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For: Normanno D, Boudarène L, Dugast-Darzacq C, Chen J, Richter C, Proux F, Bénichou O, Voituriez R, Darzacq X, Dahan M. Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher. Nat Commun 2015;6:7357. [PMID: 26151127 PMCID: PMC4507003 DOI: 10.1038/ncomms8357] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/30/2015] [Indexed: 12/17/2022]  Open
Number Cited by Other Article(s)
1
Cui JH, Kwan JZJ, Faghihi A, Nguyen TF, Teves SS. Functional divergence of TBP homologs through distinct DNA-binding dynamics. Nucleic Acids Res 2025;53:gkaf436. [PMID: 40396489 PMCID: PMC12093143 DOI: 10.1093/nar/gkaf436] [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: 11/08/2024] [Revised: 04/02/2025] [Accepted: 05/12/2025] [Indexed: 05/22/2025]  Open
2
Muñoz V, Goluguri RR, Ghosh C, Tanielian B, Sadqi M. Mechanisms for DNA Interplay in Eukaryotic Transcription Factors. Annu Rev Biophys 2025;54:121-139. [PMID: 39879549 DOI: 10.1146/annurev-biophys-071524-111008] [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: 01/31/2025]
3
Mao X, Rao G, Li G, Chen S. Insights into Extrachromosomal DNA in Cancer: Biogenesis, Methodologies, Functions, and Therapeutic Potential. Adv Biol (Weinh) 2025;9:e2400433. [PMID: 39945006 DOI: 10.1002/adbi.202400433] [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: 07/25/2024] [Revised: 02/01/2025] [Indexed: 03/17/2025]
4
Sang M, Johnson ME. Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.18.638941. [PMID: 40027831 PMCID: PMC11870488 DOI: 10.1101/2025.02.18.638941] [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: 03/05/2025]
5
Stortz M, Oses C, Lafuente AL, Presman DM, Levi V. Catching the glucocorticoid receptor in the act: Lessons from fluorescence fluctuation methods. Biochem Biophys Res Commun 2025;748:151327. [PMID: 39823895 DOI: 10.1016/j.bbrc.2025.151327] [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: 10/25/2024] [Revised: 01/10/2025] [Accepted: 01/12/2025] [Indexed: 01/20/2025]
6
Huynh D, Hoffmeister P, Friedrich T, Zhang K, Bartkuhn M, Ferrante F, Giaimo BD, Kovall RA, Borggrefe T, Oswald F, Gebhardt JCM. Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding. Nat Commun 2025;16:1259. [PMID: 39893191 PMCID: PMC11787368 DOI: 10.1038/s41467-025-56515-4] [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: 07/05/2024] [Accepted: 01/21/2025] [Indexed: 02/04/2025]  Open
7
Wagh K, Stavreva DA, Hager GL. Transcription dynamics and genome organization in the mammalian nucleus: Recent advances. Mol Cell 2025;85:208-224. [PMID: 39413793 PMCID: PMC11741928 DOI: 10.1016/j.molcel.2024.09.022] [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: 05/17/2024] [Revised: 07/31/2024] [Accepted: 09/19/2024] [Indexed: 10/18/2024]
8
Antani JD, Ward T, Emonet T, Turner PE. Microscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells. Proc Natl Acad Sci U S A 2024;121:e2410905121. [PMID: 39700139 DOI: 10.1073/pnas.2410905121] [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: 06/01/2024] [Accepted: 11/12/2024] [Indexed: 12/21/2024]  Open
9
Antani JD, Ward T, Emonet T, Turner PE. Microscopic Phage Adsorption Assay: High-throughput quantification of virus particle attachment to host bacterial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.09.617072. [PMID: 39416219 PMCID: PMC11482966 DOI: 10.1101/2024.10.09.617072] [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: 10/19/2024]
10
Garate X, Gómez-García PA, Merino MF, Angles MC, Zhu C, Castells-García A, Ed-Daoui I, Martin L, Ochiai H, Neguembor MV, Cosma MP. The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition. Nucleic Acids Res 2024;52:8146-8164. [PMID: 38850157 DOI: 10.1093/nar/gkae476] [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: 04/03/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024]  Open
11
Thonnekottu D, Chatterjee D. Probing the modulation in facilitated diffusion guided by DNA-protein interactions in target search processes. Phys Chem Chem Phys 2024. [PMID: 38922594 DOI: 10.1039/d4cp01580k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
12
Hao S, Lee YJ, Benhamou Goldfajn N, Flores E, Liang J, Fuehrer H, Demmerle J, Lippincott-Schwartz J, Liu Z, Sukenik S, Cai D. YAP condensates are highly organized hubs. iScience 2024;27:109927. [PMID: 38784009 PMCID: PMC11111833 DOI: 10.1016/j.isci.2024.109927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 10/24/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024]  Open
13
Liu Z, Gillis TG, Raman S, Cui Q. A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery. eLife 2024;12:RP92262. [PMID: 38836839 PMCID: PMC11152574 DOI: 10.7554/elife.92262] [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: 06/06/2024]  Open
14
Scherer NM, Maurel C, Graus M, McAlary L, Richter G, Radford RW, Hogan A, Don E, Lee A, Yerbury J, Francois M, Chung R, Morsch M. RNA-binding properties orchestrate TDP-43 homeostasis through condensate formation in vivo. Nucleic Acids Res 2024;52:5301-5319. [PMID: 38381071 PMCID: PMC11109982 DOI: 10.1093/nar/gkae112] [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: 06/23/2023] [Revised: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]  Open
15
Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024;25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
16
Emanuelson C, Bardhan A, Deiters A. DNA Logic Gates for Small Molecule Activation Circuits in Cells. ACS Synth Biol 2024;13:538-545. [PMID: 38306634 PMCID: PMC10877608 DOI: 10.1021/acssynbio.3c00474] [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: 08/02/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/04/2024]
17
Liu Z, Gillis T, Raman S, Cui Q. A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.06.552196. [PMID: 37662419 PMCID: PMC10473640 DOI: 10.1101/2023.08.06.552196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
18
Salomone J, Farrow E, Gebelein B. Homeodomain complex formation and biomolecular condensates in Hox gene regulation. Semin Cell Dev Biol 2024;152-153:93-100. [PMID: 36517343 PMCID: PMC10258226 DOI: 10.1016/j.semcdb.2022.11.016] [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: 07/30/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
19
Wan Y, Mu Q, Krzysztoń R, Cohen J, Coraci D, Helenek C, Tompkins C, Lin A, Farquhar K, Cross E, Wang J, Balázsi G. Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance. Proc Natl Acad Sci U S A 2023;120:e2303114120. [PMID: 38019857 DOI: 10.1073/pnas.2303114120] [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: 02/22/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023]  Open
20
Tang Q, Sensale S, Bond C, Xing J, Qiao A, Hugelier S, Arab A, Arya G, Lakadamyali M. Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets. Curr Biol 2023;33:5169-5184.e8. [PMID: 37979580 PMCID: PMC10843832 DOI: 10.1016/j.cub.2023.10.068] [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: 01/06/2023] [Revised: 08/03/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023]
21
Waigh TA, Korabel N. Heterogeneous anomalous transport in cellular and molecular biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023;86:126601. [PMID: 37863075 DOI: 10.1088/1361-6633/ad058f] [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: 12/21/2022] [Accepted: 10/20/2023] [Indexed: 10/22/2023]
22
Wagh K, Stavreva DA, Upadhyaya A, Hager GL. Transcription Factor Dynamics: One Molecule at a Time. Annu Rev Cell Dev Biol 2023;39:277-305. [PMID: 37540844 DOI: 10.1146/annurev-cellbio-022823-013847] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
23
Mazzocca M, Loffreda A, Colombo E, Fillot T, Gnani D, Falletta P, Monteleone E, Capozi S, Bertrand E, Legube G, Lavagnino Z, Tacchetti C, Mazza D. Chromatin organization drives the search mechanism of nuclear factors. Nat Commun 2023;14:6433. [PMID: 37833263 PMCID: PMC10575952 DOI: 10.1038/s41467-023-42133-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023]  Open
24
Chen L, Zhang Z, Han Q, Maity BK, Rodrigues L, Zboril E, Adhikari R, Ko SH, Li X, Yoshida SR, Xue P, Smith E, Xu K, Wang Q, Huang THM, Chong S, Liu Z. Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions. Mol Cell 2023;83:3438-3456.e12. [PMID: 37738977 PMCID: PMC10592010 DOI: 10.1016/j.molcel.2023.08.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/11/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023]
25
Manrubia S, Cuesta JA. Physics of diffusion in viral genome evolution. Proc Natl Acad Sci U S A 2023;120:e2310999120. [PMID: 37556488 PMCID: PMC10450443 DOI: 10.1073/pnas.2310999120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]  Open
26
Price RM, Budzyński MA, Shen J, Mitchell JE, Kwan JJ, Teves S. Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes. Nucleic Acids Res 2023;51:5040-5055. [PMID: 37114996 PMCID: PMC10250243 DOI: 10.1093/nar/gkad304] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023]  Open
27
Dahal L, Walther N, Tjian R, Darzacq X, Graham TG. Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023;51:557-569. [PMID: 36876879 PMCID: PMC10212543 DOI: 10.1042/bst20221242] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
28
He Y, Zhang Q, Wang S, Chen Z, Cui Z, Guo ZH, Huang DS. Predicting the Sequence Specificities of DNA-Binding Proteins by DNA Fine-Tuned Language Model With Decaying Learning Rates. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:616-624. [PMID: 35389869 DOI: 10.1109/tcbb.2022.3165592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
29
Ball DA, Jalloh B, Karpova TS. Impact of Saccharomyces cerevisiae on the Field of Single-Molecule Biophysics. Int J Mol Sci 2022;23:15895. [PMID: 36555532 PMCID: PMC9781480 DOI: 10.3390/ijms232415895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]  Open
30
Punia B, Chaudhury S. Theoretical insights into the full description of DNA target search by subdiffusing proteins. Phys Chem Chem Phys 2022;24:29074-29083. [PMID: 36440504 DOI: 10.1039/d2cp04934a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
31
Heckert A, Dahal L, Tjian R, Darzacq X. Recovering mixtures of fast-diffusing states from short single-particle trajectories. eLife 2022;11:e70169. [PMID: 36066004 PMCID: PMC9451534 DOI: 10.7554/elife.70169] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/04/2022] [Indexed: 12/15/2022]  Open
32
Stochastic particle unbinding modulates growth dynamics and size of transcription factor condensates in living cells. Proc Natl Acad Sci U S A 2022;119:e2200667119. [PMID: 35881789 PMCID: PMC9351496 DOI: 10.1073/pnas.2200667119] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
33
Mehra D, Adhikari S, Banerjee C, Puchner EM. Characterizing locus specific chromatin structure and dynamics with correlative conventional and super-resolution imaging in living cells. Nucleic Acids Res 2022;50:e78. [PMID: 35524554 PMCID: PMC9303368 DOI: 10.1093/nar/gkac314] [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: 03/31/2021] [Revised: 04/08/2022] [Accepted: 05/02/2022] [Indexed: 11/23/2022]  Open
34
Loell K, Wu Y, Staller MV, Cohen B. Activation domains can decouple the mean and noise of gene expression. Cell Rep 2022;40:111118. [PMID: 35858548 PMCID: PMC9912357 DOI: 10.1016/j.celrep.2022.111118] [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: 09/08/2021] [Revised: 01/18/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022]  Open
35
Solano A, Lou J, Scipioni L, Gratton E, Hinde E. Radial pair correlation of molecular brightness fluctuations maps protein diffusion as a function of oligomeric state within live-cell nuclear architecture. Biophys J 2022;121:2152-2167. [PMID: 35490296 PMCID: PMC9247470 DOI: 10.1016/j.bpj.2022.04.030] [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: 06/08/2021] [Revised: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022]  Open
36
Nollmann M, Bennabi I, Götz M, Gregor T. The Impact of Space and Time on the Functional Output of the Genome. Cold Spring Harb Perspect Biol 2022;14:a040378. [PMID: 34230036 PMCID: PMC8733053 DOI: 10.1101/cshperspect.a040378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
37
Kenworthy CA, Haque N, Liou SH, Chandris P, Wong V, Dziuba P, Lavis LD, Liu WL, Singer RH, Coleman RA. Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. Biophys J 2022;121:1738-1752. [PMID: 35364106 PMCID: PMC9117891 DOI: 10.1016/j.bpj.2022.03.027] [Citation(s) in RCA: 3] [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: 07/23/2021] [Revised: 09/20/2021] [Accepted: 03/24/2022] [Indexed: 11/12/2022]  Open
38
de Jonge WJ, Patel HP, Meeussen JVW, Lenstra TL. Following the tracks: how transcription factor binding dynamics control transcription. Biophys J 2022;121:1583-1592. [PMID: 35337845 PMCID: PMC9117886 DOI: 10.1016/j.bpj.2022.03.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022]  Open
39
Irgen-Gioro S, Yoshida S, Walling V, Chong S. Fixation can change the appearance of phase separation in living cells. eLife 2022;11:79903. [PMID: 36444977 PMCID: PMC9817179 DOI: 10.7554/elife.79903] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022]  Open
40
Nozaki T, Chang F, Weiner B, Kleckner N. High Temporal Resolution 3D Live-Cell Imaging of Budding Yeast Meiosis Defines Discontinuous Actin/Telomere-Mediated Chromosome Motion, Correlated Nuclear Envelope Deformation and Actin Filament Dynamics. Front Cell Dev Biol 2021;9:687132. [PMID: 34900979 PMCID: PMC8656277 DOI: 10.3389/fcell.2021.687132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022]  Open
41
Wang Z, Deng W. Dynamic transcription regulation at the single-molecule level. Dev Biol 2021;482:67-81. [PMID: 34896367 DOI: 10.1016/j.ydbio.2021.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
42
Seebauer CT, Graus MS, Huang L, McCann AJ, Wylie-Sears J, Fontaine FR, Karnezis T, Zurakowski D, Staffa SJ, Meunier FA, Mulliken JB, Bischoff J, Francois M. Non-β-blocker enantiomers of propranolol and atenolol inhibit vasculogenesis in infantile hemangioma. J Clin Invest 2021;132:151109. [PMID: 34874911 PMCID: PMC8803322 DOI: 10.1172/jci151109] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/02/2021] [Indexed: 12/02/2022]  Open
43
Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 2021;600:731-736. [PMID: 34819668 PMCID: PMC9126690 DOI: 10.1038/s41586-021-04116-8] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
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Khamis H, Rudnizky S, Melamed P, Kaplan A. Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation. Nucleic Acids Res 2021;49:10975-10987. [PMID: 34606618 PMCID: PMC8565314 DOI: 10.1093/nar/gkab843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/04/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022]  Open
45
Wiegard A, Kuzin V, Cameron DP, Grosser J, Ceribelli M, Mehmood R, Ballarino R, Valant F, Grochowski R, Karabogdan I, Crosetto N, Lindqvist A, Bizard AH, Kouzine F, Natsume T, Baranello L. Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1. Mol Cell 2021;81:5007-5024.e9. [PMID: 34767771 DOI: 10.1016/j.molcel.2021.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/26/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
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Lu F, Lionnet T. Transcription Factor Dynamics. Cold Spring Harb Perspect Biol 2021;13:a040949. [PMID: 34001530 PMCID: PMC8559544 DOI: 10.1101/cshperspect.a040949] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
47
Pan L, Hoffmeister P, Turkiewicz A, Huynh NND, Große-Berkenbusch A, Knippschild U, Gebhardt JCM, Baumann B, Borggrefe T, Oswald F. Transcription Factor RBPJL Is Able to Repress Notch Target Gene Expression but Is Non-Responsive to Notch Activation. Cancers (Basel) 2021;13:cancers13195027. [PMID: 34638511 PMCID: PMC8508133 DOI: 10.3390/cancers13195027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/01/2022]  Open
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Zentout S, Smith R, Jacquier M, Huet S. New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells. Front Cell Dev Biol 2021;9:730998. [PMID: 34589495 PMCID: PMC8473836 DOI: 10.3389/fcell.2021.730998] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023]  Open
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Mazzocca M, Colombo E, Callegari A, Mazza D. Transcription factor binding kinetics and transcriptional bursting: What do we really know? Curr Opin Struct Biol 2021;71:239-248. [PMID: 34481381 DOI: 10.1016/j.sbi.2021.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022]
50
Garcia DA, Fettweis G, Presman DM, Paakinaho V, Jarzynski C, Upadhyaya A, Hager GL. Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model. Nucleic Acids Res 2021;49:6605-6620. [PMID: 33592625 DOI: 10.1093/nar/gkab072] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]  Open
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