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For: Chen L, Chen JY, Zhang X, Gu Y, Xiao R, Shao C, Tang P, Qian H, Luo D, Li H, Zhou Y, Zhang DE, Fu XD. R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters. Mol Cell 2017;68:745-757.e5. [PMID: 29104020 PMCID: PMC5957070 DOI: 10.1016/j.molcel.2017.10.008] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/05/2017] [Accepted: 10/06/2017] [Indexed: 12/18/2022]
Number Cited by Other Article(s)
1
Zhao YM, Jiang Y, Wang JZ, Cao S, Zhu H, Wang WK, Yu J, Liu J, Hui J. GPATCH4 functions as a regulator of nucleolar R-loops in hepatocellular carcinoma cells. Nucleic Acids Res 2025;53:gkaf438. [PMID: 40401559 PMCID: PMC12096074 DOI: 10.1093/nar/gkaf438] [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: 07/15/2024] [Revised: 04/03/2025] [Accepted: 05/15/2025] [Indexed: 05/23/2025]  Open
2
Lago S, Poli V, Fol L, Botteon M, Busi F, Turdo A, Gaggianesi M, Ciani Y, D'Amato G, Fagnocchi L, Fasciani A, Demichelis F, Todaro M, Zippo A. ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent transcription replication conflicts in triple negative breast cancer. Nat Commun 2025;16:4602. [PMID: 40382323 PMCID: PMC12085574 DOI: 10.1038/s41467-025-59804-0] [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: 01/29/2024] [Accepted: 05/02/2025] [Indexed: 05/20/2025]  Open
3
Snyder RJ, Shankar U, Delker D, Soerianto W, Burdick JT, Cheung VG, Watts JA. Guanine quadruplexes mediate mitochondrial RNA polymerase pausing. BMC Biol 2025;23:129. [PMID: 40361112 PMCID: PMC12076976 DOI: 10.1186/s12915-025-02229-4] [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: 12/03/2024] [Accepted: 04/30/2025] [Indexed: 05/15/2025]  Open
4
Zhao Y, Metzler AD, Li Y, Urlich P, Wang Y, Gilbert DM, Yao B, Tang H. Interferon-dependent R-loop induction by Zika virus contributes to growth attenuation. PNAS NEXUS 2025;4:pgaf147. [PMID: 40386679 PMCID: PMC12082298 DOI: 10.1093/pnasnexus/pgaf147] [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: 08/20/2024] [Accepted: 03/31/2025] [Indexed: 05/20/2025]
5
Li Y, Sheng Y, Di C, Yao H. Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops. Mol Cell 2025;85:1686-1702.e5. [PMID: 40112807 DOI: 10.1016/j.molcel.2025.02.019] [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: 07/30/2024] [Revised: 01/30/2025] [Accepted: 02/21/2025] [Indexed: 03/22/2025]
6
Stanek TJ, Kneebone A, Lawlor MA, Cao W, Ellison CE. Complex determinants of R-loop formation at transposable elements and major DNA satellites. Genetics 2025;229:iyaf035. [PMID: 40036798 PMCID: PMC12005256 DOI: 10.1093/genetics/iyaf035] [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: 12/30/2024] [Revised: 02/19/2025] [Accepted: 02/22/2025] [Indexed: 03/06/2025]  Open
7
Palmer B, Lee CY, Yang L, Paul T, Myong S. High-frequency transcription leads to rapid R-loop formation. J Biol Chem 2025;301:108514. [PMID: 40250562 DOI: 10.1016/j.jbc.2025.108514] [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: 01/13/2025] [Revised: 03/31/2025] [Accepted: 04/09/2025] [Indexed: 04/20/2025]  Open
8
Hwang J, Lee CY, Brahmachari S, Tripathi S, Paul T, Lee H, Craig A, Ha T, Myong S. DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase. Nat Commun 2025;16:3363. [PMID: 40204744 PMCID: PMC11982182 DOI: 10.1038/s41467-025-58479-x] [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: 05/21/2024] [Accepted: 03/24/2025] [Indexed: 04/11/2025]  Open
9
Mangione RM, Pierce S, Zheng M, Martin RM, Goncalves C, Kumar A, Scaglione S, de Sousa Morgado C, Penzo A, Lancrey A, Reid RJD, Lautier O, Gaillard PH, Stirling PC, de Almeida SF, Rothstein R, Palancade B. DNA lesions can frequently precede DNA:RNA hybrid accumulation. Nat Commun 2025;16:2401. [PMID: 40064914 PMCID: PMC11893903 DOI: 10.1038/s41467-025-57588-x] [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: 06/10/2024] [Accepted: 02/26/2025] [Indexed: 03/14/2025]  Open
10
Batra S, Allwein B, Kumar C, Devbhandari S, Brüning JG, Bahng S, Lee CM, Marians KJ, Hite RK, Remus D. G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation. Science 2025;387:eadt1978. [PMID: 40048517 DOI: 10.1126/science.adt1978] [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: 09/23/2024] [Accepted: 12/15/2024] [Indexed: 03/15/2025]
11
Chen X, Mai Z, Zheng Y, Lin P, Lu Y, Zheng J, Lin Y, Zhou Z, Xu R, Zhao X, Cui L. The hidden weavers: A review of DNA/RNA R-loops in stem cell biology and therapeutic potential. Int J Biol Macromol 2025;297:139895. [PMID: 39818393 DOI: 10.1016/j.ijbiomac.2025.139895] [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: 07/22/2024] [Revised: 12/28/2024] [Accepted: 01/13/2025] [Indexed: 01/18/2025]
12
de Klein B, Eickhoff N, Zwart W. The emerging regulatory interface between DNA repair and steroid hormone receptors in cancer. Trends Mol Med 2025:S1471-4914(25)00006-1. [PMID: 39934021 DOI: 10.1016/j.molmed.2025.01.006] [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: 11/15/2024] [Revised: 01/10/2025] [Accepted: 01/15/2025] [Indexed: 02/13/2025]
13
Damasceno JD, Briggs EM, Krasilnikova M, Marques CA, Lapsley C, McCulloch R. R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania. Nat Commun 2025;16:1470. [PMID: 39922816 PMCID: PMC11807225 DOI: 10.1038/s41467-025-56785-y] [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: 05/16/2024] [Accepted: 01/31/2025] [Indexed: 02/10/2025]  Open
14
Kang Z, Xu C, Lu S, Gong J, Yan R, Luo G, Wang Y, He Q, Wu Y, Yan Y, Qian B, Han S, Bu Z, Zhang J, Xia X, Chen L, Hu Z, Lin M, Sun Z, Gu Y, Ye L. NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit. Nat Commun 2025;16:791. [PMID: 39824811 PMCID: PMC11742055 DOI: 10.1038/s41467-024-55579-y] [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: 07/04/2023] [Accepted: 12/16/2024] [Indexed: 01/20/2025]  Open
15
Sun C, Wang Z, Li Q, Sun Q, Xu W. mDRIP-seq is a high-throughput method for quantitative profiling of R-loop landscape. Sci Bull (Beijing) 2025;70:38-41. [PMID: 38821747 DOI: 10.1016/j.scib.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/07/2024] [Accepted: 05/11/2024] [Indexed: 06/02/2024]
16
Guo XL, Wang YD, Liu YJ, Chu L, Zhu H, Hu Y, Wu RY, Xie HY, Yu J, Li SP, Xiong CY, Li RY, Ke F, Chen L, Chen GQ, Chen L, Bai F, Enver T, Li GH, Li HF, Hong DL. Fetal hepatocytes protect the HSPC genome via fetuin-A. Nature 2025;637:402-411. [PMID: 39633051 PMCID: PMC11711094 DOI: 10.1038/s41586-024-08307-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: 01/04/2023] [Accepted: 10/30/2024] [Indexed: 12/07/2024]
17
Stratigi K, Siametis A, Garinis GA. Looping forward: exploring R-loop processing and therapeutic potential. FEBS Lett 2025;599:244-266. [PMID: 38844597 PMCID: PMC11771710 DOI: 10.1002/1873-3468.14947] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 01/28/2025]
18
Zhao W, Luo Q, Zhan H, Du Z, Deng T, Duan H. DDX18 influences chemotherapy sensitivity in colorectal cancer by regulating genomic stability. Exp Cell Res 2025;444:114344. [PMID: 39577603 DOI: 10.1016/j.yexcr.2024.114344] [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: 09/29/2024] [Revised: 11/18/2024] [Accepted: 11/18/2024] [Indexed: 11/24/2024]
19
Ouyang J. Transcription as a double-edged sword in genome maintenance. FEBS Lett 2025;599:147-156. [PMID: 39704019 DOI: 10.1002/1873-3468.15080] [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: 02/16/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 12/21/2024]
20
Akiki RM, Cornbrooks RG, Magami K, Greige A, Snyder KK, Wood DJ, Herrington MC, Mace P, Blidy K, Koike N, Berto S, Cowan CW, Taniguchi M. A long noncoding eRNA forms R-loops to shape emotional experience-induced behavioral adaptation. Science 2024;386:1282-1289. [PMID: 39666799 PMCID: PMC12071198 DOI: 10.1126/science.adp1562] [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: 03/19/2024] [Accepted: 10/09/2024] [Indexed: 12/14/2024]
21
Wu Y, Lin S, Chen H, Zheng X. Cross-regulation of RNA methylation modifications and R-loops: from molecular mechanisms to clinical implications. Cell Mol Life Sci 2024;82:1. [PMID: 39656315 PMCID: PMC11631829 DOI: 10.1007/s00018-024-05536-1] [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: 09/26/2024] [Revised: 11/08/2024] [Accepted: 11/29/2024] [Indexed: 12/13/2024]
22
Puzzo F, Crossley MP, Goswami A, Zhang F, Pekrun K, Garzon JL, Cimprich KA, Kay MA. AAV-mediated genome editing is influenced by the formation of R-loops. Mol Ther 2024;32:4256-4271. [PMID: 39369271 PMCID: PMC11638834 DOI: 10.1016/j.ymthe.2024.09.035] [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: 05/22/2024] [Revised: 08/05/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024]  Open
23
Anczukow O, Allain FHT, Angarola BL, Black DL, Brooks AN, Cheng C, Conesa A, Crosse EI, Eyras E, Guccione E, Lu SX, Neugebauer KM, Sehgal P, Song X, Tothova Z, Valcárcel J, Weeks KM, Yeo GW, Thomas-Tikhonenko A. Steering research on mRNA splicing in cancer towards clinical translation. Nat Rev Cancer 2024;24:887-905. [PMID: 39384951 DOI: 10.1038/s41568-024-00750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/11/2024]
24
Zhang X, Liang SB, Yi Z, Qiao Z, Xu B, Geng H, Wang H, Yin X, Tang M, Ge W, Xu YZ, Liang K, Fan YJ, Chen L. Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila. Nucleic Acids Res 2024;52:13110-13127. [PMID: 39470713 PMCID: PMC11602159 DOI: 10.1093/nar/gkae933] [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: 06/28/2024] [Revised: 09/30/2024] [Accepted: 10/08/2024] [Indexed: 10/30/2024]  Open
25
Khosraviani N, Yerlici VT, St-Germain J, Hou YY, Cao SB, Ghali C, Bokros M, Krishnan R, Hakem R, Lee S, Raught B, Mekhail K. Nucleolar Pol II interactome reveals TBPL1, PAF1, and Pol I at intergenic rDNA drive rRNA biogenesis. Nat Commun 2024;15:9603. [PMID: 39505901 PMCID: PMC11541992 DOI: 10.1038/s41467-024-54002-w] [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: 11/23/2023] [Accepted: 10/28/2024] [Indexed: 11/08/2024]  Open
26
Liu A, Wang Y, Zheng S, Bao Z, Zhu H, Yin L, Liu C, Zhao X, Zhao Z, Zhu D, Yu H. Endonuclear Circ-calm4 regulates ferroptosis via a circR-Loop of the COMP gene in pulmonary artery smooth muscle cells. Eur J Pharmacol 2024;982:176944. [PMID: 39187041 DOI: 10.1016/j.ejphar.2024.176944] [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: 03/31/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
27
Ferrero L, Zhang W, Benhamed M, Crespi M, Ariel F. Non-B DNA in plant genomes: prediction, mapping, and emerging roles. TRENDS IN PLANT SCIENCE 2024;29:1224-1244. [PMID: 39079769 DOI: 10.1016/j.tplants.2024.06.011] [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: 03/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 11/09/2024]
28
Sagi T, Sadato D, Takayasu K, Sasanuma H, Kanoh Y, Masai H. RNA-DNA hybrids on protein coding genes are stabilized by loss of RNase H and are associated with DNA damages during S-phase in fission yeast. Genes Cells 2024;29:966-982. [PMID: 39252397 DOI: 10.1111/gtc.13157] [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: 07/13/2024] [Revised: 08/15/2024] [Accepted: 08/23/2024] [Indexed: 09/11/2024]
29
Choi H, Zhou L, Zhao Y, Dean J. RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility. Nucleic Acids Res 2024;52:11973-11994. [PMID: 39162228 PMCID: PMC11514495 DOI: 10.1093/nar/gkae712] [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: 06/18/2023] [Accepted: 08/06/2024] [Indexed: 08/21/2024]  Open
30
Yadav C, Yadav R, Nanda S, Ranga S, Ahuja P. The hidden architects of the genome: a comprehensive review of R-loops. Mol Biol Rep 2024;51:1095. [PMID: 39460836 DOI: 10.1007/s11033-024-10025-6] [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: 08/08/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024]
31
Qiu Y, Man C, Zhu L, Zhang S, Wang X, Gong D, Fan Y. R-loops' m6A modification and its roles in cancers. Mol Cancer 2024;23:232. [PMID: 39425197 PMCID: PMC11487993 DOI: 10.1186/s12943-024-02148-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: 07/02/2024] [Accepted: 10/07/2024] [Indexed: 10/21/2024]  Open
32
Liu T, Shen X, Ren Y, Lu H, Liu Y, Chen C, Yu L, Xue Z. Genome-wide mapping of native co-localized G4s and R-loops in living cells. eLife 2024;13:RP99026. [PMID: 39392462 PMCID: PMC11469684 DOI: 10.7554/elife.99026] [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] [Indexed: 10/12/2024]  Open
33
Crowner A, Smith K, DeSmet M. Regulation of R-Loops in DNA Tumor Viruses. Pathogens 2024;13:863. [PMID: 39452734 PMCID: PMC11510693 DOI: 10.3390/pathogens13100863] [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: 09/11/2024] [Revised: 09/25/2024] [Accepted: 09/30/2024] [Indexed: 10/26/2024]  Open
34
Hu J, Xing Z, Yang H, Zhou Y, Guo L, Zhang X, Xu L, Liu Q, Ye J, Zhong X, Wang J, Lin R, Long E, Jiang J, Chen L, Pan Y, He L, Chen JY. Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases. iScience 2024;27:110584. [PMID: 39188986 PMCID: PMC11345597 DOI: 10.1016/j.isci.2024.110584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/17/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024]  Open
35
Yu Z, Wang Q, Zhang Q, Tian Y, Yan G, Zhu J, Zhu G, Zhang Y. Decoding the genomic landscape of chromatin-associated biomolecular condensates. Nat Commun 2024;15:6952. [PMID: 39138204 PMCID: PMC11322608 DOI: 10.1038/s41467-024-51426-2] [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: 07/28/2023] [Accepted: 08/05/2024] [Indexed: 08/15/2024]  Open
36
Xu W, Liu X, Li J, Sun C, Chen L, Zhou J, Li K, Li Q, Meng A, Sun Q. ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis. CELL INSIGHT 2024;3:100179. [PMID: 38974143 PMCID: PMC11225018 DOI: 10.1016/j.cellin.2024.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
37
Peixoto ML, Madan E. Unraveling the complexity: Advanced methods in analyzing DNA, RNA, and protein interactions. Adv Cancer Res 2024;163:251-302. [PMID: 39271265 DOI: 10.1016/bs.acr.2024.06.010] [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: 09/15/2024]
38
Ng RR, Lin Z, Zhang Y, Ti SC, Javed A, Wong JWH, Fang Q, Leung JWC, Tang AHN, Huen MSY. R-loop resolution by ARIP4 helicase promotes androgen-mediated transcription induction. SCIENCE ADVANCES 2024;10:eadm9577. [PMID: 39028815 PMCID: PMC11259169 DOI: 10.1126/sciadv.adm9577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
39
Yang BZ, Liu MY, Chiu KL, Chien YL, Cheng CA, Chen YL, Tsui LY, Lin KR, Chu HPC, Wu CSP. DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability. Nat Commun 2024;15:6009. [PMID: 39019926 PMCID: PMC11255299 DOI: 10.1038/s41467-024-50428-4] [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: 09/04/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024]  Open
40
Zhang X, Xu J, Hu J, Zhang S, Hao Y, Zhang D, Qian H, Wang D, Fu XD. Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation. Nat Commun 2024;15:6031. [PMID: 39019869 PMCID: PMC11255242 DOI: 10.1038/s41467-024-50298-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: 04/07/2023] [Accepted: 07/04/2024] [Indexed: 07/19/2024]  Open
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Kannan A, Gangadharan Leela S, Branzei D, Gangwani L. Role of senataxin in R-loop-mediated neurodegeneration. Brain Commun 2024;6:fcae239. [PMID: 39070547 PMCID: PMC11277865 DOI: 10.1093/braincomms/fcae239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024]  Open
42
Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024;223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [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: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024]  Open
43
Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024;26:1025-1036. [PMID: 38914786 PMCID: PMC12044674 DOI: 10.1038/s41556-024-01437-4] [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: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
44
Machitani M, Nomura A, Yamashita T, Yasukawa M, Ueki S, Fujita KI, Ueno T, Yamashita A, Tanzawa Y, Watanabe M, Taniguchi T, Saitoh N, Kaneko S, Kato Y, Mano H, Masutomi K. Maintenance of R-loop structures by phosphorylated hTERT preserves genome integrity. Nat Cell Biol 2024;26:932-945. [PMID: 38806647 DOI: 10.1038/s41556-024-01427-6] [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: 07/18/2023] [Accepted: 04/23/2024] [Indexed: 05/30/2024]
45
Bujosa P, Reina O, Caballé A, Casas-Lamesa A, Torras-Llort M, Pérez-Roldán J, Nacht AS, Vicent GP, Bernués J, Azorín F. Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs. Cell Rep 2024;43:114137. [PMID: 38662543 DOI: 10.1016/j.celrep.2024.114137] [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: 04/14/2023] [Revised: 12/23/2023] [Accepted: 04/08/2024] [Indexed: 06/01/2024]  Open
46
Duardo RC, Marinello J, Russo M, Morelli S, Pepe S, Guerra F, Gómez-González B, Aguilera A, Capranico G. Human DNA topoisomerase I poisoning causes R loop-mediated genome instability attenuated by transcription factor IIS. SCIENCE ADVANCES 2024;10:eadm8196. [PMID: 38787953 PMCID: PMC11122683 DOI: 10.1126/sciadv.adm8196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
47
Puzzo F, Crossley MP, Goswami A, Zhang F, Pekrun K, Garzon JL, Cimprich KA, Kay MA. AAV-mediated genome editing is influenced by the formation of R-loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592855. [PMID: 38766176 PMCID: PMC11100726 DOI: 10.1101/2024.05.07.592855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
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Galli S, Flint G, Růžičková L, Di Antonio M. Genome-wide mapping of G-quadruplex DNA: a step-by-step guide to select the most effective method. RSC Chem Biol 2024;5:426-438. [PMID: 38725910 PMCID: PMC11078208 DOI: 10.1039/d4cb00023d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/21/2024] [Indexed: 05/12/2024]  Open
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Mérida-Cerro JA, Maraver-Cárdenas P, Rondón AG, Aguilera A. Rat1 promotes premature transcription termination at R-loops. Nucleic Acids Res 2024;52:3623-3635. [PMID: 38281203 DOI: 10.1093/nar/gkae033] [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: 06/05/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/30/2024]  Open
50
Mukhopadhyay P, Miller H, Stoja A, Bishop AJR. Approaches for Mapping and Analysis of R-loops. Curr Protoc 2024;4:e1037. [PMID: 38666626 PMCID: PMC11840513 DOI: 10.1002/cpz1.1037] [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] [Indexed: 05/04/2024]
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