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For: Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell 2022;185:4574-4586.e16. [PMID: 36423580 DOI: 10.1016/j.cell.2022.10.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/10/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022]
Number Cited by Other Article(s)
1
Xiang W, Lin X, Yang Y, Huang L, Chen Y, Chen J, Liu L. Cas12h is a crRNA-guided DNA nickase that can be utilized for precise gene editing. Cell Rep 2025;44:115718. [PMID: 40372912 DOI: 10.1016/j.celrep.2025.115718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 03/20/2025] [Accepted: 04/28/2025] [Indexed: 05/17/2025]  Open
2
Silva MKDP, Nicoleti VYU, Rodrigues BDPP, Araujo ASF, Ellwanger JH, de Almeida JM, Lemos LN. Exploring deep learning in phage discovery and characterization. Virology 2025;609:110559. [PMID: 40359589 DOI: 10.1016/j.virol.2025.110559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 03/24/2025] [Accepted: 04/28/2025] [Indexed: 05/15/2025]
3
Yang C, Gao M, Wang Y, Jiang T, Ma Y, Si X, Deng Y, Liu Y, Mo M, Xiao X, Wang F, Yang Y. Low-Frequency Optical Signal Enhancement Device Combines CRISPR-Based Assay for Portable S. Pneumoniae Detection. Anal Chem 2025;97:8553-8563. [PMID: 40203058 DOI: 10.1021/acs.analchem.5c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2025]
4
Tordoff J, Alfonse LE, Makarova KS, Ornstein A, Garrity AJ, Yan WX, Scott DA, Koonin EV, Cheng DR. Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems. CRISPR J 2025;8:149-154. [PMID: 40163416 DOI: 10.1089/crispr.2024.0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]  Open
5
Xavier KVM, de Oliveira Luz AC, Silva-Junior JW, de Melo BST, de Aragão Batista MV, de Albuquerque Silva AM, de Queiroz Balbino V, Leal-Balbino TC. Molecular epidemiological study of Pseudomonas aeruginosa strains isolated from hospitals in Brazil by MLST and CRISPR/Cas system analysis. Mol Genet Genomics 2025;300:33. [PMID: 40113632 PMCID: PMC11925996 DOI: 10.1007/s00438-025-02239-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 03/02/2025] [Indexed: 03/22/2025]
6
Duan C, Zang Z, Xu Y, He H, Li S, Liu Z, Lei Z, Zheng JS, Li SZ. FGeneBERT: function-driven pre-trained gene language model for metagenomics. Brief Bioinform 2025;26:bbaf149. [PMID: 40211978 PMCID: PMC11986344 DOI: 10.1093/bib/bbaf149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 02/22/2025] [Accepted: 03/14/2025] [Indexed: 04/14/2025]  Open
7
Zheng W, Li H, Liu M, Wei Y, Liu B, Li Z, Xiong C, Huang S, Hu C, Ouyang S. Molecular insights and rational engineering of a compact CRISPR-Cas effector Cas12h1 with a broad-spectrum PAM. Signal Transduct Target Ther 2025;10:66. [PMID: 39955288 PMCID: PMC11830025 DOI: 10.1038/s41392-025-02147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 01/01/2025] [Accepted: 01/16/2025] [Indexed: 02/17/2025]  Open
8
Chen J, Lin X, Xiang W, Chen Y, Zhao Y, Huang L, Liu L. DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems. Nucleic Acids Res 2025;53:gkae1241. [PMID: 39676682 PMCID: PMC11797020 DOI: 10.1093/nar/gkae1241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 10/30/2024] [Accepted: 12/03/2024] [Indexed: 12/17/2024]  Open
9
Peng H, Chen IA, Qimron U. Engineering Phages to Fight Multidrug-Resistant Bacteria. Chem Rev 2025;125:933-971. [PMID: 39680919 PMCID: PMC11758799 DOI: 10.1021/acs.chemrev.4c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 12/04/2024] [Accepted: 12/09/2024] [Indexed: 12/18/2024]
10
Liao H, Li J, Wang YZ, Li H, An XL, Wang T, Chang RY, Zhu YG, Su JQ. Evolutionary diversification and succession of soil huge phages in glacier foreland. MICROBIOME 2025;13:18. [PMID: 39838455 PMCID: PMC11748809 DOI: 10.1186/s40168-024-02017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Accepted: 12/19/2024] [Indexed: 01/23/2025]
11
Schechter MS, Trigodet F, Veseli IA, Miller SE, Klein ML, Sever M, Maignien L, Delmont TO, Light SH, Eren AM. Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.15.633187. [PMID: 39868213 PMCID: PMC11760686 DOI: 10.1101/2025.01.15.633187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
12
Hu D, Hu L, Lu Y, Dong X, Cao X, Bai S, Zhang L, Li D, Sun Y. Intein-mediated split SaCas9 for genome editing in plants. Front Genome Ed 2025;6:1506468. [PMID: 39845892 PMCID: PMC11750852 DOI: 10.3389/fgeed.2024.1506468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 12/13/2024] [Indexed: 01/24/2025]  Open
13
Nayfach S, Bhatnagar A, Novichkov A, Estevam GO, Kim N, Hill E, Ruffolo JA, Silverstein R, Gallagher J, Kleinstiver B, Meeske AJ, Cameron P, Madani A. Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.06.631536. [PMID: 39829748 PMCID: PMC11741284 DOI: 10.1101/2025.01.06.631536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
14
Delgado-Nungaray JA, Figueroa-Yáñez LJ, Reynaga-Delgado E, Corona-España AM, Gonzalez-Reynoso O. Unveiling the endogenous CRISPR-Cas system in Pseudomonas aeruginosa PAO1. PLoS One 2024;19:e0312783. [PMID: 39739718 DOI: 10.1371/journal.pone.0312783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 10/13/2024] [Indexed: 01/02/2025]  Open
15
Li D, Zhang S, Lin S, Xing W, Yang Y, Zhu F, Su D, Chen C, Liu JJG. Cas12e orthologs evolve variable structural elements to facilitate dsDNA cleavage. Nat Commun 2024;15:10727. [PMID: 39737904 PMCID: PMC11685505 DOI: 10.1038/s41467-024-54491-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 11/11/2024] [Indexed: 01/01/2025]  Open
16
Rubio A, Garzón A, Moreno-Rodríguez A, Pérez-Pulido AJ. Biological warfare between two bacterial viruses in a defense archipelago sheds light on the spread of CRISPR-Cas systems. Cell Rep 2024;43:115085. [PMID: 39675005 DOI: 10.1016/j.celrep.2024.115085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 10/12/2024] [Accepted: 11/26/2024] [Indexed: 12/17/2024]  Open
17
Koonin EV, Makarova KS. CRISPR in mobile genetic elements: counter-defense, inter-element competition and RNA-guided transposition. BMC Biol 2024;22:295. [PMID: 39696488 DOI: 10.1186/s12915-024-02090-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 12/03/2024] [Indexed: 12/20/2024]  Open
18
Wu WY, Adiego-Pérez B, van der Oost J. Biology and applications of CRISPR-Cas12 and transposon-associated homologs. Nat Biotechnol 2024;42:1807-1821. [PMID: 39633151 DOI: 10.1038/s41587-024-02485-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 10/24/2024] [Indexed: 12/07/2024]
19
Wang F, Ma S, Zhang S, Ji Q, Hu C. CRISPR beyond: harnessing compact RNA-guided endonucleases for enhanced genome editing. SCIENCE CHINA. LIFE SCIENCES 2024;67:2563-2574. [PMID: 39012436 DOI: 10.1007/s11427-023-2566-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/11/2024] [Indexed: 07/17/2024]
20
Wu Z, Liu S, Ni J. Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum. Nat Microbiol 2024;9:3362-3375. [PMID: 39448846 DOI: 10.1038/s41564-024-01839-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 09/25/2024] [Indexed: 10/26/2024]
21
Xuan Q, Wang J, Nie Y, Fang C, Liang W. Research Progress and Application of Miniature CRISPR-Cas12 System in Gene Editing. Int J Mol Sci 2024;25:12686. [PMID: 39684395 DOI: 10.3390/ijms252312686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 11/22/2024] [Accepted: 11/22/2024] [Indexed: 12/18/2024]  Open
22
Li W, Jiang X, Wang W, Hou L, Cai R, Li Y, Gu Q, Chen Q, Ma P, Tang J, Guo M, Chuai G, Huang X, Zhang J, Liu Q. Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models. Nat Commun 2024;15:10024. [PMID: 39562558 PMCID: PMC11576732 DOI: 10.1038/s41467-024-54365-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 11/07/2024] [Indexed: 11/21/2024]  Open
23
Zhang L, Wang H, Zeng J, Cao X, Gao Z, Liu Z, Li F, Wang J, Zhang Y, Yang M, Feng Y. Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system. Nat Chem Biol 2024;20:1471-1481. [PMID: 38977786 DOI: 10.1038/s41589-024-01659-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 05/31/2024] [Indexed: 07/10/2024]
24
Čepaitė R, Klein N, Mikšys A, Camara-Wilpert S, Ragožius V, Benz F, Skorupskaitė A, Becker H, Žvejytė G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaitė L, Pausch P. Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference. Nat Commun 2024;15:9306. [PMID: 39468082 PMCID: PMC11519345 DOI: 10.1038/s41467-024-53778-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 10/23/2024] [Indexed: 10/30/2024]  Open
25
Tang H, Yu D, Zhang J, Wang M, Fu M, Qian Y, Zhang X, Ji R, Gu J, Zhang X. The new advance of exosome-based liquid biopsy for cancer diagnosis. J Nanobiotechnology 2024;22:610. [PMID: 39380060 PMCID: PMC11463159 DOI: 10.1186/s12951-024-02863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 09/16/2024] [Indexed: 10/10/2024]  Open
26
Katz MA, Sawyer EM, Oriolt L, Kozlova A, Williams MC, Margolis SR, Johnson M, Bondy-Denomy J, Meeske AJ. Diverse viral cas genes antagonize CRISPR immunity. Nature 2024;634:677-683. [PMID: 39232173 PMCID: PMC11991930 DOI: 10.1038/s41586-024-07923-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/07/2024] [Indexed: 09/06/2024]
27
Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F. Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell 2024;187:5238-5252.e20. [PMID: 39208796 PMCID: PMC11423790 DOI: 10.1016/j.cell.2024.07.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/19/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
28
Getz LJ, Maxwell KL. Diverse Antiphage Defenses Are Widespread Among Prophages and Mobile Genetic Elements. Annu Rev Virol 2024;11:343-362. [PMID: 38950439 DOI: 10.1146/annurev-virology-100422-125123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
29
Wang Y, Wang Y, Tang N, Wang Z, Pan D, Ji Q. Characterization and Engineering of a Novel Miniature Eubacterium siraeum CRISPR-Cas12f System. ACS Synth Biol 2024;13:2115-2127. [PMID: 38941613 DOI: 10.1021/acssynbio.4c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
30
Tang N, Ji Q. Miniature CRISPR-Cas12 Systems: Mechanisms, Engineering, and Genome Editing Applications. ACS Chem Biol 2024;19:1399-1408. [PMID: 38899980 DOI: 10.1021/acschembio.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
31
Hu T, Ji Q, Ke X, Zhou H, Zhang S, Ma S, Yu C, Ju W, Lu M, Lin Y, Ou Y, Zhou Y, Xiao Y, Xu C, Hu C. Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV). Commun Biol 2024;7:858. [PMID: 39003402 PMCID: PMC11246428 DOI: 10.1038/s42003-024-06537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 07/03/2024] [Indexed: 07/15/2024]  Open
32
Zhou S, Ran J, Man S, Zhang J, Yuan R, Yang X. Exploring the Effect of Steric Hindrance on Trans-cleavage Activity of CRISPR-cas12a for Ultrasensitive SERS Detection of P53 DNA. Anal Chem 2024;96:10654-10661. [PMID: 38875020 DOI: 10.1021/acs.analchem.4c01347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
33
Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024;15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
34
Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. Cell 2024;187:3249-3261.e14. [PMID: 38781968 PMCID: PMC11658890 DOI: 10.1016/j.cell.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/20/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
35
Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R. Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans. Cell Host Microbe 2024;32:875-886.e9. [PMID: 38754416 DOI: 10.1016/j.chom.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
36
Beamud B, Benz F, Bikard D. Going viral: The role of mobile genetic elements in bacterial immunity. Cell Host Microbe 2024;32:804-819. [PMID: 38870898 DOI: 10.1016/j.chom.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
37
Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024;300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]  Open
38
George NA, Zhou Z, Anantharaman K, Hug LA. Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596742. [PMID: 38854013 PMCID: PMC11160803 DOI: 10.1101/2024.05.30.596742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
39
Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024;14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
40
Xiang G, Li Y, Sun J, Huo Y, Cao S, Cao Y, Guo Y, Yang L, Cai Y, Zhang YE, Wang H. Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors. Nat Biotechnol 2024;42:745-757. [PMID: 37386294 DOI: 10.1038/s41587-023-01857-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 06/05/2023] [Indexed: 07/01/2023]
41
Zaman QU, Raza A, Lozano-Juste J, Chao L, Jones MGK, Wang HF, Varshney RK. Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops. Trends Biotechnol 2024;42:560-574. [PMID: 37993299 DOI: 10.1016/j.tibtech.2023.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
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Martínez M, Rizzuto I, Molina R. Knowing Our Enemy in the Antimicrobial Resistance Era: Dissecting the Molecular Basis of Bacterial Defense Systems. Int J Mol Sci 2024;25:4929. [PMID: 38732145 PMCID: PMC11084316 DOI: 10.3390/ijms25094929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]  Open
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Flores VS, Amgarten DE, Iha BKV, Ryon KA, Danko D, Tierney BT, Mason C, da Silva AM, Setubal JC. Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Sci Rep 2024;14:7913. [PMID: 38575625 PMCID: PMC10994904 DOI: 10.1038/s41598-024-58226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024]  Open
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Ruta GV, Ciciani M, Kheir E, Gentile MD, Amistadi S, Casini A, Cereseto A. Eukaryotic-driven directed evolution of Cas9 nucleases. Genome Biol 2024;25:79. [PMID: 38528620 PMCID: PMC10962177 DOI: 10.1186/s13059-024-03215-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/13/2024] [Indexed: 03/27/2024]  Open
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024;187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
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Rogo U, Simoni S, Fambrini M, Giordani T, Pugliesi C, Mascagni F. Future-Proofing Agriculture: De Novo Domestication for Sustainable and Resilient Crops. Int J Mol Sci 2024;25:2374. [PMID: 38397047 PMCID: PMC10888583 DOI: 10.3390/ijms25042374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]  Open
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Chen Y, Luo X, Kang R, Cui K, Ou J, Zhang X, Liang P. Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment. J Genet Genomics 2024;51:159-183. [PMID: 37516348 DOI: 10.1016/j.jgg.2023.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
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Su M, Li F, Wang Y, Gao Y, Lan W, Shao Z, Zhu C, Tang N, Gan J, Wu Z, Ji Q. Molecular basis and engineering of miniature Cas12f with C-rich PAM specificity. Nat Chem Biol 2024;20:180-189. [PMID: 37697004 DOI: 10.1038/s41589-023-01420-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
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Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon P, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert R, Knott GJ, Lapinaite A, Pausch P, Cofsky J, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Res 2024;52:D590-D596. [PMID: 37889041 PMCID: PMC10767948 DOI: 10.1093/nar/gkad890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]  Open
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Badon IW, Oh Y, Kim HJ, Lee SH. Recent application of CRISPR-Cas12 and OMEGA system for genome editing. Mol Ther 2024;32:32-43. [PMID: 37952084 PMCID: PMC10787141 DOI: 10.1016/j.ymthe.2023.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]  Open
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