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For: Corless S, Gilbert N. Investigating DNA supercoiling in eukaryotic genomes. Brief Funct Genomics 2018;16:379-389. [PMID: 28444308 PMCID: PMC5598747 DOI: 10.1093/bfgp/elx007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
Number Cited by Other Article(s)
1
Ghilain C, Vidal-Cruchez O, Joly A, Debatisse M, Gilson E, Giraud-Panis MJ. Innovative Tools for DNA Topology Probing in Human Cells Reveal a Build-Up of Positive Supercoils Following Replication Stress at Telomeres and at the FRA3B Fragile Site. Cells 2024;13:1361. [PMID: 39195250 DOI: 10.3390/cells13161361] [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: 07/24/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]  Open
2
Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024;87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [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: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
3
Lehner AF. Reactions of deoxyribonucleotide bases with sulfooxymethyl or halomethyl polycyclic aromatic hydrocarbons induce unwinding of DNA supercoils. Toxicol Mech Methods 2024;34:423-443. [PMID: 38133498 DOI: 10.1080/15376516.2023.2297836] [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: 10/31/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
4
Janissen R, Barth R, Polinder M, van der Torre J, Dekker C. Single-molecule visualization of twin-supercoiled domains generated during transcription. Nucleic Acids Res 2024;52:1677-1687. [PMID: 38084930 PMCID: PMC10899792 DOI: 10.1093/nar/gkad1181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 02/29/2024]  Open
5
Fu Z, Guo MS, Zhou W, Xiao J. Differential roles of positive and negative supercoiling in organizing the E. coli genome. Nucleic Acids Res 2024;52:724-737. [PMID: 38050973 PMCID: PMC10810199 DOI: 10.1093/nar/gkad1139] [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: 09/11/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]  Open
6
D'Alessio Y, D'Alfonso A, Camilloni G. Chromatin conformations of HSP12 during transcriptional activation in the Saccharomyces cerevisiae stationary phase. Adv Biol Regul 2023;90:100986. [PMID: 37741159 DOI: 10.1016/j.jbior.2023.100986] [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: 07/20/2023] [Revised: 08/17/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
7
Junier I, Ghobadpour E, Espeli O, Everaers R. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling. Front Microbiol 2023;14:1192831. [PMID: 37965550 PMCID: PMC10642903 DOI: 10.3389/fmicb.2023.1192831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023]  Open
8
Starr CH, Bryant Z, Spakowitz AJ. Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics. Biophys J 2022;121:1949-1962. [PMID: 35421389 PMCID: PMC9199097 DOI: 10.1016/j.bpj.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/19/2021] [Accepted: 04/06/2022] [Indexed: 11/02/2022]  Open
9
Namiecińska E, Grazul M, Sadowska B, Więckowska-Szakiel M, Hikisz P, Pasternak B, Budzisz E. Arene-Ruthenium(II) Complexes with Carbothiamidopyrazoles as a Potential Alternative for Antibiotic Resistance in Human. Molecules 2022;27:468. [PMID: 35056783 PMCID: PMC8781304 DOI: 10.3390/molecules27020468] [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: 12/11/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 11/25/2022]  Open
10
Rezaei-Lotfi S, Vujovic F, Simonian M, Hunter N, Farahani RM. Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes. Genome Biol 2021;22:334. [PMID: 34886891 PMCID: PMC8656028 DOI: 10.1186/s13059-021-02555-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/22/2021] [Indexed: 12/31/2022]  Open
11
Vujovic F, Rezaei-Lotfi S, Hunter N, Farahani RM. The fate of notch-1 transcript is linked to cell cycle dynamics by activity of a natural antisense transcript. Nucleic Acids Res 2021;49:10419-10430. [PMID: 34520549 PMCID: PMC8501981 DOI: 10.1093/nar/gkab800] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/08/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022]  Open
12
Fogg JM, Judge AK, Stricker E, Chan HL, Zechiedrich L. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 2021;12:5683. [PMID: 34584096 PMCID: PMC8478907 DOI: 10.1038/s41467-021-25936-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]  Open
13
Shelar SB, Dey A, Gawali SL, Dhinakaran S, Barick KC, Basu M, Uppal S, Hassan PA. Spontaneous Formation of Cationic Vesicles in Aqueous DDAB-Lecithin Mixtures for Efficient Plasmid DNA Complexation and Gene Transfection. ACS APPLIED BIO MATERIALS 2021;4:6005-6015. [DOI: 10.1021/acsabm.1c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
14
Desai RV, Chen X, Martin B, Chaturvedi S, Hwang DW, Li W, Yu C, Ding S, Thomson M, Singer RH, Coleman RA, Hansen MMK, Weinberger LS. A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions. Science 2021;373:science.abc6506. [PMID: 34301855 DOI: 10.1126/science.abc6506] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/08/2021] [Indexed: 12/13/2022]
15
Guo MS, Kawamura R, Littlehale ML, Marko JF, Laub MT. High-resolution, genome-wide mapping of positive supercoiling in chromosomes. eLife 2021;10:e67236. [PMID: 34279217 PMCID: PMC8360656 DOI: 10.7554/elife.67236] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022]  Open
16
Patel YD, Brown AJ, Zhu J, Rosignoli G, Gibson SJ, Hatton D, James DC. Control of Multigene Expression Stoichiometry in Mammalian Cells Using Synthetic Promoters. ACS Synth Biol 2021;10:1155-1165. [PMID: 33939428 PMCID: PMC8296667 DOI: 10.1021/acssynbio.0c00643] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 01/22/2023]
17
Birnie A, Dekker C. Genome-in-a-Box: Building a Chromosome from the Bottom Up. ACS NANO 2021;15:111-124. [PMID: 33347266 PMCID: PMC7844827 DOI: 10.1021/acsnano.0c07397] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
18
Zhang Y, Zhang X, Zhang W, Zhang W. Effects of Psoralen on Histone-DNA Interactions Studied by Using Atomic Force Microscopy. Macromol Rapid Commun 2020;41:e2000017. [PMID: 32686170 DOI: 10.1002/marc.202000017] [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: 01/07/2020] [Revised: 06/26/2020] [Indexed: 11/09/2022]
19
Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication. Int J Mol Sci 2020;21:ijms21124504. [PMID: 32599919 PMCID: PMC7349988 DOI: 10.3390/ijms21124504] [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: 06/06/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022]  Open
20
Ivanov IE, Wright AV, Cofsky JC, Aris KDP, Doudna JA, Bryant Z. Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling. Proc Natl Acad Sci U S A 2020;117:5853-5860. [PMID: 32123105 PMCID: PMC7084090 DOI: 10.1073/pnas.1913445117] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
21
Klindziuk A, Meadowcroft B, Kolomeisky AB. A Mechanochemical Model of Transcriptional Bursting. Biophys J 2020;118:1213-1220. [PMID: 32049059 DOI: 10.1016/j.bpj.2020.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]  Open
22
Kaczmarczyk A, Meng H, Ordu O, Noort JV, Dekker NH. Chromatin fibers stabilize nucleosomes under torsional stress. Nat Commun 2020;11:126. [PMID: 31913285 PMCID: PMC6949304 DOI: 10.1038/s41467-019-13891-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/25/2019] [Indexed: 01/11/2023]  Open
23
Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint. PLoS One 2019;14:e0224936. [PMID: 31747397 PMCID: PMC6867626 DOI: 10.1371/journal.pone.0224936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/30/2019] [Indexed: 12/22/2022]  Open
24
Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology. PLANTS 2019;8:plants8080270. [PMID: 31390788 PMCID: PMC6724115 DOI: 10.3390/plants8080270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/29/2019] [Accepted: 08/04/2019] [Indexed: 12/19/2022]
25
Scott S, Xu ZM, Kouzine F, Berard DJ, Shaheen C, Gravel B, Saunders L, Hofkirchner A, Leroux C, Laurin J, Levens D, Benham CJ, Leslie SR. Visualizing structure-mediated interactions in supercoiled DNA molecules. Nucleic Acids Res 2019;46:4622-4631. [PMID: 29684182 PMCID: PMC5961182 DOI: 10.1093/nar/gky266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/03/2018] [Indexed: 01/23/2023]  Open
26
Machine Learning Models Combined with Virtual Screening and Molecular Docking to Predict Human Topoisomerase I Inhibitors. Molecules 2019;24:molecules24112107. [PMID: 31167344 PMCID: PMC6601036 DOI: 10.3390/molecules24112107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/20/2019] [Accepted: 05/28/2019] [Indexed: 12/15/2022]  Open
27
Bizard AH, Allemand JF, Hassenkam T, Paramasivam M, Sarlós K, Singh MI, Hickson ID. PICH and TOP3A cooperate to induce positive DNA supercoiling. Nat Struct Mol Biol 2019;26:267-274. [PMID: 30936532 DOI: 10.1038/s41594-019-0201-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
28
Cinelli MA. Topoisomerase 1B poisons: Over a half-century of drug leads, clinical candidates, and serendipitous discoveries. Med Res Rev 2018;39:1294-1337. [PMID: 30456874 DOI: 10.1002/med.21546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022]
29
Ghoshdastidar D, Bansal M. Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies. Brief Funct Genomics 2018;18:192-204. [DOI: 10.1093/bfgp/ely026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/23/2018] [Accepted: 07/09/2018] [Indexed: 12/23/2022]  Open
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