Genome Editing in Drug Discovery. Группа авторов

for Specificity. Mol. Cell 62: 824–833.

      162 Nussenzweig, P.M. and Marraffini, L.A. (2020). Molecular mechanisms of CRISPR‐Cas immunity in bacteria. Annu. Rev. Genet. 54: 93–120.

      163 Nussenzweig, P.M., Mcginn, J., and Marraffini, L.A. (2019). Cas9 cleavage of viral genomes primes the acquisition of new immunological memories. Cell Host Microbe 26: 515–526. e6.

      164 Osakabe, K., Wada, N., Miyaji, T. et al. (2020). Genome editing in plants using CRISPR type I‐D nuclease. Commun. Biol. 3: 648.

      165 Osawa, T., Inanaga, H., Sato, C., and Numata, T. (2015). Crystal structure of the CRISPR‐Cas RNA silencing Cmr complex bound to a target analog. Mol. Cell 58: 418–430.

      166 Ozcan, A., Pausch, P., Linden, A. et al. (2019). Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum. Nat. Microbiol. 4: 89–96.

      167 Patchsung, M., Jantarug, K., Pattama, A. et al. (2020). Clinical validation of a Cas13‐based assay for the detection of SARS‐CoV‐2 RNA. Nat. Biomed. Eng. 4: 1140–1149.

      168 Pausch, P., Al‐Shayeb, B., Bisom‐Rapp, E. et al. (2020). CRISPR‐CasPhi from huge phages is a hypercompact genome editor. Science 369: 333–337.

      169 Perez‐Pinera, P., Kocak, D.D., Vockley, C.M. et al. (2013). RNA‐guided gene activation by CRISPR‐Cas9‐based transcription factors. Nat. Methods 10: 973–976.

      170 Pinilla‐Redondo, R., Mayo‐Munoz, D., Russel, J. et al. (2020). Type IV CRISPR‐Cas systems are highly diverse and involved in competition between plasmids. Nucleic Acids Res. 48: 2000–2012.

      171 Pougach, K., Semenova, E., Bogdanova, E. et al. (2010). Transcription, processing and function of CRISPR cassettes in Escherichia coli. Mol. Microbiol. 77: 1367–1379.

      172 Pourcel, C., Salvignol, G., and Vergnaud, G. (2005). CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiol. (Reading) 151: 653–663.

      173 Pul, U., Wurm, R., Arslan, Z. et al. (2010). Identification and characterization of E. coli CRISPR‐cas promoters and their silencing by H‐NS. Mol. Microbiol. 75: 1495–1512.

      174 Pyenson, N.C., Gayvert, K., Varble, A. et al. (2017). Broad targeting specificity during bacterial Type III CRISPR‐Cas immunity constrains viral escape. Cell Host Microbe 22: 343–353. e3.

      175 Pyne, M.E., Bruder, M.R., MOO‐Young, M. et al. (2016). Harnessing heterologous and endogenous CRISPR‐Cas machineries for efficient markerless genome editing in Clostridium. Sci. Rep. 6: 25666.

      176 Qi, L.S., Larson, M.H., Gilbert, L.A. et al. (2013). Repurposing CRISPR as an RNA‐guided platform for sequence‐specific control of gene expression. Cell 152: 1173–1183.

      177 Ramachandran, A., Summerville, L., Learn, B.A. et al. (2020). Processing and integration of functionally oriented prespacers in the Escherichia coli CRISPR system depends on bacterial host exonucleases. J. Biol. Chem. 295: 3403–3414.

      178 Ran, F.A., Cong, L., Yan, W.X. et al. (2015). in vivo genome editing using Staphylococcus aureus Cas9. Nature 520: 186–191.

      179 Raper, A.T., Stephenson, A.A., and Suo, Z. (2018). Functional insights revealed by the kinetic mechanism of CRISPR/Cas9. J. Am. Chem. Soc. 140: 2971–2984.

      180 Redding, S., Sternberg, S.H., Marshall, M. et al. (2015). Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR‐Cas System. Cell 163: 854–865.

      181 Roberts, R.J. (2005). How restriction enzymes became the workhorses of molecular biology. Proc. Natl. Acad. Sci. U. S. A. 102: 5905–5908.

      182 Rollie, C., Graham, S., Rouillon, C., and White, M.F. (2018). Prespacer processing and specific integration in a Type I‐A CRISPR system. Nucleic Acids Res. 46: 1007–1020.

      183 Rostol, J.T. and Marraffini, L.A. (2019). Non‐specific degradation of transcripts promotes plasmid clearance during type III‐A CRISPR‐Cas immunity. Nat. Microbiol. 4: 656–662.

      184 Samai, P., Pyenson, N., Jiang, W. et al. (2015). Co‐transcriptional DNA and RNA cleavage during Type III CRISPR‐Cas immunity. Cell 161: 1164–1174.

      185 Sampson, T.R., Saroj, S.D., Llewellyn, A.C. et al. (2013). A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497: 254–257.

      186 Sashital, D.G., Jinek, M., and Doudna, J.A. (2011). An RNA‐induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat. Struct. Mol. Biol. 18: 680–687.

      187 Sashital, D.G., Wiedenheft, B., and Doudna, J.A. (2012). Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol. Cell 46: 606–615.

      188 Savitskaya, E., Semenova, E., Dedkov, V. et al. (2013). High‐throughput analysis of type I‐E CRISPR/Cas spacer acquisition in E. coli. RNA Biol. 10: 716–725.

      189 Schmid‐Burgk, J.L., Gao, L., Li, D. et al. (2020). Highly parallel profiling of Cas9 variant specificity. Mol. Cell 78: 794–800. e8.

      190 Sefcikova, J., Roth, M., Yu, G., and Li, H. (2017). Cas6 processes tight and relaxed repeat RNA via multiple mechanisms: a hypothesis. BioEssays 39.

      191 Shah, S.A., Erdmann, S., Mojica, F.J., and Garrett, R.A. (2013). Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol. 10: 891–899.

      192 Shao, Y., Richter, H., Sun, S. et al. (2016). A non‐stem‐loop CRISPR RNA is processed by dual binding Cas6. Structure 24: 547–554.

      193 Shiimori, M., Garrett, S.C., Graveley, B.R., and Terns, M.P. (2018). Cas4 nucleases define the PAM, length, and orientation of DNA fragments integrated at CRISPR loci. Mol. Cell 70: 814–824. e6.

      194 Shmakov, S., Abudayyeh, O.O., Makarova, K.S. et al. (2015). Discovery and functional characterization of diverse class 2 CRISPR‐Cas systems. Mol. Cell 60: 385–397.

      195 Shmakov, S., Smargon, A., Scott, D. et al. (2017). Diversity and evolution of class 2 CRISPR‐Cas systems. Nat. Rev. Microbiol. 15: 169–182.

      196 Silas, S., Mohr, G., Sidote, D.J. et al. (2016). Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase‐Cas1 fusion protein. Science 351: aad4234–aad4234.

      197 Singh, D., Mallon, J., Poddar, A. et al. (2018). Real‐time observation of DNA target interrogation and product release by the RNA‐guided endonuclease CRISPR Cpf1 (Cas12a). Proc. Natl. Acad. Sci. U. S. A. 115: 5444–5449.

      198 Sinkunas, T., Gasiunas, G., Fremaux, C. et al. (2011). Cas3 is a single‐stranded DNA nuclease and ATP‐dependent helicase in the CRISPR/Cas immune system. EMBO J. 30: 1335–1342.

      199 Sinkunas, T., Gasiunas, G., Waghmare, S.P. et al. (2013). in vitro reconstitution of Cascade‐mediated CRISPR immunity in Streptococcus thermophilus. EMBO J. 32: 385–394.

      200 Slaymaker, I.M., Gao, L., Zetsche, B. et al. (2016). Rationally engineered Cas9 nucleases with improved specificity. Science 351: 84–88.

      201 Slaymaker, I.M., Mesa, P., Kellner, M.J. et al. (2019). High‐Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage. Cell Rep. 26: 3741–3751. e5.

      202 Smargon, A.A., Cox, D.B.T., Pyzocha, N.K. et al. (2017). Cas13b Is a Type VI‐B CRISPR‐associated RNA‐guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol. Cell 65: 618–630. e7.

      203 Staals, R.H., Zhu, Y., Taylor, D.W. et al. (2014). RNA targeting by the type III‐A CRISPR‐Cas Csm complex of thermus thermophilus. Mol. Cell 56: 518–530.

      204 Staals, R.H., Jackson, S.A., Biswas, A. et al. (2016). Interference‐driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR‐Cas system. Nat. Commun. 7: 12853.

      205 Stella, S., Mesa, P., Thomsen, J. et al. (2018). Conformational activation promotes CRISPR‐Cas12a catalysis and resetting of the endonuclease activity. Cell 175: 1856–1871. e21.

      206 Sternberg,