39: 92759282.CrossRefGoogle ScholarPubMed
Shen, Z, Zhang, X, Chai, Y, et al. 2014. Conditional knockouts generated by engineered CRISPR-Cas9 endonuclease reveal the roles of coronin in C. elegans neural development. Dev Cell 30: 625636.CrossRefGoogle Scholar
Shmakov, S, Abudayyeh, OO, Makarova, KS, et al. 2015. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 60: 385397.CrossRefGoogle ScholarPubMed
Sternberg, SH, Redding, S, Jinek, M, Greene, EC, Doudna, JA. 2014. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507: 6267.CrossRefGoogle ScholarPubMed
Sulston, JE, Schierenberg, E, White, JG, Thomson, JN. 1983. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol 100: 64119.CrossRefGoogle ScholarPubMed
Tanenbaum, ME, Gilbert, LA, Qi, LS, Weissman, JS, Vale, RD. 2014. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159: 635646.CrossRefGoogle ScholarPubMed
Thompson, O, Edgley, M, Strasbourger, P, et al. 2013. The Million Mutation Project: a new approach to genetics in Caenorhabditis elegans. Genome Res 23: 17491762.CrossRefGoogle Scholar
Thyme, SB, Schier, AF. 2016. Polq-mediated end joining is essential for surviving DNA double-strand breaks during early zebrafish development. Cell Rep 15: 16111613.CrossRefGoogle ScholarPubMed
Tian, D, Diao, M, Jiang, Y, et al. 2015. Anillin regulates neuronal migration and neurite growth by linking RhoG to the actin cytoskeleton. Curr Biol 25: 11351145.CrossRefGoogle ScholarPubMed
Tsai, SQ, Zheng, Z, Nguyen, NT, et al. 2015. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33: 187197.CrossRefGoogle ScholarPubMed
Urnov, FD, Rebar, EJ, Holmes, MC, Zhang, HS, Gregory, PD. 2010. Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11: 636646.CrossRefGoogle ScholarPubMed
van Schendel, R, Roerink, SF, Portegijs, V, van den Heuvel, S, Tijsterman, M. 2015. Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis. Nat Commun 6: 7394.CrossRefGoogle ScholarPubMed
Waaijers, S, Portegijs, V, Kerver, J, et al. 2013. CRISPR/Cas9-targeted mutagenesis in Caenorhabditis elegans. Genetics 195: 11871191.CrossRefGoogle ScholarPubMed
Wang, S, Su, J-H, Zhang, F, Zhuang, X. 2016. An RNA-aptamer-based two-color CRISPR labeling system. Sci Rep 6: 26857.CrossRefGoogle ScholarPubMed
Wang, T, Wei, JJ, Sabatini, DM, Lander, ES. 2014. Genetic screens in human cells using the CRISPR-Cas9 system. Science 343: 8084.CrossRefGoogle ScholarPubMed
Ward, JD. 2015. Rapid and precise engineering of the Caenorhabditis elegans genome with lethal mutation co-conversion and inactivation of NHEJ repair. Genetics 199: 363377.CrossRefGoogle ScholarPubMed
Wei, Q, Shen, Y, Chen, X, Shifman, Y, Ellis, RE. 2014. Rapid creation of forward-genetics tools for C. briggsae using TALENs: lessons for nonmodel organisms. Mol Biol Evol 31: 468473.CrossRefGoogle ScholarPubMed
Witte, H, Moreno, E, Rödelsperger, C, et al. 2015. Gene inactivation using the CRISPR/Cas9 system in the nematode Pristionchus pacificus. Dev Genes Evol 225: 5562.CrossRefGoogle ScholarPubMed
Wood, AJ, Lo, T-W, Zeitler, B, et al. 2011. Targeted genome editing across species using ZFNs and TALENs. Science 333: 307.CrossRefGoogle ScholarPubMed
Wu, X, Scott, DA, Kriz, AJ, et al. 2014. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32: 670676.CrossRefGoogle ScholarPubMed
Zalatan, JG, Lee, ME, Almeida, R, et al. 2015. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160: 339350.CrossRefGoogle ScholarPubMed
Zetsche, B, Gootenberg, JS, Abudayyeh, OO, et al. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163: 759771.CrossRefGoogle ScholarPubMed
Zhang, L, Ward, JD, Cheng, Z, Dernburg, AF. 2015. The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans. Dev Camb Engl 142: 43744384.Google ScholarPubMed
Zhao, P, Zhang, Z, Ke, H, Yue, Y, Xue, D. 2014. Oligonucleotide-based targeted gene editing in C. elegans via the CRISPR/Cas9 system. Cell Res 24: 247250.CrossRefGoogle Scholar
Zhao, P, Zhang, Z, Lv, X, et al. 2016. One-step homozygosity in precise gene editing by an improved CRISPR/Cas9 system. Cell Res 26: 633636.CrossRefGoogle ScholarPubMed

References

Chen, B, Gilbert, LA, Cimini, BA, et al. 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155: 14791491.CrossRefGoogle ScholarPubMed
Choulika, A, Perrin, A, Dujon, B, Nicolas, JF. 1995. Induction of homologous recombination in mammalian chromosomes by using the I-Scei system of Saccharomyces cerevisiae. Mol Cell Biol 15: 19681973.CrossRefGoogle ScholarPubMed
Christian, M, Cermak, T, Doyle, EL, et al. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757761.CrossRefGoogle ScholarPubMed
Crosetto, N, Mitra, A, Silva, MJ, et al. 2013. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods 10: 361365.CrossRefGoogle ScholarPubMed
Frock, RL, Hu, J, Meyers, RM, et al. 2015. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol 33: 179186.CrossRefGoogle ScholarPubMed
Fu, Y, Foden, JA, Khayter, C, et al. 2013. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31: 822826.CrossRefGoogle ScholarPubMed
Fu, Y, Sander, JD, Reyon, D, et al. 2014. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32: 279284.CrossRefGoogle ScholarPubMed
Gabriel, R, Lombardo, A, Arens, A, et al. 2011. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol 29: 816823.CrossRefGoogle ScholarPubMed
Gaj, T, Gersbach, CA, Barbas, CF III. 2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31: 397405.CrossRefGoogle ScholarPubMed
Gao, F, Shen, XZ, Jiang, F, Wu, Y, Han, C. 2016. DNA-guided genome editing using the Natronobacterium gregoryi Argonaute. Nat Biotechnol 34: 768773.CrossRefGoogle ScholarPubMed
Guilinger, JP, Pattanayak, V, Reyon, D, et al. 2014a. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat Methods 11: 429435.CrossRefGoogle ScholarPubMed
Guilinger, JP, Thompson, DB, Liu, DR. 2014b. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 32: 577582.CrossRefGoogle ScholarPubMed
Guschin, DY, Waite, AJ, Katibah, GE, et al. 2010. A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol 649: 247256.CrossRefGoogle ScholarPubMed
Hacein-Bey-Abina, S, Von Kalle, C, Schmidt, M, et al. 2003. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. N Engl J Med 348: 255256.CrossRefGoogle ScholarPubMed
Honma, M, Sakuraba, M, Koizumi, T, et al. 2007. Non-homologous end-joining for repairing I-SceI-induced DNA double strand breaks in human cells. DNA Repair (Amst) 6: 781788.CrossRefGoogle ScholarPubMed
Hsu, PD, Scott, DA, Weinstein, JA, et al. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827832.CrossRefGoogle ScholarPubMed
Jinek, M, Chylinski, K, Fonfara, I, et al. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816821.CrossRefGoogle ScholarPubMed
Kim, D, Bae, S, Park, J, et al. 2015. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods 12: 237243, 1 p following 243.CrossRefGoogle ScholarPubMed
Kim, YG, Cha, J, Chandrasegaran, S. 1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 93: 11561160.CrossRefGoogle ScholarPubMed
Komor, AC, Kim, YB, Packer, MS, Zuris, JA, Liu, DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533: 420424.CrossRefGoogle ScholarPubMed
Lieber, MR. 2010. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79: 181211.CrossRefGoogle ScholarPubMed
Lin, YN, Cradick, TJ, Brown, MT, et al. 2014. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res 42: 74737485.CrossRefGoogle ScholarPubMed
Mojica, FJ, Diez-Villasenor, C, Garcia-Martinez, J, Almendros, C. 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155: 733740.CrossRefGoogle ScholarPubMed
Nelles, DA, Fang, MY, O’Connell, MR, et al. 2016. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165: 488496.CrossRefGoogle ScholarPubMed
Osborn, MJ, Starker, CG, McElroy, AN, et al. 2013. TALEN-based gene correction for epidermolysis bullosa. Mol Ther 21: 11511159.CrossRefGoogle ScholarPubMed
Paruzynski, A, Arens, A, Gabriel, R, et al. 2010. Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. Nat Protoc 5: 13791395.CrossRefGoogle ScholarPubMed
Pierson, TC, Kieffer, TL, Ruff, CT, et al. 2002. Intrinsic stability of episomal circles formed during human immunodeficiency virus type 1 replication. J Virol 76: 41384144.CrossRefGoogle ScholarPubMed
Ran, FA, Cong, L, Yan, WX, et al. 2015. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520: 186191.CrossRefGoogle ScholarPubMed
Ran, FA, Hsu, PD, Lin, CY, et al. 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154: 13801389.CrossRefGoogle ScholarPubMed
Saenz, DT, Loewen, N, Peretz, M, et al. 2004. Unintegrated lentivirus DNA persistence and accessibility to expression in nondividing cells: analysis with class I integrase mutants. J Virol 78: 29062920.CrossRefGoogle ScholarPubMed
Shah, SA, Erdmann, S, Mojica, FJ, Garrett, RA. 2013. Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol 10: 891899.CrossRefGoogle ScholarPubMed
Shen, B, Zhang, W, Zhang, J, et al. 2014. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods 11: 399402.CrossRefGoogle ScholarPubMed
Shrivastav, M, De Haro, LP, Nickoloff, JA. 2008. Regulation of DNA double-strand break repair pathway choice. Cell Res 18: 134147.CrossRefGoogle ScholarPubMed
Silva, G, Poirot, L, Galetto, R, et al. 2011. Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy. Curr Gene Ther 11: 1127.CrossRefGoogle ScholarPubMed
Smith, C, Gore, A, Yan, W, et al. 2014. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 15: 1213.CrossRefGoogle ScholarPubMed
Tsai, SQ, Zheng, Z, Nguyen, NT, et al. 2015. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33: 187197.CrossRefGoogle ScholarPubMed
Veres, A, Gosis, BS, Ding, Q, et al. 2014. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 15: 2730.CrossRefGoogle ScholarPubMed
Vigna, E, Naldini, L. 2000. Lentiviral vectors: excellent tools for experimental gene transfer and promising candidates for gene therapy. J Gene Med 2: 308316.3.0.CO;2-3>CrossRefGoogle ScholarPubMed
Wang, X, Wang, Y, Wu, X, et al. 2015. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat Biotechnol 33: 175178.CrossRefGoogle ScholarPubMed
Wanisch, K, Yanez-Munoz, RJ. 2009. Integration-deficient lentiviral vectors: a slow coming of age. Mol Ther 17: 13161332.CrossRefGoogle ScholarPubMed
Weinstock, DM, Jasin, M. 2006. Alternative pathways for the repair of RAG-induced DNA breaks. Mol Cell Biol 26: 131139.CrossRefGoogle ScholarPubMed
Wu, X, Scott, DA, Kriz, AJ, et al. 2014. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32: 670676.CrossRefGoogle ScholarPubMed
Wyman, C, Kanaar, R. 2006. DNA double-strand break repair: all’s well that ends well. Annu Rev Genet 40: 363383.CrossRefGoogle ScholarPubMed
Zhou, Y, Zhu, S, Cai, C, et al. 2014. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509: 487491.CrossRefGoogle ScholarPubMed

References

Agarwal, V, Bell, GW, Nam, JW, Bartel, DP. 2015. Predicting effective microRNA target sites in mammalian mRNAs. Elife 4: e05005.CrossRefGoogle ScholarPubMed
Alexiou, P, Maragkakis, M, Papadopoulos, GL, Reczko, M, Hatzigeorgiou, AG. 2009. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25: 30493055.CrossRefGoogle ScholarPubMed
Bartel, DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281297.CrossRefGoogle ScholarPubMed
Bartel, DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136: 215233.CrossRefGoogle ScholarPubMed
Bassett, A, Liu, JL. 2014. CRISPR/Cas9 mediated genome engineering in Drosophila. Methods 69: 128136.CrossRefGoogle ScholarPubMed
Bassett, AR, Azzam, G, Wheatley, L, et al. 2014. Understanding functional miRNA-target interactions in vivo by site-specific genome engineering. Nat Commun 5: 4640.CrossRefGoogle ScholarPubMed
Bassett, AR, Tibbit, C, Ponting, CP, Liu, JL. 2013. Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 4: 220228.CrossRefGoogle ScholarPubMed
Bell, CC, Magor, GW, Gillinder, KR, Perkins, AC. 2014. A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing. BMC Genomics 15: 1002.CrossRefGoogle ScholarPubMed
Bibikova, M, Golic, M, Golic, KG, Carroll, D. 2002. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161: 11691175.CrossRefGoogle ScholarPubMed
Brinkman, EK, Chen, T, Amendola, M, van Steensel, B. 2014. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res 42: e168.CrossRefGoogle ScholarPubMed
Bushati, N, Cohen, SM. 2007. microRNA functions. Annu Rev Cell Dev Biol 23: 175205.CrossRefGoogle ScholarPubMed
Cacchiarelli, D, Incitti, T, Martone, J, et al. 2011. miR-31 modulates dystrophin expression: new implications for Duchenne muscular dystrophy therapy. EMBO Rep 12: 136141.CrossRefGoogle ScholarPubMed
Carrington, B, Varshney, GK, Burgess, SM, Sood, R. 2015. CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity. Nucleic Acids Res 43: e157.CrossRefGoogle ScholarPubMed
Choi, WY, Giraldez, AJ, Schier, AF. 2007. Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430. Science 318: 271274.CrossRefGoogle ScholarPubMed
Cloonan, N. 2015. Re-thinking miRNA-mRNA interactions: intertwining issues confound target discovery. Bioessays 37: 379388.CrossRefGoogle ScholarPubMed
Cong, L, Ran, FA, Cox, D, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819823.CrossRefGoogle ScholarPubMed
Croce, CM, Calin, GA. 2005. miRNAs, cancer, and stem cell division. Cell 122: 67.CrossRefGoogle ScholarPubMed
Esteller, M. 2011. Non-coding RNAs in human disease. Nat Rev Genet 12: 861874.CrossRefGoogle ScholarPubMed
Farh, KK, Grimson, A, Jan, C, et al. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 18171821.CrossRefGoogle ScholarPubMed
Gehrke, S, Imai, Y, Sokol, N, Lu, B. 2010. Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression. Nature 466: 637641.CrossRefGoogle ScholarPubMed
Hafner, M, Landthaler, M, Burger, L, et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129141.CrossRefGoogle ScholarPubMed
Helwak, A, Kudla, G, Dudnakova, T, Tollervey, D. 2013. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153: 654665.CrossRefGoogle ScholarPubMed
Hwang, WY, Fu, Y, Reyon, D, et al. 2013. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31: 227229.CrossRefGoogle ScholarPubMed
Jin, Y, Chen, Z, Liu, X, Zhou, X. 2013. Evaluating the microRNA targeting sites by luciferase reporter gene assay. Methods Mol Biol 936: 117127.CrossRefGoogle ScholarPubMed
Jinek, M, Chylinski, K, Fonfara, I, et al. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816821.CrossRefGoogle ScholarPubMed
Jinek, M, Doudna, JA. 2009. A three-dimensional view of the molecular machinery of RNA interference. Nature 457: 405412.CrossRefGoogle ScholarPubMed
John, B, Enright, AJ, Aravin, A, et al. 2005. Human microRNA targets. PLoS Biol 3: e264.CrossRefGoogle Scholar
Kim, JM, Kim, D, Kim, S, Kim, JS. 2014a. Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat Commun 5: 3157.CrossRefGoogle ScholarPubMed
Kim, S, Kim, D, Cho, SW, Kim, J, Kim, JS. 2014b. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 24: 10121019.CrossRefGoogle ScholarPubMed
Krutzfeldt, J, Rajewsky, N, Braich, R, et al. 2005. Silencing of microRNAs in vivo with “antagomirs”. Nature 438: 685689.CrossRefGoogle ScholarPubMed
Lewis, BP, Burge, CB, Bartel, DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 1520.CrossRefGoogle ScholarPubMed
Lewis, BP, Shih, IH, Jones-Rhoades, MW, et al. 2003. Prediction of mammalian microRNA targets. Cell 115: 787798.CrossRefGoogle ScholarPubMed
Lim, LP, Lau, NC, Garrett-Engele, P, et al. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769773.CrossRefGoogle ScholarPubMed
Liu, CG, Calin, GA, Volinia, S, Croce, CM. 2008. MicroRNA expression profiling using microarrays. Nat Protoc 3: 563578.CrossRefGoogle ScholarPubMed
Mali, P, Yang, L, Esvelt, KM, et al. 2013. RNA-guided human genome engineering via Cas9. Science 339: 823826.CrossRefGoogle ScholarPubMed
Mendell, JT. 2005. MicroRNAs: critical regulators of development, cellular physiology and malignancy. Cell Cycle 4: 11791184.CrossRefGoogle ScholarPubMed
Michaels, YS, Wu, Q, Fulga, TA. 2017. Interrogation of functional miRNA-target interactions by CRISPR/Cas9 genome engineering. Meth Mol Biol 1580: 7997.CrossRefGoogle ScholarPubMed
Park, CY, Choi, YS, McManus, MT. 2010. Analysis of microRNA knockouts in mice. Hum Mol Genet 19: R169R175.CrossRefGoogle ScholarPubMed
Pillai, RS, Artus, CG, Filipowicz, W. 2004. Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA 10: 15181525.CrossRefGoogle ScholarPubMed
Port, F, Muschalik, N, Bullock, SL. 2015. Systematic evaluation of Drosophila CRISPR tools reveals safe and robust alternatives to autonomous gene drives in basic research. G3 (Bethesda) 5: 14931502.CrossRefGoogle ScholarPubMed
Rajewsky, N. 2006. microRNA target predictions in animals. Nat Genet 38(Suppl.): S8S13.CrossRefGoogle ScholarPubMed
Ran, FA, Hsu, PD, Wright, J, et al. 2013. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8: 22812308.CrossRefGoogle ScholarPubMed
Staton, AA, Giraldez, AJ. 2011. Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo. Nat Protoc 6: 20352049.CrossRefGoogle ScholarPubMed
Sun, K, Lai, EC. 2013. Adult-specific functions of animal microRNAs. Nat Rev Genet 14: 535548.CrossRefGoogle ScholarPubMed
Thomas, M, Lieberman, J, Lal, A. 2010. Desperately seeking microRNA targets. Nat Struct Mol Biol 17: 11691174.CrossRefGoogle ScholarPubMed
Thomson, DW, Bracken, CP, Goodall, GJ. 2011. Experimental strategies for microRNA target identification. Nucleic Acids Res 39: 68456853.CrossRefGoogle ScholarPubMed
Wang, Z. 2011. The guideline of the design and validation of MiRNA mimics. Methods Mol Biol 676: 211223.CrossRefGoogle ScholarPubMed
Wu, Q, Ferry, QRV, Michaels, YS, et al. 2017. In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering. Nat Comms 8: 2109.CrossRefGoogle ScholarPubMed
Zhang, Y, Ge, X, Yang, F, et al. 2014. Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells. Sci Rep 4: 5405.CrossRefGoogle ScholarPubMed

References

Abudayyeh, OO, Gootenberg, JS, Konermann, S, et al. 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353(6299): aaf5573CrossRefGoogle ScholarPubMed
Ala, U, Karreth, FA, Bosia, C, et al. 2013. Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci USA 110: 71547159.CrossRefGoogle ScholarPubMed
Armstrong, GA, Liao, M, You, Z, et al. 2016. Homology directed knockin of point mutations in the zebrafish tardbp and fus genes in ALS using the CRISPR/Cas9 system. PLoS One 11: e0150188.CrossRefGoogle ScholarPubMed
Bartel, DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281297.CrossRefGoogle ScholarPubMed
Bartel, DP, Chen, CZ. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5: 396400.CrossRefGoogle ScholarPubMed
Bibikova, M, Carroll, D, Segal, DJ, et al. 2001. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21: 289297.CrossRefGoogle ScholarPubMed
Bikard, D, Jiang, W, Samai, P, et al. 2013. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res 41: 74297437.CrossRefGoogle ScholarPubMed
Bitinaite, J, Wah, DA, Aggarwal, AK, Schildkraut, I. 1998. FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95: 1057010575.CrossRefGoogle ScholarPubMed
Boch, J. 2011. TALEs of genome targeting. Nat Biotechnol 29: 135136.CrossRefGoogle ScholarPubMed
Boch, J, Scholze, H, Schornack, S, et al. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326: 15091512.CrossRefGoogle ScholarPubMed
Bosson, AD, Zamudio, JR, Sharp, PA. 2014. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell 56: 347359.CrossRefGoogle ScholarPubMed
Cade, L, Reyon, D, Hwang, WY, et al. 2012. Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs. Nucleic Acids Res 40: 80018010.CrossRefGoogle ScholarPubMed
Calin, GA, Croce, CM. 2006. MicroRNA signatures in human cancers. Nat Rev Cancer 6: 857866.CrossRefGoogle ScholarPubMed
Calin, GA, Dumitru, CD, Shimizu, M, et al. 2002. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99: 1552415529.CrossRefGoogle ScholarPubMed
Carlson, DF, Tan, W, Lillico, SG, et al. 2012. Efficient TALEN-mediated gene knockout in livestock. Proc Natl Acad Sci USA 109: 1738217387.CrossRefGoogle ScholarPubMed
Carninci, P, Kasukawa, T, Katayama, S, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 15591563.CrossRefGoogle ScholarPubMed
Cech, TR, Steitz, JA. 2014. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157: 7794.CrossRefGoogle ScholarPubMed
Chen, B, Chen, X, Wu, X, et al. 2015. Disruption of microRNA-21 by TALEN leads to diminished cell transformation and increased expression of cell-environment interaction genes. Cancer Lett 356: 506516.CrossRefGoogle ScholarPubMed
Chiu, HS, Llobet-Navas, D, Yang, X, et al. 2015. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Res 25: 257267.CrossRefGoogle ScholarPubMed
Christian, M, Cermak, T, Doyle, EL, et al. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757761.CrossRefGoogle ScholarPubMed
Cong, L, Ran, FA, Cox, D, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819823.CrossRefGoogle ScholarPubMed
Djebali, S, Davis, CA, Merkel, A, et al. 2012. Landscape of transcription in human cells. Nature 489: 101108.CrossRefGoogle ScholarPubMed
Fedorov, Y, Anderson, EM, Birmingham, A, et al. 2006. Off-target effects by siRNA can induce toxic phenotype. RNA 12: 11881196.CrossRefGoogle ScholarPubMed
Fire, A, Xu, S, Montgomery, MK, et al. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806811.CrossRefGoogle ScholarPubMed
Gilbert, LA, Larson, MH, Morsut, L, et al. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154: 442451.CrossRefGoogle ScholarPubMed
Gupta, A, Christensen, RG, Rayla, AL, et al. 2012. An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods 9: 588590.CrossRefGoogle ScholarPubMed
Gutschner, T, Baas, M, Diederichs, S. 2011. Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases. Genome Res 21: 19441954.CrossRefGoogle ScholarPubMed
Ha, M, Kim, VN. 2014. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15: 509524.CrossRefGoogle ScholarPubMed
Hansen, TB, Jensen, TI, Clausen, BH, et al. 2013. Natural RNA circles function as efficient microRNA sponges. Nature 495: 384388.CrossRefGoogle ScholarPubMed
Hausser, J, Syed, AP, Bilen, B, Zavolan, M. 2013. Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res 23: 604615.CrossRefGoogle ScholarPubMed
Heintze, J, Luft, C, Ketteler, R. 2013. A CRISPR CASe for high-throughput silencing. Front Genet 4: 193.CrossRefGoogle ScholarPubMed
Hu, R, Wallace, J, Dahlem, TJ, Grunwald, DJ, O’Connell, RM. 2013. Targeting human microRNA genes using engineered Tal-effector nucleases (TALENs). PLoS One 8: e63074.CrossRefGoogle ScholarPubMed
Inui, M, Miyado, M, Igarashi, M, et al. 2014. Rapid generation of mouse models with defined point mutations by the CRISPR/Cas9 system. Sci Rep 4: 5396.CrossRefGoogle ScholarPubMed
Jinek, M, Chylinski, K, Fonfara, I, et al. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816821.CrossRefGoogle ScholarPubMed
Karreth, FA, Reschke, M, Ruocco, A, et al. 2015. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 161: 319332.CrossRefGoogle ScholarPubMed
Karreth, FA, Tay, Y, Perna, D, et al. 2011. In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147: 382395.CrossRefGoogle Scholar
Khan, AA, Betel, D, Miller, ML, et al. 2009. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 27: 549555.CrossRefGoogle ScholarPubMed
Kim, H, Kim, JS. 2014. A guide to genome engineering with programmable nucleases. Nat Rev Genet 15: 321334.CrossRefGoogle ScholarPubMed
Kim, JS, Lee, HJ, Carroll, D. 2010. Genome editing with modularly assembled zinc-finger nucleases. Nat Methods 7: 91; author reply 9192.CrossRefGoogle ScholarPubMed
Kim, Y, Kweon, J, Kim, JS. 2013a. TALENs and ZFNs are associated with different mutation signatures. Nat Methods 10: 185.CrossRefGoogle ScholarPubMed
Kim, YK, Wee, G, Park, J, et al. 2013b. TALEN-based knockout library for human microRNAs. Nat Struct Mol Biol 20: 14581464.CrossRefGoogle ScholarPubMed
Lee, RC, Feinbaum, RL, Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843854.CrossRefGoogle Scholar
Liu, XH, Sun, M, Nie, FQ, et al. 2014. Lnc RNA HOTAIR functions as a competing endogenous RNA to regulate HER2 expression by sponging miR-331-3p in gastric cancer. Mol Cancer 13: 92.CrossRefGoogle ScholarPubMed
Lu, M, Zhang, Q, Deng, M, et al. 2008. An analysis of human microRNA and disease associations. PLoS One 3: e3420.CrossRefGoogle ScholarPubMed
Maeder, ML, Thibodeau-Beganny, S, Osiak, A, et al. 2008. Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31: 294301.CrossRefGoogle ScholarPubMed
Memczak, S, Jens, M, Elefsinioti, A, et al. 2013. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495: 333338.CrossRefGoogle ScholarPubMed
Miranda, KC, Huynh, T, Tay, Y, et al. (2006). A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126: 12031217.CrossRefGoogle ScholarPubMed
Moehle, EA, Rock, JM, Lee, YL, et al. 2007. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci USA 104: 30553060.CrossRefGoogle ScholarPubMed
Mojica, FJ, Diez-Villasenor, C, Garcia-Martinez, J, Soria, E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60: 174182.CrossRefGoogle ScholarPubMed
Nelles, DA, Fang, MY, O’Connell, MR, et al. 2016. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165: 488496.CrossRefGoogle ScholarPubMed
O’Connell, MR, Oakes, BL, Sternberg, SH, et al. 2014. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516: 263266.CrossRefGoogle ScholarPubMed
Orlando, SJ, Santiago, Y, Dekelver, RC, et al. 2010. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res 38: e152.CrossRefGoogle ScholarPubMed
Orom, UA, Nielsen, FC, Lund, AH. 2008. MicroRNA-10a binds the 5’UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30: 460471.CrossRefGoogle Scholar
Plaisier, CL, Pan, M, Baliga, NS. 2012. A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res 22: 23022314.CrossRefGoogle ScholarPubMed
Poliseno, L, Salmena, L, Zhang, J, et al. 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465: 10331038.CrossRefGoogle ScholarPubMed
Qi, LS, Larson, MH, Gilbert, LA, et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152: 11731183.CrossRefGoogle ScholarPubMed
Reyon, D, Tsai, SQ, Khayter, C, et al. 2012. FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30: 460465.CrossRefGoogle ScholarPubMed
Salmena, L, Poliseno, L, Tay, Y, Kats, L, Pandolfi, PP. 2011. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146: 353358.CrossRefGoogle ScholarPubMed
Santiago, Y, Chan, E, Liu, PQ, et al. 2008. Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci USA 105: 58095814.CrossRefGoogle ScholarPubMed
Shechner, DM, Hacisuleyman, E, Younger, ST, Rinn, JL. 2015. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods 12: 664670.CrossRefGoogle ScholarPubMed
Sumazin, P, Yang, X, Chiu, HS, et al. 2011. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147: 370381.CrossRefGoogle ScholarPubMed
Takada, S, Sato, T, Ito, Y, et al. 2013. Targeted gene deletion of miRNAs in mice by TALEN system. PLoS One 8: e76004.CrossRefGoogle ScholarPubMed
Tay, Y, Kats, L, Salmena, L, et al. 2011. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147: 344357.CrossRefGoogle ScholarPubMed
Tay, Y, Rinn, J, Pandolfi, PP. 2014. The multilayered complexity of ceRNA crosstalk and competition. Nature 505: 344352.CrossRefGoogle ScholarPubMed
Uhde-Stone, C, Sarkar, N, Antes, T, et al. 2014. A TALEN-based strategy for efficient bi-allelic miRNA ablation in human cells. RNA 20: 948955.CrossRefGoogle ScholarPubMed
Urnov, FD, Miller, JC, Lee, YL, et al. 2005. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435: 646651.CrossRefGoogle ScholarPubMed
Wang, J, Liu, X, Wu, H, et al. 2010. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 38: 53665383.CrossRefGoogle ScholarPubMed
Wightman, B, Ha, I, Ruvkun, G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855862.CrossRefGoogle ScholarPubMed
Wyman, C, Kanaar, R. 2006. DNA double-strand break repair: all’s well that ends well. Annu Rev Genet 40: 363383.CrossRefGoogle ScholarPubMed
Xiao, H, Tang, K, Liu, P, et al. 2015. LncRNA MALAT1 functions as a competing endogenous RNA to regulate ZEB2 expression by sponging miR-200s in clear cell kidney carcinoma. Oncotarget 6: 3800538015.CrossRefGoogle ScholarPubMed
Zalatan, JG, Lee, ME, Almeida, R, et al. 2015. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160: 339350.CrossRefGoogle ScholarPubMed

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