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For: Bou-Nader C, Bothra A, Garboczi DN, Leppla SH, Zhang J. Structural basis of R-loop recognition by the S9.6 monoclonal antibody. Nat Commun 2022;13:1641. [PMID: 35347133 PMCID: PMC8960830 DOI: 10.1038/s41467-022-29187-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Mamar H, Fajka-Boja R, Mórocz M, Jurado EP, Zentout S, Mihuţ A, Kopasz AG, Mérey M, Smith R, Sharma AB, Lakin ND, Bowman AJ, Haracska L, Huet S, Timinszky G. The loss of DNA polymerase epsilon accessory subunits POLE3-POLE4 leads to BRCA1-independent PARP inhibitor sensitivity. Nucleic Acids Res 2024:gkae439. [PMID: 38828775 DOI: 10.1093/nar/gkae439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024]  Open
2
Leisegang MS, Warwick T, Stötzel J, Brandes RP. RNA-DNA triplexes: molecular mechanisms and functional relevance. Trends Biochem Sci 2024;49:532-544. [PMID: 38582689 DOI: 10.1016/j.tibs.2024.03.009] [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: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
3
Liu Z, Ajit K, Wu Y, Zhu WG, Gullerova M. The GATAD2B-NuRD complex drives DNA:RNA hybrid-dependent chromatin boundary formation upon DNA damage. EMBO J 2024;43:2453-2485. [PMID: 38719994 PMCID: PMC11183058 DOI: 10.1038/s44318-024-00111-7] [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: 11/10/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/19/2024]  Open
4
Zhang X, Guo J, Shi X, Zhou X, Chen Q. LUC7L3 is a downstream factor of SRSF1 and prevents genomic instability. CELL INSIGHT 2024;3:100170. [PMID: 38590928 PMCID: PMC10999515 DOI: 10.1016/j.cellin.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024]
5
Geraud M, Cristini A, Salimbeni S, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, Marinello J, Cordelier P, Trouche D, Favre G, Nicolas E, Capranico G, Sordet O. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep 2024;43:114214. [PMID: 38761375 DOI: 10.1016/j.celrep.2024.114214] [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: 03/02/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]  Open
6
Hou Y, Zhang C, Liu L, Yu Y, Shi L, Qin Y. WDR61 ablation triggers R-loop accumulation and suppresses breast cancer progression. FEBS J 2024. [PMID: 38708718 DOI: 10.1111/febs.17145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/09/2024] [Accepted: 04/12/2024] [Indexed: 05/07/2024]
7
Xiao H, Chen W, Lin M, Jiang S, Cui X, Zhao S. Rapid immunoassay for dual-mode detection of HPV16 and HPV18 DNA based on Au@PdPt nanoparticles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024;16:1862-1869. [PMID: 38463013 DOI: 10.1039/d3ay02307a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
8
Wang P, Wei X, Shen L, Xu K, Wen Z, Gao N, Fan T, Xun S, Zhu Q, Qu X, Zhu Y. Amplification-Free Analysis of Bladder Cancer MicroRNAs on Wrinkled Silica Nanoparticles with DNA-Functionalized Quantum Dots. Anal Chem 2024;96:4860-4867. [PMID: 38478499 DOI: 10.1021/acs.analchem.3c05204] [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: 03/27/2024]
9
Dowling JW, Smith JR, Forero A. Protocol for detection of in vitro R-loop formation using dot blots. STAR Protoc 2024;5:102857. [PMID: 38285737 PMCID: PMC10839531 DOI: 10.1016/j.xpro.2024.102857] [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: 10/18/2023] [Revised: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024]  Open
10
Parsons AM, Su K, Daniels M, Bouma GJ, Vanden Heuvel GB, Larson ED. Human PKD1 sequences form R-loop structures in vitro. MICROPUBLICATION BIOLOGY 2024;2024:10.17912/micropub.biology.001058. [PMID: 38371318 PMCID: PMC10873753 DOI: 10.17912/micropub.biology.001058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/08/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
11
Feró O, Varga D, Nagy É, Karányi Z, Sipos É, Engelhardt J, Török N, Balogh I, Vető B, Likó I, Fóthi Á, Szabó Z, Halmos G, Vécsei L, Arányi T, Székvölgyi L. DNA methylome, R-loop and clinical exome profiling of patients with sporadic amyotrophic lateral sclerosis. Sci Data 2024;11:123. [PMID: 38267456 PMCID: PMC10808109 DOI: 10.1038/s41597-024-02985-y] [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: 09/21/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]  Open
12
Zhang W, Yang Z, Wang W, Sun Q. Primase promotes the competition between transcription and replication on the same template strand resulting in DNA damage. Nat Commun 2024;15:73. [PMID: 38168108 PMCID: PMC10761990 DOI: 10.1038/s41467-023-44443-0] [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: 06/20/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]  Open
13
Bothra A, Perry ML, Wei E, Moayeri M, Ma Q, Biamonte MA, Siirin M, Leppla SH. S9.6-based hybrid capture immunoassay for pathogen detection. Sci Rep 2023;13:22562. [PMID: 38110611 PMCID: PMC10728093 DOI: 10.1038/s41598-023-49881-w] [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: 10/20/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]  Open
14
Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023;214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [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: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
15
Stylianakis E, Chan JPK, Law PP, Jiang Y, Khadayate S, Karimi MM, Festenstein R, Vannier JB. Mouse HP1γ regulates TRF1 expression and telomere stability. Life Sci 2023;331:122030. [PMID: 37598977 DOI: 10.1016/j.lfs.2023.122030] [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: 11/29/2022] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
16
Liu J, Shi J, Feng Q, Fan W, Liu C. An immunoassay-like recognition mechanism-based lateral flow strategy for rapid microRNA analysis. Chem Commun (Camb) 2023;59:11851-11854. [PMID: 37718643 DOI: 10.1039/d3cc03788f] [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: 09/19/2023]
17
Thompson VF, Wieland DR, Mendoza-Leon V, Janis HI, Lay MA, Harrell LM, Schwartz JC. Binding of the nuclear ribonucleoprotein family member FUS to RNA prevents R-loop RNA:DNA hybrid structures. J Biol Chem 2023;299:105237. [PMID: 37690693 PMCID: PMC10556777 DOI: 10.1016/j.jbc.2023.105237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]  Open
18
Sharma AB, Ramlee MK, Kosmin J, Higgs MR, Wolstenholme A, Ronson GE, Jones D, Ebner D, Shamkhi N, Sims D, Wijnhoven PWG, Forment JV, Gibbs-Seymour I, Lakin ND. C16orf72/HAPSTR1/TAPR1 functions with BRCA1/Senataxin to modulate replication-associated R-loops and confer resistance to PARP disruption. Nat Commun 2023;14:5003. [PMID: 37591890 PMCID: PMC10435583 DOI: 10.1038/s41467-023-40779-9] [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: 02/06/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023]  Open
19
Wu T, Hou H, Dey A, Bachu M, Chen X, Wisniewski J, Kudoh F, Chen C, Chauhan S, Xiao H, Pan R, Ozato K. BRD4 directs mitotic cell division by inhibiting DNA damage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547436. [PMID: 37546888 PMCID: PMC10401944 DOI: 10.1101/2023.07.02.547436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
20
Hagkarim NC, Hajkarim MC, Suzuki T, Fujiwara T, Winkler GS, Stewart GS, Grand RJ. Disruption of the Mammalian Ccr4-Not Complex Contributes to Transcription-Mediated Genome Instability. Cells 2023;12:1868. [PMID: 37508532 PMCID: PMC10378556 DOI: 10.3390/cells12141868] [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: 08/10/2022] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]  Open
21
Wei E, Bou-Nader C, Perry ML, Fattah R, Zhang J, Leppla SH, Bothra A. S9.6 Antibody-Enzyme Conjugates for the Detection of DNA-RNA Hybrids. Bioconjug Chem 2023;34:834-844. [PMID: 37194248 DOI: 10.1021/acs.bioconjchem.2c00609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
22
Gong D, Wang L, Zhou H, Gao J, Zhang W, Zheng P. Long noncoding RNA Lnc530 localizes on R-loops and regulates R-loop formation and genomic stability in mouse embryonic stem cells. Stem Cell Reports 2023;18:952-968. [PMID: 36931280 PMCID: PMC10147553 DOI: 10.1016/j.stemcr.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023]  Open
23
Laspata N, Kaur P, Mersaoui S, Muoio D, Liu Z, Bannister MH, Nguyen H, Curry C, Pascal J, Poirier G, Wang H, Masson JY, Fouquerel E. PARP1 associates with R-loops to promote their resolution and genome stability. Nucleic Acids Res 2023;51:2215-2237. [PMID: 36794853 PMCID: PMC10018367 DOI: 10.1093/nar/gkad066] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]  Open
24
Fang M, Liu F, Fang D, Chen Y, Xiang Y, Zhang H, Huang M, Qin X, Pan LH, Yang F. Primer exchange reaction-amplified protein-nucleic acid interactions for ultrasensitive and specific microRNA detection. Biosens Bioelectron 2023;230:115274. [PMID: 37004284 DOI: 10.1016/j.bios.2023.115274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023]
25
Dey A, Prakash J, Das R, Shelar S, Saini A, Cherian S, Patel SC, Hassan PA, Khandekar A, Dasgupta K, Misra HS, Uppal S. Development of a rapid and ultra-sensitive RNA:DNA hybrid immunocapture based biosensor for visual detection of SARS-CoV-2 RNA. PNAS NEXUS 2023;2:pgad031. [PMID: 36909823 PMCID: PMC9998032 DOI: 10.1093/pnasnexus/pgad031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/23/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
26
The Epidemiology of Infectious Diseases Meets AI: A Match Made in Heaven. Pathogens 2023;12:pathogens12020317. [PMID: 36839589 PMCID: PMC9963936 DOI: 10.3390/pathogens12020317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]  Open
27
Scheuren M, Möhner J, Zischler H. R-loop landscape in mature human sperm: Regulatory and evolutionary implications. Front Genet 2023;14:1069871. [PMID: 37139234 PMCID: PMC10149866 DOI: 10.3389/fgene.2023.1069871] [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: 10/14/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023]  Open
28
Zhou J, Zhang W, Sun Q. R-loop: The new genome regulatory element in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022;64:2275-2289. [PMID: 36223078 DOI: 10.1111/jipb.13383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
29
Watts JA, Grunseich C, Rodriguez Y, Liu Y, Li D, Burdick J, Bruzel A, Crouch RJ, Mahley RW, Wilson S, Cheung V. A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE. Nucleic Acids Res 2022;50:12497-12514. [PMID: 36453989 PMCID: PMC9757052 DOI: 10.1093/nar/gkac1107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]  Open
30
Lee H, You SY, Han DW, La H, Park C, Yoo S, Kang K, Kang MH, Choi Y, Hong K. Dynamic Change of R-Loop Implicates in the Regulation of Zygotic Genome Activation in Mouse. Int J Mol Sci 2022;23:ijms232214345. [PMID: 36430821 PMCID: PMC9699122 DOI: 10.3390/ijms232214345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]  Open
31
Marinello J, Arleo A, Russo M, Delcuratolo M, Ciccarelli F, Pommier Y, Capranico G. Topoisomerase I poison-triggered immune gene activation is markedly reduced in human small-cell lung cancers by impairment of the cGAS/STING pathway. Br J Cancer 2022;127:1214-1225. [PMID: 35794238 PMCID: PMC9519573 DOI: 10.1038/s41416-022-01894-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 12/27/2022]  Open
32
NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis. Nat Commun 2022;13:5058. [PMID: 36030240 PMCID: PMC9420119 DOI: 10.1038/s41467-022-32709-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 08/11/2022] [Indexed: 11/11/2022]  Open
33
Li Q, Lin C, Luo Z, Li H, Li X, Sun Q. Cryo-EM structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids. J Genet Genomics 2022;49:677-680. [PMID: 35550870 DOI: 10.1016/j.jgg.2022.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 11/29/2022]
34
Shinriki S, Hirayama M, Nagamachi A, Yokoyama A, Kawamura T, Kanai A, Kawai H, Iwakiri J, Liu R, Maeshiro M, Tungalag S, Tasaki M, Ueda M, Tomizawa K, Kataoka N, Ideue T, Suzuki Y, Asai K, Tani T, Inaba T, Matsui H. DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells. Leukemia 2022;36:2605-2620. [PMID: 36229594 PMCID: PMC9613458 DOI: 10.1038/s41375-022-01708-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
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