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For: Shi G, Liu L, Hyeon C, Thirumalai D. Interphase human chromosome exhibits out of equilibrium glassy dynamics. Nat Commun 2018;9:3161. [PMID: 30089831 PMCID: PMC6082855 DOI: 10.1038/s41467-018-05606-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/05/2018] [Indexed: 01/01/2023]  Open
Number Cited by Other Article(s)
1
Vidi PA, Liu J, Bonin K, Bloom K. Closing the loops: chromatin loop dynamics after DNA damage. Nucleus 2025;16:2438633. [PMID: 39720924 DOI: 10.1080/19491034.2024.2438633] [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] [Revised: 11/29/2024] [Accepted: 11/30/2024] [Indexed: 12/26/2024]  Open
2
Vercellone F, Chiariello AM, Esposito A, Conte M, Abraham A, Fontana A, Di Pierno F, Tafuri F, Guha S, Kundu S, Di Carluccio C, Nicodemi M, Bianco S. A Multiscale Perspective on Chromatin Architecture through Polymer Physics. Physiology (Bethesda) 2025;40:0. [PMID: 39601793 DOI: 10.1152/physiol.00050.2024] [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: 10/18/2024] [Accepted: 11/08/2024] [Indexed: 11/29/2024]  Open
3
Vinayak V, Basir R, Golloshi R, Toth J, Sant'Anna L, Lakadamyali M, McCord RP, Shenoy VB. Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression. Nat Commun 2025;16:3816. [PMID: 40268925 PMCID: PMC12019571 DOI: 10.1038/s41467-025-59001-z] [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: 09/27/2024] [Accepted: 04/08/2025] [Indexed: 04/25/2025]  Open
4
Thirumalai D, Shi G, Shin S, Hyeon C. Organization and Dynamics of Chromosomes. Annu Rev Phys Chem 2025;76:565-588. [PMID: 39971382 DOI: 10.1146/annurev-physchem-082423-024123] [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: 02/21/2025]
5
Oliveira RJ, Oliveira Junior AB, Contessoto VG, Onuchic JN. The synergy between compartmentalization and motorization in chromatin architecture. J Chem Phys 2025;162:114116. [PMID: 40105139 DOI: 10.1063/5.0239634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 02/20/2025] [Indexed: 03/20/2025]  Open
6
Lee S, Liu X, Ziabkin I, Zidovska A. Image-based analysis of the genome's fractality during the cell cycle. Biophys J 2025:S0006-3495(25)00105-5. [PMID: 40007120 DOI: 10.1016/j.bpj.2025.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 02/13/2025] [Accepted: 02/14/2025] [Indexed: 02/27/2025]  Open
7
Fontana A, Tafuri F, Abraham A, Bianco S, Esposito A, Conte M, Vercellone F, Pierno FD, Guha S, Carluccio CD, Chiariello AM. Polymer models of chromatin organization in virally infected cells. Biochem Soc Trans 2025;53:BST20240598. [PMID: 39927819 DOI: 10.1042/bst20240598] [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: 01/28/2025] [Revised: 01/16/2025] [Accepted: 01/21/2025] [Indexed: 02/11/2025]
8
Brennan L, Kim HK, Colmenares S, Ego T, Ryu JK, Karpen G. HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.10.18.618981. [PMID: 39868136 PMCID: PMC11761810 DOI: 10.1101/2024.10.18.618981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
9
Sadeghi A, Hyeon C, Jung Y, Ha BY. Compaction and clustering of a heterogeneous polymer by biomolecular crowding. J Chem Phys 2024;161:184904. [PMID: 39530373 DOI: 10.1063/5.0226892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024]  Open
10
Chu FY, Clavijo AS, Lee S, Zidovska A. Transcription-dependent mobility of single genes and genome-wide motions in live human cells. Nat Commun 2024;15:8879. [PMID: 39438437 PMCID: PMC11496510 DOI: 10.1038/s41467-024-51149-4] [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: 04/22/2020] [Accepted: 07/31/2024] [Indexed: 10/25/2024]  Open
11
Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Di Pierno F, Dekker J, Nicodemi M. Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations. Int J Mol Sci 2024;25:10215. [PMID: 39337699 PMCID: PMC11432541 DOI: 10.3390/ijms251810215] [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: 07/14/2024] [Revised: 09/17/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024]  Open
12
Lao Z, Kamat KD, Jiang Z, Zhang B. OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 2024;13:RP93223. [PMID: 39146200 PMCID: PMC11326778 DOI: 10.7554/elife.93223] [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: 08/17/2024]  Open
13
Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M. Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603769. [PMID: 39071404 PMCID: PMC11275793 DOI: 10.1101/2024.07.16.603769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
14
Liu S, Athreya A, Lao Z, Zhang B. From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization. Annu Rev Biophys 2024;53:221-245. [PMID: 38346246 PMCID: PMC11369498 DOI: 10.1146/annurev-biophys-030822-032650] [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: 07/18/2024]
15
Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Cell type- and transcription-independent spatial proximity between enhancers and promoters. Mol Biol Cell 2024;35:ar96. [PMID: 38717453 PMCID: PMC11244156 DOI: 10.1091/mbc.e24-02-0082] [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: 02/23/2024] [Revised: 04/12/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024]  Open
16
Sahoo S, Kadam S, Padinhateeri R, Kumar PBS. Nonequilibrium switching of segmental states can influence compaction of chromatin. SOFT MATTER 2024;20:4621-4632. [PMID: 38819321 DOI: 10.1039/d4sm00274a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
17
Korabel N, Warmenhoven JW, Henthorn NT, Ingram S, Fedotov S, Heaven CJ, Kirkby KJ, Taylor MJ, Merchant MJ. Modelling Heterogeneous Anomalous Dynamics of Radiation-Induced Double-Strand Breaks in DNA during Non-Homologous End-Joining Pathway. ENTROPY (BASEL, SWITZERLAND) 2024;26:502. [PMID: 38920510 PMCID: PMC11202905 DOI: 10.3390/e26060502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024]
18
Kant A, Guo Z, Vinayak V, Neguembor MV, Li WS, Agrawal V, Pujadas E, Almassalha L, Backman V, Lakadamyali M, Cosma MP, Shenoy VB. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nat Commun 2024;15:4338. [PMID: 38773126 PMCID: PMC11109243 DOI: 10.1038/s41467-024-48698-z] [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: 04/24/2023] [Accepted: 05/06/2024] [Indexed: 05/23/2024]  Open
19
Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nat Commun 2024;15:4178. [PMID: 38755200 PMCID: PMC11099156 DOI: 10.1038/s41467-024-48562-0] [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: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024]  Open
20
Lao Z, Kamat K, Jiang Z, Zhang B. OpenNucleome for high resolution nuclear structural and dynamical modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562451. [PMID: 37905090 PMCID: PMC10614770 DOI: 10.1101/2023.10.16.562451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
21
Jeong D, Shi G, Li X, Thirumalai D. Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion. eLife 2024;12:RP88564. [PMID: 38502563 PMCID: PMC10950330 DOI: 10.7554/elife.88564] [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: 03/21/2024]  Open
22
Shin S, Shi G, Cho HW, Thirumalai D. Transcription-induced active forces suppress chromatin motion. Proc Natl Acad Sci U S A 2024;121:e2307309121. [PMID: 38489381 PMCID: PMC10963020 DOI: 10.1073/pnas.2307309121] [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: 05/02/2023] [Accepted: 02/06/2024] [Indexed: 03/17/2024]  Open
23
Wei J, Xue Y, Liu Y, Tian H, Shao Y, Gao YQ. Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins. J Chem Phys 2024;160:054904. [PMID: 38341710 DOI: 10.1063/5.0189692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024]  Open
24
Das R, Sakaue T, Shivashankar GV, Prost J, Hiraiwa T. Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics. PHYSICAL REVIEW LETTERS 2024;132:058401. [PMID: 38364140 DOI: 10.1103/physrevlett.132.058401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
25
Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet 2024;25:123-141. [PMID: 37673975 PMCID: PMC11127719 DOI: 10.1038/s41576-023-00638-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 09/08/2023]
26
Jung Y, Sadeghi A, Ha BY. Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS. Sci Rep 2024;14:139. [PMID: 38167921 PMCID: PMC10762067 DOI: 10.1038/s41598-023-50355-2] [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: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]  Open
27
Singh A, Chakrabarti S. Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture. PLoS Comput Biol 2023;19:e1011725. [PMID: 38109423 PMCID: PMC10760866 DOI: 10.1371/journal.pcbi.1011725] [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: 07/24/2023] [Revised: 01/02/2024] [Accepted: 12/01/2023] [Indexed: 12/20/2023]  Open
28
Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566470. [PMID: 38014222 PMCID: PMC10680651 DOI: 10.1101/2023.11.09.566470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
29
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]
30
Dutta S, Ghosh A, Boettiger AN, Spakowitz AJ. Leveraging polymer modeling to reconstruct chromatin connectivity from live images. Biophys J 2023;122:3532-3540. [PMID: 37542372 PMCID: PMC10502477 DOI: 10.1016/j.bpj.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/19/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]  Open
31
Liu S, Wang C, Latham AP, Ding X, Zhang B. OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates. PLoS Comput Biol 2023;19:e1011442. [PMID: 37695778 PMCID: PMC10513381 DOI: 10.1371/journal.pcbi.1011442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/21/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]  Open
32
Eshghi I, Zidovska A, Grosberg AY. Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023;46:69. [PMID: 37540478 DOI: 10.1140/epje/s10189-023-00327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
33
Chiariello AM, Abraham A, Bianco S, Esposito A, Vercellone F, Conte M, Fontana A, Nicodemi M. Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550709. [PMID: 37546924 PMCID: PMC10402158 DOI: 10.1101/2023.07.27.550709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
34
Eshghi I, Zidovska A, Grosberg AY. Activity-Driven Phase Transition Causes Coherent Flows of Chromatin. PHYSICAL REVIEW LETTERS 2023;131:048401. [PMID: 37566839 DOI: 10.1103/physrevlett.131.048401] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 08/13/2023]
35
Li Z, Portillo-Ledesma S, Schlick T. Brownian dynamics simulations of mesoscale chromatin fibers. Biophys J 2023;122:2884-2897. [PMID: 36116007 PMCID: PMC10397810 DOI: 10.1016/j.bpj.2022.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022]  Open
36
Kadam S, Kumari K, Manivannan V, Dutta S, Mitra MK, Padinhateeri R. Predicting scale-dependent chromatin polymer properties from systematic coarse-graining. Nat Commun 2023;14:4108. [PMID: 37433821 PMCID: PMC10336007 DOI: 10.1038/s41467-023-39907-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023]  Open
37
Tolokh IS, Kinney NA, Sharakhov IV, Onufriev AV. Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin. Epigenetics Chromatin 2023;16:21. [PMID: 37254161 PMCID: PMC10228000 DOI: 10.1186/s13072-023-00492-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/04/2023] [Indexed: 06/01/2023]  Open
38
Amin A, Kadam S, Mieczkowski J, Ahmed I, Bhat YA, Shah F, Tolstorukov MY, Kingston RE, Padinhateeri R, Wani AH. Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility. Life Sci Alliance 2023;6:e202201768. [PMID: 36849253 PMCID: PMC9973501 DOI: 10.26508/lsa.202201768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023]  Open
39
Dey A, Shi G, Takaki R, Thirumalai D. Structural changes in chromosomes driven by multiple condensin motors during mitosis. Cell Rep 2023;42:112348. [PMID: 37027299 DOI: 10.1016/j.celrep.2023.112348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/10/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023]  Open
40
Liu S, Wang C, Latham A, Ding X, Zhang B. OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537533. [PMID: 37131742 PMCID: PMC10153273 DOI: 10.1101/2023.04.19.537533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
41
Erdel F. Phase transitions in heterochromatin organization. Curr Opin Struct Biol 2023;80:102597. [PMID: 37087823 DOI: 10.1016/j.sbi.2023.102597] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
42
Kamat K, Lao Z, Qi Y, Wang Y, Ma J, Zhang B. Compartmentalization with nuclear landmarks yields random, yet precise, genome organization. Biophys J 2023;122:1376-1389. [PMID: 36871158 PMCID: PMC10111368 DOI: 10.1016/j.bpj.2023.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]  Open
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Abdulla AZ, Salari H, Tortora MMC, Vaillant C, Jost D. 4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling. Curr Opin Genet Dev 2023;79:102033. [PMID: 36893485 DOI: 10.1016/j.gde.2023.102033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023]
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Shi G, Thirumalai D. A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants. Nat Commun 2023;14:1150. [PMID: 36854665 PMCID: PMC9974990 DOI: 10.1038/s41467-023-36412-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023]  Open
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Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling. Int J Mol Sci 2023;24:ijms24043660. [PMID: 36835064 PMCID: PMC9967178 DOI: 10.3390/ijms24043660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]  Open
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Contessoto VG, Dudchenko O, Aiden EL, Wolynes PG, Onuchic JN, Di Pierro M. Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nat Commun 2023;14:326. [PMID: 36658127 PMCID: PMC9852290 DOI: 10.1038/s41467-023-35909-2] [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: 02/16/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023]  Open
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The spatial organization of transcriptional control. Nat Rev Genet 2023;24:53-68. [PMID: 36104547 DOI: 10.1038/s41576-022-00526-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2022] [Indexed: 12/27/2022]
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Finn EH, Misteli T. Nuclear position modulates long-range chromatin interactions. PLoS Genet 2022;18:e1010451. [PMID: 36206323 PMCID: PMC9581366 DOI: 10.1371/journal.pgen.1010451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/19/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022]  Open
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Jiang Z, Qi Y, Kamat K, Zhang B. Phase Separation and Correlated Motions in Motorized Genome. J Phys Chem B 2022;126:5619-5628. [PMID: 35858189 PMCID: PMC9899348 DOI: 10.1021/acs.jpcb.2c03238] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Locatelli M, Lawrimore J, Lin H, Sanaullah S, Seitz C, Segall D, Kefer P, Salvador Moreno N, Lietz B, Anderson R, Holmes J, Yuan C, Holzwarth G, Bloom KS, Liu J, Bonin K, Vidi PA. DNA damage reduces heterogeneity and coherence of chromatin motions. Proc Natl Acad Sci U S A 2022;119:e2205166119. [PMID: 35858349 PMCID: PMC9304018 DOI: 10.1073/pnas.2205166119] [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: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 01/14/2023]  Open
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