Biomics

The article discusses various applications of CRISPR loci and their components: a) for genotyping of certain bacteria strains (CRISPR-cassettes); b) for studying of fundamental questions of the individual genes function and gene networks and also RNA transcripts (CRISPR/dCas system); c) for highly sensitive CRISPR-Dx detection of specific sequences of nucleic acids (nuclease Cas13a).

CRISPR/Cas system, CRISPR-loci, CRISPR-cassettes, spoligotyping, recombinase polymerase amplification, RPA, CRISPR-Dx, CRISPR/dCas9, Cas13a, CRISPRi, CRISPRa, CRISPRi/a

1. Баймиев Ан.Х., Чемерис Д.А., Кирьянова О.Ю., Матниязов Р.Т., Валеев А.Ш., Баймиев Ал.Х., Губайдуллин И.М., Чемерис А.В. Биоинформатические ресурсы для in silico поиска CRISPR локусов в геномах прокариот // Биомика. 2017. Т.9. С.229-244.
2. Баймиев Ан.Х., Кулуев Б.Р., Вершинина З.Р. Князев А.В., Чемерис Д.А., Рожнова Н.А., Геращенков Г.А., Михайлова Е.В., Баймиев Ал.Х., Чемерис А.В. CRISPR/Cas редактирование геномов (растений) и общество // Биомика. 2017а. Т.9. С.183-202.
3. Вершинина З.Р., Кулуев Б.Р., Геращенков Г.А., Князев А.В., Чемерис Д.А., Гумерова Г.Р., Баймиев Ал.Х., Чемерис А.В. Эволюция методов редактирования геномов // Биомика. 2017. Т.9. С.245-270 .
4. Кулуев Б.Р., Геращенков Г.А., Рожнова Н.А., Баймиев Ан.Х., Вершинина З.Р., Князев А.В., Матниязов Р.Т., Гумерова Г.Р., Михайлова Е.В., Никоноров Ю.М., Чемерис Д.А., Баймиев Ал.Х., Чемерис А.В. CRISPR/Cas редактирование геномов растений // Биомика. 2017. Т.9. С.155-182.
5. Чемерис Д.А., Кирьянова О.Ю., Геращенков Г.А., Кулуев Б.Р., Рожнова Н.А., Матниязов Р.Т., Баймиев Ан.Х., Баймиев Ал.Х., Губайдуллин И.М., Чемерис А.В. Биоинформатические ресурсы для CRISPR/Cas редактирования геномов // Биомика. 2017. Т.9. С.203-228.
6. Abudayyeh O.O., Gootenberg J.S., Konermann S., Joung J., Slaymaker I.M., Cox D.B., Shmakov S., Makarova K.S., Semenova E.,Minakhin L., Severinov K., Regev A., Lander E.S., Koonin E.V., Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPReffector // Science. 2016. V. 353:aaf
7. Aranaz A., Liébana E., Mateos A., Dominguez L, Vidal D, Domingo M, Gonzolez O, Rodriguez-Ferri EF, Bunschoten AE, Van Embden JD,Cousins D. Spacer oligonucleotide typing of Mycobacterium bovis strains from cattle and other animals: a tool for studying epidemiology of tuberculosis // J. Clin Microbiol. V. 34. P. 2734-2740.
8. Barrangou R., Dudley E.G. CRISPR-based typing and next-generation tracking technologies // Annu. Rev. Food Sci. Technol. 2016. V. 7. P. 395-411.
9. Bespyatykh J.A., Zimenkov D.V., Shitikov E.A., Kulagina E.V., Lapa S.A., Gryadunov D.A., Ilina E.N., Govorun V.M. Spoligotyping of Mycobacterium tuberculosis complex isolates using hydrogel oligonucleotide microarrays // Infect. Genet. Evol. 2014. V. 26. P. 41-46.
10. Botelho A., Canto A., Leão C., Cunha M.V. Clustered regularly interspaced short palindromic repeats (CRISPRs) analysis of members of the Mycobacterium tuberculosis complex // Methods Mol. Biol. 2015. V. 1247. P. 373-389.
11. Brudey K., Driscoll J.R., Rigouts L., Prodinger W.M., Gori A., Al-Hajoj S.A., Allix C., Aristimuño L., Arora J., Baumanis V., Binder L., Cafrune P., Cataldi A., Cheong S., Diel R., Ellermeier C., Evans J.T., Fauville-Dufaux M., Ferdinand S., Garcia de Viedma D., Garzelli C., Gazzola L., Gomes H.M., Guttierez M.C., Hawkey P.M., van Helden P.D., Kadival G.V., Kreiswirth B.N., Kremer K., Kubin M., Kulkarni S.P., Liens B., Lillebaek T., Ho M.L., Martin C., Martin C., Mokrousov I., Narvskaïa O., Ngeow Y.F., Naumann L., Niemann S., Parwati I., Rahim Z., Rasolofo-Razanamparany V., Rasolonavalona T., Rossetti M.L., Rüsch-Gerdes S., Sajduda A., Samper S., Shemyakin I.G., Singh U.B., Somoskovi A., Skuce R.A., van Soolingen D., Streicher E.M., Suffys P.N., Tortoli E., Tracevska T., Vincent V., Victor T.C., Warren R.M., Yap S.F., Zaman K., Portaels F., Rastogi N., Sola C. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology // BMC Microbiol. 2006. V. 6:23.
12. Canver M.C., Bauer D.E., Orkin S.H. Functional interrogation of non-coding DNA through CRISPR genome editing // Methods. 2017. V. 121-122. P. 118-129.
13. Ceasar S.A., Rajan V., Prykhozhij S.V., Berman J.N., Ignacimuthu S. Insert, remove or replace: A highly advanced genome editing system usingCRISPR/Cas9 // Biochim. Biophys. Acta. 2016. V. 1863. P. 2333-2344.
14. Chandu D., Paul S., Parker M., Dudin Y., King-Sitzes J., Perez T., Mittanck D.W., Shah M., Glenn K.C., Piepenburg O. Development of a rapid point-of-use DNA test for the screening of Genuity® Roundup Ready 2 Yield® soybean in seed samples // Biomed Res. Int. 2016:3145921.
15. Chen B., Huang B. Imaging genomic elements in living cells using CRISPR/Cas9 // Methods Enzymol. 2014. V. 546. P. 337-354.
16. Clancy E., Higgins O., Forrest M.S., Boo T.W., Cormican M., Barry T., Piepenburg O., Smith T.J. Development of a rapid recombinase polymerase amplification assay for the detection of Streptococcus pneumoniae in whole blood // BMC Infect. Dis. 2015. V. 15:481.
17. Compton J. Nucleic acid sequence-based amplification // Nature. V.350. P.91-92.
18. Cowan L.S., Diem L., Brake M.C., Crawford J.T. Transfer of a Mycobacterium tuberculosis genotyping method, spoligotyping, from a reverse line-blot hybridization, membrane-based assay to the Luminex multianalyte profiling system // J. Clin. Microbiol. 2004. V. 42. P. 474-477.
19. Cox D.B.T., Gootenberg J.S., Abudayyeh O.O., Franklin B., Kellner M.J., Joung J., Zhang F. RNA editing with CRISPR-Cas13 // Science. pii: eaaq0180.
20. Crannell Z.A., Rohrman B., Richards-Kortum R. Equipment-free incubation of recombinase polymerase amplification reactions using body heat // PLoS One. 2014. V. 9:e112146.
21. Cui Y., Li Y., Gorgé O., Platonov M.E., Yan Y., Guo Z., Pourcel C., Dentovskaya S.V., Balakhonov S.V., Wang X., Song Y., Anisimov A.P., Vergnaud G., Yang R. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats // PLoS One. 2008. V.9;3(7):e
22. Daher R.K., Stewart G., Boissinot M., Bergeron M.G. Recombinase polymerase amplification for diagnostic applications // Clin. Chem. 2016. V.62. P.947-958.
23. Dale J.W., Brittain D., Cataldi A.A., Cousins D., Crawford J.T., Driscoll J., Heersma H., Lillebaek T., Quitugua T., Rastogi N., Skuce R.A., Sola C., Van Soolingen D., Vincent V. Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature // Int. J. Tuberc. Lung Dis. 2001. V.5. P.216-219.
24. Demay C., Liens B., Burguière T., Hill V., Couvin D., Millet J., Mokrousov I., Sola C., Zozio T., Rastogi N. SITVITWEB - a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology // Infect. Evol. 2012. V.12. P.755-766.
25. Deng W., Shi X., Tjian R., Lionnet T., Singer R.H. CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells // Proc. Natl. Acad. Sci. USA. 2015. V. 112. P. 11870-11875.
26. Dominguez A.A., Lim W.A., Qi L.S. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation // Nat. Rev. Mol. Cell. Biol. 2016. V. 17. P. 5-15.
27. Donohoue P.D., Barrangou R., May A.P. Advances in industrial biotechnology using CRISPR-Cas Systems // Trends Biotechnol. 2017. pii: S0167-7799(17)30187-7.
28. Dreissig S., Schiml S., Schindele P., Weiss O., Rutten T., Schubert V., Gladilin E., Mette M.F., Puchta H., Houben A. Live-cell CRISPR imaging in plants reveals dynamic telomere movements // Plant J. 2017. V. 91. P. 565-573.
29. Driscoll J.R. Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex // Methods Mol. Biol. 2009. V. 551. P. 117-128.
30. East-Seletsky A., O'Connell M.R., Knight S.C., Burstein D., Cate J.H., Tjian R., Doudna J.A. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection // Nature. 2016. V. 538. P. 270-273.
31. East-Seletsky A., O'Connell M.R., Burstein D., Knott G.J., Doudna J.A. RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes // Mol. Cell. 2017. V. 66. P. 373-383.e3.
32. Enríquez P. CRISPR-Mediated epigenome editing // Yale J. Biol. Med. 2016. V.89. P.471-486.
33. Euler M., Wang Y., Otto P., Tomaso H., Escudero R., Anda P., Hufert F.T., Weidmann M. Recombinase polymerase amplification assay for rapid detection of Francisella tularensis // J. Clin. Microbiol. 2012. V. 50. P. 2234-2238.
34. Euler M., Wang Y., Heidenreich D., Patel P., Strohmeier O., Hakenberg S., Niedrig M., Hufert F.T., Weidmann M. Development of a panel of recombinase polymerase amplification assays for detection of biothreat agents // J. Clin. Microbiol. 2013. V. 51. P. 1110-1117.
35. Filliol I., Driscoll J.R., Van Soolingen D., Kreiswirth B.N., Kremer K., Valétudie G., Anh D.D., Barlow R., Banerjee D., Bifani P.J., Brudey K., Cataldi A., Cooksey R.C., Cousins D.V., Dale J.W., Dellagostin O.A., Drobniewski F., Engelmann G., Ferdinand S., Gascoyne-Binzi D., Gordon M., Gutierrez M.C., Haas W.H., Heersma H., Källenius G., Kassa-Kelembho E., Koivula T., Ly H.M., Makristathis A., Mammina C., Martin G., Moström P., Mokrousov I., Narbonne V., Narvskaya O., Nastasi A., Niobe-Eyangoh S.N., Pape J.W., Rasolofo-Razanamparany V., Ridell M., Rossetti M.L., Stauffer F., Suffys P.N., Takiff H., Texier-Maugein J., Vincent V., De Waard J.H., Sola C., Rastogi N. Global distribution of Mycobacterium tuberculosis spoligotypes // Emerg. Infect. Dis. 2002. V.8. P.1347-1349.
36. Filliol I., Driscoll J.R., van Soolingen D., Kreiswirth B.N., Kremer K., Valétudie G., Dang D.A., Barlow R., Banerjee D., Bifani P.J., Brudey K., Cataldi A., Cooksey R.C., Cousins D.V., Dale J.W., Dellagostin O.A., Drobniewski F., Engelmann G., Ferdinand S., Gascoyne-Binzi D., Gordon M., Gutierrez M.C., Haas W.H., Heersma H., Kassa-Kelembho E., Ho M.L., Makristathis A., Mammina C., Martin G., Moström P., Mokrousov I., Narbonne V., Narvskaya O., Nastasi A., Niobe-Eyangoh S.N., Pape J.W., Rasolofo-Razanamparany V., Ridell M., Rossetti M.L., Stauffer F., Suffys P.N., Takiff H., Texier-Maugein J., Vincent V., de Waard J.H., Sola C., Rastogi N. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study // J. Clin. Microbiol. V. 41. P. 1963-1970.
37. Fujita T., Fujii H. Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR // Biochem. Biophys. Res. Commun. 2013. V.439. P.132-136.
38. Fuller S.L., Savory E.A., Weisberg A.J., Buser J.Z., Gordon M.I., Putnam M.L., Chang J.H. Isothermal amplification and lateral-flow assay for detecting crown-gall-causing Agrobacterium spp. // Phytopathology. 2017. V.107. P.1062-1068.
39. Gilbert L.A., Larson M.H., Morsut L., Liu Z., Brar G.A., Torres S.E., Stern-Ginossar N., Brandman O., Whitehead E.H., Doudna J.A., Lim W.A., Weissman J.S., Qi L.S. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes // Cell. 2013. V.154. P.442-451.
40. Gilbert L.A., Horlbeck M.A., Adamson B., Villalta J.E., Chen Y., Whitehead E.H., Guimaraes C., Panning B., Ploegh H.L., Bassik M.C., Qi L.S., Kampmann M., Weissman J.S. Genome-scale CRISPR-mediated control of gene repression and activation // Cell. 2014. V.159. P.647-661.
41. Goguet de la Salmonière Y.O., Li H.M., Torrea G., Bunschoten A., van Embden J., Gicquel B. Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis // J. Clin. Microbiol. 1997. V. 35. P. 2210-2214.
42. Gomgnimbou M.K., Abadia E., Zhang J., Refrégier G., Panaiotov S., Bachiyska E., Sola C. "Spoligoriftyping," a dual-priming-oligonucleotide-based direct-hybridization assay for tuberculosis control with a multianalyte microbead-based hybridization system // J. Clin. Microbiol. 2012. V. 50. P. 3172-3179.
43. Gootenberg J.S., Abudayyeh O.O., Lee J.W., Essletzbichler P., Dy A.J., Joung J., Verdine V., Donghia N., Daringer N.M., Freije C.A., Myhrvold C., Bhattacharyya R.P., Livny J., Regev A., Koonin E.V., Hung D.T., Sabeti P.C., Collins J.J., Zhang F. Nucleic acid detection with CRISPR-Cas13a/C2c2 // Science. 2017. V. 356. P. 438-442.
44. Goyal M., Saunders N.A., van Embden J.D., Young D.B., Shaw R.J. Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism // J. Clin. Microbiol. 1997. V. 35. P. 647-651.
45. Grissa I., Bouchon P., Pourcel C., Vergnaud G. On-line resources for bacterial micro-evolution studies using MLVA or CRISPRtyping // Biochimie. 2008. V. 90. P. 660-668.
46. Grissa I., Vergnaud G., Pourcel C. Clustered regularly interspaced short palindromic repeats (CRISPRs) for the genotyping of bacterial pathogens // Methods Mol Biol. 2009. V.551. P.105-116.
47. Groenen P.M., Bunschoten A.E., van Soolingen D., van Embden J.D. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method // Mol. Microbiol. 1993. V.10. P.1057-1065.
48. Guatelli J.C., Whitfield K.M., Kwoh D.Y., Barringer K.J., Richman D.D., Gingeras T.R. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication // Proc. Natl. Acad. Sci. USA. 1990. V.87. P.1874-1878. – Erratum - Guatelli J.C., Whitfield K.M., Kwoh D.Y., Barringer K.J., Richman D.D., Gingeras T.R. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication // Proc. Natl. Acad. Sci. USA. 1990. V.87. P.7797.
49. Hermans P.W., van Soolingen D., Bik E.M., de Haas P.E., Dale J.W., van Embden J.D. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains // Infect. Immun. 1991. V.59. P.2695-2705.
50. Honisch C., Mosko M., Arnold C., Gharbia S.E., Diel R., Niemann S. Replacing reverse line blot hybridization spoligotyping of the Mycobacterium tuberculosis complex // J. Clin. Microbiol. 2010. V.48. P.1520-1526.
51. Ishino Y., Shinagawa H., Makino K., Amemura M., Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product // J. Bacteriol. 1987. V. 169. P. 5429–5433.
52. James A., Macdonald J. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics // Expert. Rev. Mol. Diagn. 2015. V.15. P.1475-1489.
53. Kamerbeek J., Schouls L., Kolk A., van Agterveld M., van Soolingen D., Kuijper S., Bunschoten A., Molhuizen H., Shaw R., Goyal M., van Embden J. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology // J. Clin. Microbiol. 1997. V. 35. P. 907-914.
54. Kim S.K., Han G.H., Seong W., Kim H., Kim S.W., Lee D.H., Lee S.G. CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production // Metab. Eng. 2016. V. 38. P. 228-240.
55. Knott G.J., East-Seletsky A., Cofsky J.C., Holton J.M., Charles E., O'Connell M.R., Doudna J.A. Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme // Nat. Struct. Mol. Biol. 2017. V.24. P.825-833.
56. Konermann S., Brigham M.D., Trevino A.E., Joung J., Abudayyeh O.O., Barcena C., Hsu P.D., Habib N., Gootenberg J.S., Nishimasu H., Nureki O., Zhang F. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex // Nature. 2015. V.517. P.583-588.
57. Kwoh D.Y., Davis G.R., Whitfield K.M., Chappelle H.L., DiMichele L.J., Gingeras T.R. Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format // Proc. Acad. Sci. USA. 1989. V.86. P.1173-1177.
58. La Russa M.F., Qi L.S. The new state of the Art: Cas9 for gene activation and repression // Mol. Cell Biol. 2015. V.35. P.3800-3809.
59. Li W., Raoult D., Fournier P.E. Bacterial strain typing in the genomic era // FEMS Microbiol. Rev. 2009. V.33. P.892-916.
60. Liljander A., Yu M., O'Brien E., Heller M., Nepper J.F., Weibel D.B., Gluecks I., Younan M., Frey J., Falquet L., Jores J. Field-applicable recombinase polymerase amplification assay for rapid detection of Mycoplasma capricolum Capripneumoniae // J. Clin. Microbiol. 2015. V. 53. P. 2810-2815.
61. Lillis L., Siverson J., Lee A., Cantera J., Parker M., Piepenburg O., Lehman D.A., Boyle D.S. Factors influencing Recombinase polymerase amplification (RPA) assay outcomes at point of care // Mol. Cell. Probes. 2016. V. 30. P. 74-78.
62. Liu H., Wei Z., Dominguez A., Li Y., Wang X., Qi L.S. CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation // Bioinformatics. 2015. V. 31. P. 3676–3678.
63. Liu X.S., Wu H., Ji X., Stelzer Y., Wu X., Czauderna S., Shu J., Dadon D., Young R.A., Jaenisch R. Editing DNA methylation in the mammalian genome // Cell. 2016. 167. P.233-247.e17.
64. Liu X., Xie C., Si H., Yang J. CRISPR/Cas9-mediated genome editing in plants // Methods. 2017. V. 121-122. P. 94-102.
65. Liu X., Zhang Y., Chen Y., Li M., Zhou F., Li K., Cao H., Ni M., Liu Y., Gu Z., Dickerson K.E., Xie S., Hon G.C., Xuan Z., Zhang M.Q.,Shao Z., Xu J. In Situ capture of chromatin interactions by biotinylated dCas9 // Cell. 2017a. V. 170: 1028-1043.e19.
66. Lowder L.G., Zhang D., Baltes N.J., Paul J.W., Tang X., Zheng X., Voytas D.F., Hsieh T.F., Zhang Y., Qi Y. A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation // Plant Physiol. 2015. V. 169. P. 971-985.
67. Ma Q., Liu H., Ye F., Xiang G., Shan W., Xing W. Rapid and visual detection of Mycobacterium tuberculosis complex using recombinase polymerase amplification combined with lateral flow strips // Mol. Cell. Probes. 2017. pii: S0890-8508(17)30080-4.
68. Marchisio M.A., Huang Z. CRISPR-Cas type II-based synthetic biology applications in eukaryotic cells // RNA Biol. 2017. V. 31. P. 1-8.
69. Miles T.D., Martin F.N., Coffey M.D. Development of rapid isothermal amplification assays for detection of Phytophthora in plant tissue // Phytopathology. 2015. V.105. P.265-278.
70. Miles L.A., Garippa R.J., Poirier J.T. Design, execution, and analysis of pooled in vitro CRISPR/Cas9 screens // FEBS J. 2016. V. 283. P. 3170-3180.
71. Mojica F.J., Juez G., Rodríguez-Valera F. Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites // Mol. Microbiol. 1993. V. 9. P. 613–621.
72. Mokrousov I., Limeschenko E., Vyazovaya A., Narvskaya O. Corynebacterium diphtheriae spoligotyping based on combined use of two CRISPR loci // Biotechnol. J. 2007. V. 2. P. 901-906.
73. Mokrousov I., Rastogi N. Spacer-based macroarrays for CRISPR genotyping // Methods Mol. Biol. 2015. V. 1311. P. 111-131.
74. Mokrousov I., Vyazovaya A., Kolodkina V., Limeschenko E., Titov L., Narvskaya O. Novel macroarray-based method of Corynebacterium diphtheriae genotyping: evaluation in a field study in Belarus // Eur. J. Clin. Microbiol. Infect. Dis. 2009. V. 28. P. 701-703.
75. Molhuizen H.O., Bunschoten A.E., Schouls L.M., van Embden J.D. Rapid detection and simultaneous strain differentiation of Mycobacterium tuberculosis complex bacteria by spoligotyping // Methods Mol. Biol. 1998. V. 101. P. 381-394.
76. Mondal D., Ghosh P., Khan M.A., Hossain F., Böhlken-Fascher S., Matlashewski G., Kroeger A., Olliaro P., Abd E., Wahed A. Mobile suitcase laboratory for rapid detection of Leishmania donovani usingrecombinase polymerase amplification assay // Parasit. Vectors. 2016. V.9:281.
77. Moore M.D., Jaykus L.A. Development of a recombinase polymerase amplification assay for detection of epidemic human noroviruses // Sci. Rep. 2017. V.7:40244.
78. Noman A., Aqeel M., He S. CRISPR-Cas9: Tool for qualitative and quantitative plant genome editing // Front Plant Sci. 2016. V. 7:1740.
79. Piepenburg O., Williams C.H., Stemple D.L., Armes N.A. DNA detection using recombination proteins // PLoS Biol. 2006. V. 4:e204.
80. Plummer R.J., Guo Y., Peng Y. A CRISPR reimagining: new twists and turns of CRISPR beyond the genome-engineering revolution // J. Cell. Biochem. 2017.
81. Pourcel C., Salvignol G., Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies // Microbiology. 2005. V.151. P.653-663.
82. Puchta H. Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes // Plant J. 2016. V. 87. P. 5-15.
83. Qi L.S., Larson M.H., Gilbert L.A., Doudna J.A., Weissman J.S., Arkin A.P., Lim W.A. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression // Cell. 2013. V.152. P.1173-1183.
84. Radzisheuskaya A., Shlyueva D., Müller I., Helin K. Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression // Nucleic Acids Res. 2016. V. 44:e141.
85. Ruettger A., Nieter J. Skrypnyk A., Engelmann I., Ziegler A., Moser I., Monecke S., Ehricht R., Sachse K. Rapid spoligotyping of Mycobacterium tuberculosis complex bacteria by use of a microarray system with automatic data processing and assignment // J. Clin. Microbiol. 2012. V.50. P.2492-2495.
86. Sebban M., Mokrousov I., Rastogi N., Sola C. A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis // Bioinformatics. V. 18. P. 235-243.
87. Seth K., Harish. Current status of potential applications of repurposed Cas9 for structural and functional genomics of plants // Biochem. Biophys. Res. Commun. 2016. pii: S0006-291X(16)31825-3.
88. Shariat N., Dudley E.G. CRISPRs: molecular signatures used for pathogen subtyping // Appl. Environ. Microbiol. 2014. V. 80. P. 430-439.
89. Sola C., Horgen L., Maïsetti J., Devallois A., Goh K.S., Rastogi N. Spoligotyping followed by double-repetitive-element PCR as rapid alternative to IS6110 fingerprinting for epidemiological studies of tuberculosis // J. Clin. Microbiol. 1998. V. 36. P. 1122-1124.
90. Sola C. Clustured regularly interspersed short palindromic repeats (CRISPR) genetic diversity studies as a mean to reconstruct the evolution of the Mycobacterium tuberculosis complex // Tuberculosis (Edinb). 2015. V. 95. P. 159-166.
91. Suzana S., Shanmugam S., Uma Devi K.R., Swarna Latha P.N., Michael J.S. Spoligotyping of Mycobacterium tuberculosis isolates at a tertiary care hospital in India // Trop. Med. Int. Health. 2017. V. 22. P. 703-707.
92. Tang C., Reyes J.F., Luciani F., Francis A.R., Tanaka M.M. spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex // Bioinformatics. 2008. V. 24. P. 2414-2415.
93. Tang X., Lowder L.G., Zhang T., Malzahn A.A., Zheng X., Voytas D.F., Zhong Z., Chen Y., Ren Q., Li Q., Kirkland E.R., Zhang Y., Qi Y. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants // Nat. Plants. 2017. V.3:17103.
94. Tu Y., Zeng X., Li H., Zheng R., Xu Y., Li Q. A strip array for spoligotyping of Mycobacterium tuberculosis complex isolates // J. Microbiol. Methods. 2016. V.122. P.23-26.
95. Vojta A., Dobrinić P., Tadić V., Bočkor L., Korać P., Julg B., Klasić M., Zoldoš V. Repurposing the CRISPR-Cas9 system for targeted DNA methylation // Nucleic Acids Res. 2016. 44. P. 5615-5628.
96. Vora S., Tuttle M., Cheng J., Church G. Next stop for the CRISPR revolution: RNA-guided epigenetic regulators // FEBS J. 2016. V.283. P.3181-3193.
97. Wang F., Qi L.S. Applications of CRISPR genome engineering in cell biology // Trends Cell. Biol. 2016. V.26. P.875-888.
98. Wang J.C., Liu L.B., Han Q.A., Wang J.F, Yuan W.Z. An exo probe-based recombinase polymerase amplification assay for the rapid detection of porcine parvovirus // J. Virol. 2017. V.248. P.145-147.
99. Wu Y.D., Xu M.J., Wang Q.Q., Zhou C.X., Wang M., Zhu X.Q., Zhou D.H. Recombinase polymerase amplification (RPA) combined with lateral flow (LF) strip for detection of Toxoplasma gondii in the environment // Vet. Parasitol. 2017. V.243. P.199-203.
100. Xu C., Li L., Jin W., Wan Y. Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops // Int. J. Mol. Sci. 2014. V. 15. P. 18197-18205.
101. Xu H., Xiao T., Chen C.H., Li W., Meyer C.A., Wu Q., Wu D., Cong L., Zhang F., Liu J.S., Brown M., Liu X.S. Sequence determinants of improved CRISPR sgRNA design // Genome Res. 2015. V.25. P.1147-1157.
102. Xu X., Tao Y., Gao X., Zhang L., Li X., Zou W., Ruan K., Wang F., Xu G.L, Hu R. A CRISPR-based approach for targeted DNA demethylation // Cell Discov. 2016. V.2:16009.
103. Zhang J., Abadia E., Refregier G., Tafaj S., Boschiroli M.L., Guillard B., Andremont A., Ruimy R., Sola C. Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay // J. Med. Microbiol. 2010. V.59. P.285-294.
104. Zhang X., Wang J., Cheng Q., Zheng X., Zhao G., Wang J. Multiplex gene regulation by CRISPR-ddCpf1 // Cell. Discov. 2017. V.3:17018.