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For: Yin X, Romero-Campero FJ, Yang M, Baile F, Cao Y, Shu J, Luo L, Wang D, Sun S, Yan P, Gong Z, Mo X, Qin G, Calonje M, Zhou Y. Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome. Plant Cell 2023;35:2484-2503. [PMID: 37070946 PMCID: PMC10291032 DOI: 10.1093/plcell/koad112] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Number Cited by Other Article(s)
1
Xue Y, Cao X, Chen X, Deng X, Deng XW, Ding Y, Dong A, Duan CG, Fang X, Gong L, Gong Z, Gu X, He C, He H, He S, He XJ, He Y, He Y, Jia G, Jiang D, Jiang J, Lai J, Lang Z, Li C, Li Q, Li X, Liu B, Liu B, Luo X, Qi Y, Qian W, Ren G, Song Q, Song X, Tian Z, Wang JW, Wang Y, Wu L, Wu Z, Xia R, Xiao J, Xu L, Xu ZY, Yan W, Yang H, Zhai J, Zhang Y, Zhao Y, Zhong X, Zhou DX, Zhou M, Zhou Y, Zhu B, Zhu JK, Liu Q. Epigenetics in the modern era of crop improvements. SCIENCE CHINA. LIFE SCIENCES 2025;68:1570-1609. [PMID: 39808224 DOI: 10.1007/s11427-024-2784-3] [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: 08/23/2024] [Accepted: 11/15/2024] [Indexed: 01/16/2025]
2
Kurbidaeva A, Gupta S, Zaidem M, Castanera R, Sato Y, Joly‐Lopez Z, Casacuberta JM, Purugganan MD. Topologically associating domains and the evolution of three-dimensional genome architecture in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025;122:e70139. [PMID: 40384625 PMCID: PMC12086760 DOI: 10.1111/tpj.70139] [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] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 02/17/2025] [Accepted: 03/25/2025] [Indexed: 05/20/2025]
3
Liu Y, Xiao S, Yang M, Guo G, Zhou Y. The Impact of Polycomb Group Proteins on 3D Chromatin Structure and Environmental Stresses in Plants. PLANTS (BASEL, SWITZERLAND) 2025;14:1038. [PMID: 40219106 PMCID: PMC11990978 DOI: 10.3390/plants14071038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/19/2025] [Accepted: 03/25/2025] [Indexed: 04/14/2025]
4
Shu J, Xiao S, Wang D, Yang M, Zhou Y. Protocol for capturing genome-wide chromatin interactions in Arabidopsis. STAR Protoc 2025;6:103702. [PMID: 40096089 PMCID: PMC11957576 DOI: 10.1016/j.xpro.2025.103702] [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: 12/23/2024] [Revised: 02/18/2025] [Accepted: 02/25/2025] [Indexed: 03/19/2025]  Open
5
Song Z, Xia Q, Yang M, Yang T, Liu Y, Wang D, Shu J, Liu Z, Chi Y, Xu H, Xing D, Zhou Y. Dynamic changes in 3D chromatin structure during male gametogenesis in Arabidopsis thaliana. Genome Biol 2025;26:27. [PMID: 39930459 PMCID: PMC11808980 DOI: 10.1186/s13059-025-03496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 02/05/2025] [Indexed: 02/14/2025]  Open
6
Lee H, Seo PJ. Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants. Gigascience 2025;14:giaf020. [PMID: 40117178 PMCID: PMC11927400 DOI: 10.1093/gigascience/giaf020] [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: 09/25/2024] [Revised: 01/06/2025] [Accepted: 02/12/2025] [Indexed: 03/23/2025]  Open
7
Su XM, Yuan DY, Liu N, Zhang ZC, Yang M, Li L, Chen S, Zhou Y, He XJ. ALFIN-like proteins link histone H3K4me3 to H2A ubiquitination and coordinate diverse chromatin modifications in Arabidopsis. MOLECULAR PLANT 2025;18:130-150. [PMID: 39668562 DOI: 10.1016/j.molp.2024.12.007] [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: 07/10/2024] [Revised: 11/15/2024] [Accepted: 12/08/2024] [Indexed: 12/14/2024]
8
Wang D, Xiao S, Shu J, Luo L, Yang M, Calonje M, He H, Song B, Zhou Y. Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis. Genome Biol 2024;25:324. [PMID: 39741350 DOI: 10.1186/s13059-024-03465-7] [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: 05/28/2024] [Accepted: 12/19/2024] [Indexed: 01/02/2025]  Open
9
Shu J, Sun L, Wang D, Yin X, Yang M, Yang Z, Gao Z, He Y, Calonje M, Lai J, Deng XW, He H, Zhou Y. EMF1 functions as a 3D chromatin modulator in Arabidopsis. Mol Cell 2024;84:4729-4739.e6. [PMID: 39566504 DOI: 10.1016/j.molcel.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: 06/17/2024] [Revised: 08/30/2024] [Accepted: 10/24/2024] [Indexed: 11/22/2024]
10
Yang T, Wang D, Luo L, Yin X, Song Z, Yang M, Zhou Y. PWOs repress gene transcription by regulating chromatin structures in Arabidopsis. Nucleic Acids Res 2024;52:12918-12929. [PMID: 39526374 PMCID: PMC11602166 DOI: 10.1093/nar/gkae958] [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: 04/26/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024]  Open
11
Liu P, Vigneau J, Craig RJ, Barrera-Redondo J, Avdievich E, Martinho C, Borg M, Haas FB, Liu C, Coelho SM. 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization. Nat Commun 2024;15:9590. [PMID: 39505852 PMCID: PMC11541908 DOI: 10.1038/s41467-024-53453-5] [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: 04/23/2024] [Accepted: 10/08/2024] [Indexed: 11/08/2024]  Open
12
Göbel AM, Zhou S, Wang Z, Tzourtzou S, Himmelbach A, Zheng S, Pradillo M, Liu C, Jiang H. Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana. Nat Commun 2024;15:9308. [PMID: 39468060 PMCID: PMC11519323 DOI: 10.1038/s41467-024-53760-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: 08/09/2024] [Accepted: 10/22/2024] [Indexed: 10/30/2024]  Open
13
Li Z, Sun L, Xu X, Liu Y, He H, Deng XW. Light control of three-dimensional chromatin organization in soybean. PLANT BIOTECHNOLOGY JOURNAL 2024;22:2596-2611. [PMID: 38762905 PMCID: PMC11331798 DOI: 10.1111/pbi.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
14
Go D, Lu B, Alizadeh M, Gazzarrini S, Song L. Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation. FRONTIERS IN PLANT SCIENCE 2024;15:1416216. [PMID: 39166233 PMCID: PMC11333834 DOI: 10.3389/fpls.2024.1416216] [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] [Accepted: 06/20/2024] [Indexed: 08/22/2024]
15
Baile F, Calonje M. Dynamics of polycomb group marks in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2024;80:102553. [PMID: 38776572 DOI: 10.1016/j.pbi.2024.102553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
16
Candela-Ferre J, Diego-Martin B, Pérez-Alemany J, Gallego-Bartolomé J. Mind the gap: Epigenetic regulation of chromatin accessibility in plants. PLANT PHYSIOLOGY 2024;194:1998-2016. [PMID: 38236303 PMCID: PMC10980423 DOI: 10.1093/plphys/kiae024] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 01/19/2024]
17
Sun L, Zhou J, Xu X, Liu Y, Ma N, Liu Y, Nie W, Zou L, Deng XW, He H. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL. Nat Commun 2024;15:35. [PMID: 38167349 PMCID: PMC10762229 DOI: 10.1038/s41467-023-44347-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: 02/17/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024]  Open
18
Deng L, Zhou Q, Zhou J, Zhang Q, Jia Z, Zhu G, Cheng S, Cheng L, Yin C, Yang C, Shen J, Nie J, Zhu JK, Li G, Zhao L. 3D organization of regulatory elements for transcriptional regulation in Arabidopsis. Genome Biol 2023;24:181. [PMID: 37550699 PMCID: PMC10405511 DOI: 10.1186/s13059-023-03018-4] [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: 11/19/2022] [Accepted: 07/20/2023] [Indexed: 08/09/2023]  Open
19
Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023;65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
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