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For: Biernacka A, Zhu Y, Skrzypczak M, Forey R, Pardo B, Grzelak M, Nde J, Mitra A, Kudlicki A, Crosetto N, Pasero P, Rowicka M, Ginalski K. i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks. Commun Biol 2018;1:181. [PMID: 30393778 PMCID: PMC6208412 DOI: 10.1038/s42003-018-0165-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 09/11/2018] [Indexed: 01/05/2023]  Open
Number Cited by Other Article(s)
1
Ben-Tov D, Mafessoni F, Cucuy A, Honig A, Melamed-Bessudo C, Levy AA. Uncovering the dynamics of precise repair at CRISPR/Cas9-induced double-strand breaks. Nat Commun 2024;15:5096. [PMID: 38877047 PMCID: PMC11178868 DOI: 10.1038/s41467-024-49410-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: 02/06/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024]  Open
2
Andrés CMC, de la Lastra JMP, Juan CA, Plou FJ, Pérez-Lebeña E. Chemical Insights into Oxidative and Nitrative Modifications of DNA. Int J Mol Sci 2023;24:15240. [PMID: 37894920 PMCID: PMC10607741 DOI: 10.3390/ijms242015240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]  Open
3
Zhang ZH, Qian SH, Wei D, Chen ZX. In vivo dynamics and regulation of DNA G-quadruplex structures in mammals. Cell Biosci 2023;13:117. [PMID: 37381029 DOI: 10.1186/s13578-023-01074-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]  Open
4
Tartas A, Lundholm L, Scherthan H, Wojcik A, Brzozowska B. The order of sequential exposure of U2OS cells to gamma and alpha radiation influences the formation and decay dynamics of NBS1 foci. PLoS One 2023;18:e0286902. [PMID: 37307266 DOI: 10.1371/journal.pone.0286902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023]  Open
5
Wang H, Wang Y, Luo Z, Lin X, Liu M, Wu F, Shao H, Zhang W. Advances in Off-Target Detection for CRISPR-Based Genome Editing. Hum Gene Ther 2023;34:112-128. [PMID: 36453226 DOI: 10.1089/hum.2022.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
6
Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023;14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023]  Open
7
Vergara X, Schep R, Medema RH, van Steensel B. From fluorescent foci to sequence: Illuminating DNA double strand break repair by high-throughput sequencing technologies. DNA Repair (Amst) 2022;118:103388. [PMID: 36037787 DOI: 10.1016/j.dnarep.2022.103388] [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: 06/08/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
8
Precision digital mapping of endogenous and induced genomic DNA breaks by INDUCE-seq. Nat Commun 2022;13:3989. [PMID: 35810156 PMCID: PMC9271039 DOI: 10.1038/s41467-022-31702-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 06/30/2022] [Indexed: 11/08/2022]  Open
9
Rucinski A, Biernacka A, Schulte R. Applications of nanodosimetry in particle therapy planning and beyond. Phys Med Biol 2021;66. [PMID: 34731854 DOI: 10.1088/1361-6560/ac35f1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/03/2021] [Indexed: 12/28/2022]
10
Atkins A, Chung CH, Allen AG, Dampier W, Gurrola TE, Sariyer IK, Nonnemacher MR, Wigdahl B. Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy. Front Genome Ed 2021;3:673022. [PMID: 34713260 PMCID: PMC8525399 DOI: 10.3389/fgeed.2021.673022] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022]  Open
11
Berzsenyi I, Pantazi V, Borsos BN, Pankotai T. Systematic overview on the most widespread techniques for inducing and visualizing the DNA double-strand breaks. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021;788:108397. [PMID: 34893162 DOI: 10.1016/j.mrrev.2021.108397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
12
Kara N, Krueger F, Rugg-Gunn P, Houseley J. Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. PLoS Biol 2021;19:e3000886. [PMID: 33760805 PMCID: PMC8021198 DOI: 10.1371/journal.pbio.3000886] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/05/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]  Open
13
Emmanouilidis I, Fili N, Cook AW, Hari-Gupta Y, dos Santos Á, Wang L, Martin-Fernandez ML, Ellis PJI, Toseland CP. A Targeted and Tuneable DNA Damage Tool Using CRISPR/Cas9. Biomolecules 2021;11:288. [PMID: 33672015 PMCID: PMC7919286 DOI: 10.3390/biom11020288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]  Open
14
Biernacka A, Skrzypczak M, Zhu Y, Pasero P, Rowicka M, Ginalski K. High-resolution, ultrasensitive and quantitative DNA double-strand break labeling in eukaryotic cells using i-BLESS. Nat Protoc 2021;16:1034-1061. [PMID: 33349705 PMCID: PMC8088906 DOI: 10.1038/s41596-020-00448-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/09/2020] [Indexed: 11/09/2022]
15
Rybin MJ, Ramic M, Ricciardi NR, Kapranov P, Wahlestedt C, Zeier Z. Emerging Technologies for Genome-Wide Profiling of DNA Breakage. Front Genet 2021;11:610386. [PMID: 33584810 PMCID: PMC7873462 DOI: 10.3389/fgene.2020.610386] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022]  Open
16
Forey R, Barthe A, Tittel-Elmer M, Wery M, Barrault MB, Ducrot C, Seeber A, Krietenstein N, Szachnowski U, Skrzypczak M, Ginalski K, Rowicka M, Cobb JA, Rando OJ, Soutourina J, Werner M, Dubrana K, Gasser SM, Morillon A, Pasero P, Lengronne A, Poli J. A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization. Mol Cell 2020;81:183-197.e6. [PMID: 33278361 DOI: 10.1016/j.molcel.2020.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023]
17
Bouwman BAM, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V, Crosetto N. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 2020;15:3894-3941. [PMID: 33139954 DOI: 10.1038/s41596-020-0397-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023]
18
Analyzing Homologous Recombination at a Genome-Wide Level. Methods Mol Biol 2020. [PMID: 32840796 DOI: 10.1007/978-1-0716-0644-5_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
19
Promonet A, Padioleau I, Liu Y, Sanz L, Biernacka A, Schmitz AL, Skrzypczak M, Sarrazin A, Mettling C, Rowicka M, Ginalski K, Chedin F, Chen CL, Lin YL, Pasero P. Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites. Nat Commun 2020;11:3940. [PMID: 32769985 PMCID: PMC7414224 DOI: 10.1038/s41467-020-17858-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 07/14/2020] [Indexed: 12/30/2022]  Open
20
Li W, Sancar A. Methodologies for detecting environmentally induced DNA damage and repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020;61:664-679. [PMID: 32083352 PMCID: PMC7442611 DOI: 10.1002/em.22365] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/08/2020] [Accepted: 02/16/2020] [Indexed: 05/07/2023]
21
Langen B, Helou K, Forssell-Aronsson E. The IRI-DICE hypothesis: ionizing radiation-induced DSBs may have a functional role for non-deterministic responses at low doses. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2020;59:349-355. [PMID: 32583290 PMCID: PMC7368863 DOI: 10.1007/s00411-020-00854-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
22
Mitrentsi I, Yilmaz D, Soutoglou E. How to maintain the genome in nuclear space. Curr Opin Cell Biol 2020;64:58-66. [PMID: 32220808 DOI: 10.1016/j.ceb.2020.02.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/28/2020] [Accepted: 02/23/2020] [Indexed: 01/27/2023]
23
Hulke ML, Massey DJ, Koren A. Genomic methods for measuring DNA replication dynamics. Chromosome Res 2020;28:49-67. [PMID: 31848781 PMCID: PMC7131883 DOI: 10.1007/s10577-019-09624-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
24
Vítor AC, Huertas P, Legube G, de Almeida SF. Studying DNA Double-Strand Break Repair: An Ever-Growing Toolbox. Front Mol Biosci 2020;7:24. [PMID: 32154266 PMCID: PMC7047327 DOI: 10.3389/fmolb.2020.00024] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/04/2020] [Indexed: 12/29/2022]  Open
25
Kordon MM, Zarębski M, Solarczyk K, Ma H, Pederson T, Dobrucki JW. STRIDE-a fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells. Nucleic Acids Res 2020;48:e14. [PMID: 31832687 PMCID: PMC7026605 DOI: 10.1093/nar/gkz1118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/24/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]  Open
26
Puig Lombardi E, Londoño-Vallejo A. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Res 2020;48:1-15. [PMID: 31754698 PMCID: PMC6943126 DOI: 10.1093/nar/gkz1097] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022]  Open
27
Homouz D, Kudlicki AS. Maximum parsimony interpretation of chromatin capture experiments. PLoS One 2019;14:e0225578. [PMID: 31765406 PMCID: PMC6876987 DOI: 10.1371/journal.pone.0225578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/08/2019] [Indexed: 11/18/2022]  Open
28
Mavragani IV, Nikitaki Z, Kalospyros SA, Georgakilas AG. Ionizing Radiation and Complex DNA Damage: From Prediction to Detection Challenges and Biological Significance. Cancers (Basel) 2019;11:E1789. [PMID: 31739493 PMCID: PMC6895987 DOI: 10.3390/cancers11111789] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]  Open
29
Arnould C, Legube G. The Secret Life of Chromosome Loops upon DNA Double-Strand Break. J Mol Biol 2019;432:724-736. [PMID: 31401119 PMCID: PMC7057266 DOI: 10.1016/j.jmb.2019.07.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022]
30
Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates? DNA Repair (Amst) 2019;81:102661. [PMID: 31331819 DOI: 10.1016/j.dnarep.2019.102661] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
31
Zhu Y, Biernacka A, Pardo B, Dojer N, Forey R, Skrzypczak M, Fongang B, Nde J, Yousefi R, Pasero P, Ginalski K, Rowicka M. qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing. Nat Commun 2019;10:2313. [PMID: 31127121 PMCID: PMC6534554 DOI: 10.1038/s41467-019-10332-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/30/2019] [Indexed: 12/04/2022]  Open
32
Bouwman BAM, Crosetto N. Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling. Genes (Basel) 2018;9:E632. [PMID: 30558210 PMCID: PMC6316733 DOI: 10.3390/genes9120632] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/07/2023]  Open
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