Understanding of natural DNA repair processes in cells has led to development of a variety of genome editing platforms. Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) are proving to be precise tools for genome engineering. These are basically chimeric nucleases, comprising interchangeable target-dependent, sequence-specific DNA-binding domains linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a number of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining (NHEJ) or homology-directed (HR) repair, at the specific targeted genomic loci. Clustered regularly interspaced short palindromic repeat (CRISPR) loci have a protective function in prokaryotes, against invasion by phage and plasmid DNA, acting through a genetic interference pathway. CRISPR loci have been located in 40% bacterial and 90% of archaeal genomes. These are observed to evolve and adapt rapidly by acquiring new spacer sequences on exposure to highly dynamic genomes of phages. This bacterial immune system matches the spacer sequences located between CRISPR repeat sequences and the invading DNA, to carry out its interference activity. Each CRISPR cluster is constituted of genetically linked subset of Cas (CRISPR-associated) genes, which collectively encode more than 40 families of proteins, involved in adaptation and interference. CRISPR loci are transcribed and converted into small CRISPR RNAs (crRNAs) that contain a full spacer sequence, flanked by partial repeat sequences of a complex of Cas proteins termed cascade (Cas-complex for antivirus defense). CrRNA spacers are known to bind target invading “protospacer” DNA by direct Watson–Crick base pairing leading to its degradation. The mechanism of CRISPR self-/non-self-discrimination involves target/crRNA mismatches at specific positions outside of the spacer sequence to identify foreign DNA for degradation, whereas extended pairing between crRNA and CRISPR DNA repeats is protective and prevents self-degradation. Various applications already built up on the platform technologies in different fields such as generation of animal models, treatment of infectious diseases, correction of genetic disorders, functional genome screening, and stem cell gene editing have been discussed.
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This work was supported by grant from the DBT-Punjabi University Interdisciplinary Life Science Programme for advanced research and education (DBT-IPLS Project) No. BT/PR-4548/INF/22/146/2012.
Cermak T, Doyle EL, Christian M et al (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39(12):e82CrossRefPubMedPubMedCentralGoogle Scholar
Denomy JB, Davidson AR (2014) To acquire or resist: the complex biological effects of CRISPR–Cas systems. Trends Microbiol 22(4):218–225CrossRefGoogle Scholar
Ding Q, Lee YK, Schaefer EA, Peters DT et al (2013) A TALEN genome-editing system for generating human stem cell-based disease models. Stem Cells 12(2):225–238Google Scholar
Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096CrossRefPubMedGoogle Scholar
Hockemeyer D, Soldner F, Beard C et al (2009) Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol 27(9):851–857CrossRefPubMedPubMedCentralGoogle Scholar
Ishino Y, Shinagawa H, Makino K et al (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169:5429–5433CrossRefPubMedPubMedCentralGoogle Scholar
Iwase H, Liu H, Wijkstrom M et al (2015) Pig kidney graft survival in a baboon for 136 days: longest life-supporting organ graft survival to date. Xenotransplantation 22(4):302–309CrossRefPubMedPubMedCentralGoogle Scholar
Li T, Huang S, Jiang WZ et al (2011) TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 39:359–372CrossRefPubMedGoogle Scholar
Li T, Liu B, Spalding MH et al (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392CrossRefPubMedGoogle Scholar
Liu Q, Segal DJ, Ghiara JB, Barbas CF (1997) Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proc Natl Acad Sci USA 94(11):5525–5530CrossRefPubMedGoogle Scholar
Liu J, Li C, Yu Z, Huang P et al (2012) Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy. J Genet Genomics 39:209–215CrossRefPubMedGoogle Scholar
Lombardo A, Genovese P, Beausejour CM et al (2007) Gene editing in human stem cells using zinc-finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol 25(11):1298–1306CrossRefGoogle Scholar
Mahfouz MM, Li L, Shamimuzzaman M, Wibowo A et al (2011) De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc Natl Acad Sci USA 108:2623–2628CrossRefPubMedGoogle Scholar
Makarova KS, Grishin NV, Shabalina SA et al (2006) A putative RNA interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1:7CrossRefPubMedPubMedCentralGoogle Scholar
Makarova KS, Haft DH, Barrangou R et al (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9(6):467–477CrossRefPubMedGoogle Scholar
Makarova KS, Wolf YI, Koonin EV (2013) The basic building blocks and evolution of CRISPR-cas systems. Biochem Soc T 41:1392–1400CrossRefGoogle Scholar
Perez EE, Wang J, Miller JC et al (2008) Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 26(7):808–816CrossRefPubMedPubMedCentralGoogle Scholar
Urnov FD, Rebar EJ, Holmes MC et al (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11(9):636–646CrossRefPubMedGoogle Scholar
Wang J, Friedman G, Doyon Y et al (2012) Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme. Genome Res 22(7):1316–1326CrossRefPubMedPubMedCentralGoogle Scholar
Wiedenheft B, Samuel H, Sternberg, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331–338CrossRefPubMedGoogle Scholar
Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M et al (2015) Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160:339–350CrossRefPubMedGoogle Scholar