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For: Owen JA, Osmanović D, Mirny L. Design principles of 3D epigenetic memory systems. Science 2023;382:eadg3053. [PMID: 37972190 PMCID: PMC11075759 DOI: 10.1126/science.adg3053] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Number Cited by Other Article(s)
1
Ziogas A, Novakovic B, Ventriglia L, Galang N, Tran KA, Li W, Matzaraki V, van Unen N, Schlüter T, Ferreira AV, Moorlag SJCFM, Koeken VACM, Moyo M, Li X, Baltissen MPA, Martens JHA, Li Y, Divangahi M, Joosten LAB, Mhlanga MM, Netea MG. Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory. Cell 2025;188:2992-3012.e16. [PMID: 40318634 DOI: 10.1016/j.cell.2025.03.048] [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: 04/26/2024] [Revised: 01/08/2025] [Accepted: 03/31/2025] [Indexed: 05/07/2025]
2
Playter C, Golloshi R, Garretson JH, Rodriguez Gonzalez A, Olajide TH, Saad A, Benson SJ, McCord RP. Deciphering pre-existing and induced 3D genome architecture changes involved in constricted melanoma migration. iScience 2025;28:112346. [PMID: 40292313 PMCID: PMC12032941 DOI: 10.1016/j.isci.2025.112346] [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: 08/22/2024] [Revised: 01/22/2025] [Accepted: 03/31/2025] [Indexed: 04/30/2025]  Open
3
Pellon A, Palacios A, Abecia L, Rodríguez H, Anguita J. Friends to remember: innate immune memory regulation by the microbiota. Trends Microbiol 2025;33:510-520. [PMID: 39794207 DOI: 10.1016/j.tim.2024.12.002] [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: 10/18/2024] [Revised: 11/28/2024] [Accepted: 12/11/2024] [Indexed: 01/13/2025]
4
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
5
Paldi F, Cavalli G. 3D genome folding in epigenetic regulation and cellular memory. Trends Cell Biol 2025:S0962-8924(25)00065-0. [PMID: 40221344 DOI: 10.1016/j.tcb.2025.03.001] [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: 01/07/2025] [Revised: 03/07/2025] [Accepted: 03/11/2025] [Indexed: 04/14/2025]
6
Mikulski P, Tehrani SSH, Kogan A, Abdul-Zani I, Shell E, James L, Ryan BJ, Jansen LET. Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signaling. Nat Struct Mol Biol 2025:10.1038/s41594-025-01522-8. [PMID: 40186025 DOI: 10.1038/s41594-025-01522-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/20/2025] [Indexed: 04/07/2025]
7
Smaruj PN, Xiao Y, Fudenberg G. Recipes and ingredients for deep learning models of 3D genome folding. Curr Opin Genet Dev 2025;91:102308. [PMID: 39862604 PMCID: PMC11867851 DOI: 10.1016/j.gde.2024.102308] [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: 09/12/2024] [Revised: 12/19/2024] [Accepted: 12/31/2024] [Indexed: 01/27/2025]
8
Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2025;292:1833-1852. [PMID: 38944686 DOI: 10.1111/febs.17211] [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: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
9
Stepanova D, Brunet Guasch M, Byrne HM, Alarcón T. Understanding How Chromatin Folding and Enzyme Competition Affect Rugged Epigenetic Landscapes. Bull Math Biol 2025;87:59. [PMID: 40153141 DOI: 10.1007/s11538-025-01434-0] [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: 09/20/2024] [Accepted: 03/03/2025] [Indexed: 03/30/2025]
10
Falk MJ, Strupp AT, Scellier B, Murugan A. Temporal Contrastive Learning through implicit non-equilibrium memory. Nat Commun 2025;16:2163. [PMID: 40038254 PMCID: PMC11880436 DOI: 10.1038/s41467-025-57043-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: 02/01/2024] [Accepted: 02/10/2025] [Indexed: 03/06/2025]  Open
11
Lin H, Wang D, Wang Q, Mao J, Yang L, Bai Y, Qu J. Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics. Mol Syst Biol 2025;21:294-314. [PMID: 39820016 PMCID: PMC11876630 DOI: 10.1038/s44320-025-00087-4] [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: 07/30/2024] [Revised: 12/29/2024] [Accepted: 01/07/2025] [Indexed: 01/19/2025]  Open
12
Mimura I, Chen Z, Natarajan R. Epigenetic alterations and memory: key players in the development/progression of chronic kidney disease promoted by acute kidney injury and diabetes. Kidney Int 2025;107:434-456. [PMID: 39725223 DOI: 10.1016/j.kint.2024.10.031] [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: 02/25/2024] [Revised: 09/20/2024] [Accepted: 10/08/2024] [Indexed: 12/28/2024]
13
Kollenstart L, Biran A, Alcaraz N, Reverón-Gómez N, Solis-Mezarino V, Völker-Albert M, Jenkinson F, Flury V, Groth A. Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability. SCIENCE ADVANCES 2025;11:eadr1453. [PMID: 39970210 PMCID: PMC11837984 DOI: 10.1126/sciadv.adr1453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 01/15/2025] [Indexed: 02/21/2025]
14
Tsukamoto S, Mofrad MRK. Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function. J Chem Phys 2025;162:054122. [PMID: 39918128 DOI: 10.1063/5.0232328] [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: 08/06/2024] [Accepted: 11/18/2024] [Indexed: 05/08/2025]  Open
15
Bell CC, Faulkner GJ, Gilan O. Chromatin-based memory as a self-stabilizing influence on cell identity. Genome Biol 2024;25:320. [PMID: 39736786 DOI: 10.1186/s13059-024-03461-x] [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: 07/24/2024] [Accepted: 12/16/2024] [Indexed: 01/01/2025]  Open
16
Pease NA, Denecke KM, Chen L, Gerges PH, Kueh HY. A timed epigenetic switch balances T and ILC lineage proportions in the thymus. Development 2024;151:dev203016. [PMID: 39655434 PMCID: PMC11664168 DOI: 10.1242/dev.203016] [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: 05/04/2024] [Accepted: 11/04/2024] [Indexed: 01/11/2025]
17
Song A, Wang Y, Liu C, Yu J, Zhang Z, Lan L, Lin H, Zhao J, Li G. Replication-coupled inheritance of chromatin states. CELL INSIGHT 2024;3:100195. [PMID: 39391004 PMCID: PMC11462216 DOI: 10.1016/j.cellin.2024.100195] [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: 05/05/2024] [Revised: 08/05/2024] [Accepted: 08/05/2024] [Indexed: 10/12/2024]
18
Movilla Miangolarra A, Howard M. Theory of epigenetic switching due to stochastic histone mark loss during DNA replication. Phys Biol 2024;22:016005. [PMID: 39556945 PMCID: PMC11605279 DOI: 10.1088/1478-3975/ad942c] [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: 09/02/2024] [Revised: 11/12/2024] [Accepted: 11/18/2024] [Indexed: 11/20/2024]
19
Dekker J, Mirny LA. The chromosome folding problem and how cells solve it. Cell 2024;187:6424-6450. [PMID: 39547207 PMCID: PMC11569382 DOI: 10.1016/j.cell.2024.10.026] [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: 08/11/2024] [Revised: 10/15/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
20
Li H, Playter C, Das P, McCord RP. Chromosome compartmentalization: causes, changes, consequences, and conundrums. Trends Cell Biol 2024;34:707-727. [PMID: 38395734 PMCID: PMC11339242 DOI: 10.1016/j.tcb.2024.01.009] [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: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
21
Chen Z, Malek V, Natarajan R. Update: the role of epigenetics in the metabolic memory of diabetic complications. Am J Physiol Renal Physiol 2024;327:F327-F339. [PMID: 38961840 PMCID: PMC11460341 DOI: 10.1152/ajprenal.00115.2024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]  Open
22
Playter C, Golloshi R, Garretson JH, Gonzalez AR, Olajide TH, Saad A, Benson SJ, McCord RP. Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609017. [PMID: 39229109 PMCID: PMC11370405 DOI: 10.1101/2024.08.21.609017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
23
Stephens RK, Miroshnikova YA. Nuclear periphery and its mechanical regulation in cell fate transitions. Curr Opin Struct Biol 2024;87:102867. [PMID: 38889500 DOI: 10.1016/j.sbi.2024.102867] [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: 12/29/2023] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
24
Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS, Ragunathan K. Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1. Nat Commun 2024;15:6276. [PMID: 39054315 PMCID: PMC11272775 DOI: 10.1038/s41467-024-50538-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: 11/28/2023] [Accepted: 07/10/2024] [Indexed: 07/27/2024]  Open
25
Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024;187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [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: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
26
Manivannan V, Inamdar MM, Padinhateeri R. Role of diffusion and reaction of the constituents in spreading of histone modification marks. PLoS Comput Biol 2024;20:e1012235. [PMID: 38991050 PMCID: PMC11265668 DOI: 10.1371/journal.pcbi.1012235] [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: 12/29/2023] [Revised: 07/23/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024]  Open
27
Akilli N, Cheutin T, Cavalli G. Phase separation and inheritance of repressive chromatin domains. Curr Opin Genet Dev 2024;86:102201. [PMID: 38701672 DOI: 10.1016/j.gde.2024.102201] [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: 12/08/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
28
Movilla Miangolarra A, Saxton DS, Yan Z, Rine J, Howard M. Two-way feedback between chromatin compaction and histone modification state explains Saccharomyces cerevisiae heterochromatin bistability. Proc Natl Acad Sci U S A 2024;121:e2403316121. [PMID: 38593082 PMCID: PMC11032488 DOI: 10.1073/pnas.2403316121] [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: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 04/11/2024]  Open
29
Daniel B, Chen AY, Sandor K, Zhang W, Miao Z, Lareau CA, Yost KE, Chang HY, Satpathy AT. Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582872. [PMID: 38496446 PMCID: PMC10942375 DOI: 10.1101/2024.02.29.582872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
30
Murphy SE, Boettiger AN. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Nat Genet 2024;56:493-504. [PMID: 38361032 DOI: 10.1038/s41588-024-01661-6] [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: 01/06/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
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