植物三维基因组学研究进展

doi:10.3969/j.issn.1009-7791.2025.05.013

亚热带植物科学 ›› 2025, Vol. 54 ›› Issue (5): 578-586.DOI: 10.3969/j.issn.1009-7791.2025.05.013

植物三维基因组学研究进展

李秋佳1，邱秉慧1，李凌雨1，陈爽2，余克琴1*

(1. 襄阳职业技术学院，湖北襄阳 441050；2. 襄阳市植物保护站，湖北襄阳 441021)

收稿日期:2025-04-27 接受日期:2025-09-01 出版日期:2025-10-31 发布日期:2025-12-17
通讯作者: 余克琴
基金资助:
襄阳职业技术学院高层次人才科研启动经费资助项目(XYZYZZ06、XYZYZZ11)

Advances in Plant Three-Dimensional Genomics Research

LI Qiu-jia1, QIU Bing-hui1, LI Ling-yu1, CHEN Shuang2, YU Ke-qin1*

(1. Xiangyang Vocational and Technical College, Xiangyang 441050, Hubei China; 2. Xiangyang Plant Protection Station, Xiangyang 441021, Hubei China)

Received:2025-04-27 Accepted:2025-09-01 Online:2025-10-31 Published:2025-12-17
Contact: YU Ke-qin

摘要/Abstract

摘要： 三维基因组学作为后基因组学时代的研究热点，致力于揭示基因组在细胞核内的三维空间结构及其与基因表达调控等生物过程的关联。相较于动物，植物三维基因组学起步较晚且面临诸多技术难题，但近年来取得显著进展。本文系统梳理植物三维基因组学研究的技术手段发展、植物基因组的三维层级结构特征，并探讨研究过程中面临的技术挑战。

关键词: 三维基因组学, 染色质构象, 表观遗传调控, 植物基因组, 基因表达

Abstract: As a research hotspot in the post-genomics era, 3D genomics is dedicated to revealing the three-dimensional spatial structure of the genome within the cell nucleus and its associations with biological processes. Compared with animals, plant 3D genomics, despite starting later and facing numerous technical challenges, has achieved significant progress in recent years. This paper systematically reviews the development of technical approaches in plant 3D genomics research, the characteristics of the three-dimensional hierarchical structure of plant genomes, and explores the technical challenges encountered in the research process, aiming to provide theoretical support and practical guidance for the future development of this field.

Key words: 3D genomics, chromatin conformation, epigenetic regulation, plant genome, gene expression

中图分类号:

Q943

李秋佳, 邱秉慧, 李凌雨, 陈爽, 余克琴. 植物三维基因组学研究进展[J]. 亚热带植物科学, 2025, 54(5): 578-586.

LI Qiu-jia, QIU Bing-hui, LI Ling-yu, CHEN Shuang, YU Ke-qin. Advances in Plant Three-Dimensional Genomics Research[J]. Subtropical Plant Science, 2025, 54(5): 578-586.

参考文献

[1] 李国亮, 阮一骏, 谷瑞升, 杜生明. 起航三维基因组学研究[J]. 科学通报, 2014, 59: 1165–1174.
[2] Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation [J]. Science, 2002, 295: 1306–1311.
[3] Lieberman-Aiden E, Van Berkum N L, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B R, Sabo P J, Dorschner M O. Comprehensive mapping of long-range interactions reveals folding principles of the human genome [J]. Science, 2009, 326(5950): 289.
[4] Rao S S, Huntley M H, Durand N C, Stamenova E K, Bochkov I D, Robinson J T, Sanborn A L, Machol I, Omer A D, Lander E S. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping [J]. Cell, 2014, 159(7): 1665–1680.
[5] Hughes J R, Roberts N, Mcgowan S, Hay D, Giannoulatou E, Lynch M, De Gobbi M, Taylor S, Gibbons R, Higgs D R. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment [J]. Nature Genetics, 2014, 46(2): 205–212.
[6] Ma W, Ay F, Lee C, Duan Z. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes [J]. Nature Methods, 2014, 12(1): 71–78.
[7] Nagano T, Lubling Y, Stevens T J, Schoenfelder S, Yaffe E, Dean W, Laue E D, Tanay A, Fraser P. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure [J]. Nature, 2013, 502(7469): 59.
[8] Fang R, Yu M, Li G, Chee S, Liu T, Schmitt A D, Ren B. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq [J]. Cell Research, 2016, 26(12): 1345–1348.
[9] Fullwood M J, Liu M H, Pan Y F, Liu J, Al H X E. An oestrogen- receptor-alpha-bound human chromatin interactome [J]. Nature, 2009, 462(7269): 58.
[10] Mumbach M R, Rubin A J, Flynn R A, Dai C, Chang H Y. HiChIP: efficient and sensitive analysis of protein-directed genome architecture [J]. Nature Methods, 2016, 13(11): 919–922.
[11] Li X, Luo O J, Wang P, Zheng M, Wang D, Piecuch E, Zhu J J, Tian S Z, Tang Z, Li G. Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions [J]. Nature Protocols, 2017, 12(5): 899–915.
[12] Sridhar B, Rivas-Astroza M, Nguyen T C, Chen W, Yan Z, Cao X, Hebert L, Zhong S. Systematic mapping of RNA-chromatin interactions in Vivo [J]. Current Biology, 2017, 27(4): 602–609.
[13] Helwak A, Kudla G, Dudnakova T, Tollervey D. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding [J]. Cell, 2013, 153(3): 654–665.
[14] Keene J D, Komisarow J M, Friedersdorf M B. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts [J]. Nature Protocols, 2006, 1(1): 302–307.
[15] Yin Z, Shujuan X, Hui X U, Lianghu Q U. CLIP: viewing the RNA world from an RNA–protein interactome perspective [J]. Science China, 2015, 58(1): 75–88.
[16] Li X, Zhou B, Chen L, Gou L T, Li H, Fu X D. GRID-seq reveals the global RNA-chromatin interactome [J]. Nature Biotechnology, 2017, 35(10): 940–950.
[17] Quinodoz S A, Noah O, Barbara T, Ali P, Marten S J, Elizabeth D, Lai M M, Shishkin A A, Prashant B, Yodai T. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus [J]. Cell, 2018, 174(3): 744–757.
[18] You Q, Cheng A Y, Gu X, Harada B T, He C. Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution [J]. Nature Biotechnology, 2020, 39(2): 225–235.
[19] Zheng M, Tian S Z, Capurso D, Kim M, Maurya R, Lee B, Piecuch E, Gong L, Zhu J J, Li Z, Wong C H, Ngan C Y, Wang P, Ruan X, Wei C L, Ruan Y. Multiplex chromatin interactions with single-molecule precision [J]. Nature, 2019, 566(7745): 558–562.
[20] Ouyang W, Xiong D, Li G. Unraveling the 3D Genome Architecture in plants: present and future [J]. Molecular Plant, 2020, 13(12): 1676–1693.
[21] Pontvianne F, Liu C. Chromatin domains in space and their functional implications [J]. Current Opinion In Plant Biology, 2020, 54: 1–10.
[22] Long Y, Wendel J F, Zhang X, Wang M. Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants [J]. Trends in Plant Science, 2024, 29(6): 638–649.
[23] Chen C, Wu S, Sun Y, Zhou J, Chen Y, Zhang J, Birchler J A, Han F, Yang N, Su H. Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus [J]. Genome Biology, 2024, 25(1): 63.
[24] Domb K, Wang N, Hummel G, Liu C. Spatial features and functional implications of plant 3D genome organization [J]. Annual Review of Plant Biology, 2022, 73: 173–200.
[25] Wang M J, Lin P C, Ye M, Li Z X, Tu G L. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton [J]. Nature Plants, 2018, 4(2): 90–97.
[26] Sun L, Jing Y, Liu X, Li Q, Xue Z, Cheng Z, Wang D, He H, Qian W. Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis [J]. Nature Communications, 2020, 11(1): 1886.
[27] Dong P, Tu X, Chu P Y, Lü P, Zhu N, Grierson D, Du B, Li P, Zhong S. 3D Chromatin architecture of large plant genomes determined by local A/B compartments [J]. Molecular Plant, 2017, 10(12): 1497.
[28] Zhang Y, Mccord R, Ho Y J, Lajoie B, Hildebrand D, Simon A, Becker M, Alt F, Dekker J. Spatial Organization of the mouse genome and its role in recurrent chromosomal translocations [J]. Cell, 2012, 148(5): 908–921.
[29] Ren G, Jin W F, Cui K R, Rodrigez J, Zhang G Q. CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression [J]. Molecular Cell, 2017, 67(6): 1049–1058.
[30] Ulianov S V, Khrameeva E E, Gavrilov A A, Flyamer I M, Kos P, Mikhaleva E A, Penin A A, Logacheva M D, Imakaev M V, Chertovich A. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains [J]. Genome Research, 2015, 26(1): 70–84.
[31] Van Steensel B, Furlong E E M. The role of transcription in shaping the spatial organization of the genome [J]. Nature Reviews Molecular Cell Biology, 2019, 20(6): 327–337.
[32] Liao Y, Wang J, Zhu Z, Liu Y, Chen J, Zhou Y, Liu F, Lei J, Gaut B S, Cao B. The 3D architecture of the pepper genome and its relationship to function and evolution [J]. Nature Communications, 2022, 13(1): 3479.
[33] Wang M, Li J, Qi Z, Long Y, Pei L, Huang X, Grover C E, Du X, Xia C, Wang P, Liu Z, You J, Tian X, Ma Y, Wang R, Chen X, He X, Fang D D, Sun Y, Tu L, Jin S, Zhu L, Wendel J F, Zhang X. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium [J]. Nature Genetics, 2022, 54(12): 1959–1971.
[34] Sun Y, Dong L, Zhang Y, Lin D, Yang F. 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize [J]. Genome Biology, 2020, 21(1): 143.
[35] Zhou S, Jiang W, Zhao Y, Zhou D X. Single-cell three-dimensional genome structures of rice gametes and unicellular zygotes [J]. Nature Plants, 2019, 5(8): 795–800.
[36] Moissiard G, Cokus S J, Cary J, Feng S, Billi A C, Stroud H, Husmann D, Zhan Y, Lajoie B R, Mccord R P. MORC family ATPases required for heterochromatin condensation and gene silencing [J]. American Association for the Advancement of Science, 2012, 336(6087): 1448–1451.
[37] Feng S, Cokus S J, Schubert V, Zhai J, Pellegrini M, Jacobsen S E. Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis [J]. Molecular Cell, 2014, 55(5): 694–707.
[38] Grob S, Schmid M W, Grossniklaus U. Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila [J]. Molecular Cell, 2014, 55(5): 678–693.
[39] Wang C, Liu C, Roqueiro D, Grimm D, Schwab R, Becker C, Lanz C, Weigel D. Genome-wide analysis of local chromatin packing in Arabidopsis thaliana [J]. Genome Research, 2015, 25(2): 246–256.
[40] Liu C, Wang C, Wang G, Becker C, Zaidem M, Weigel D. Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution [J]. Genome Research, 2016, 26(8): 1057–1068.
[41] Hu B, Wang N, Bi X, Karaaslan E S, Liu C. Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery [J]. Genome biology, 2019, 20(1): 87.
[42] Xie T, Zhang F G, Zhang H Y, Wang X T, Wu X M. Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization [J]. Nature Plants, 2019, 5(8): 822–832.
[43] Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication [J]. Nature Genetics, 2017, 49(4): 579.
[44] Liu C, Cheng Y J, Wang J W, Weigel D. Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis [J]. Nature plants, 2017, 3(9): 742–748.
[45] Dong Q, Li N, Li X, Yuan Z, Xie D, Wang X, Li J, Yu Y, Wang J, Ding B. Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice [J]. Plant Journal, 2018, 94(6): 1141–1156.
[46] Dong P, Tu X, Li H, Zhang J, Grierson D, Li P, Zhong S. Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains [J]. Journal of Integrative Plant Biology, 2020, 62(2): 201–217.
[47] Zhou S, Jiang W, Zhao Y, Zhou D X. Single-cell three-dimensional genome structures of rice gametes and unicellular zygotes [J]. Nature Plants, 2019, 5(8): 795–800.
[48] Peng Y, Xiong D, Zhao L, Ouyang W, Li X. Chromatin interaction maps reveal genetic regulation for quantitative traits in maize [J]. Nature Communications, 2019, 10(1): 2632.
[49] Li E, Liu H, Huang L, Zhang X, Dong X, Song W, Zhao H, Lai J. Long-range interactions between proximal and distal regulatory regions in maize [J]. Nature Communications, 2019, 10(1): 2633.
[50] Ricci W A, Lu Z, Ji L, Marand A P, Zhang X. Widespread long-range cis-regulatory elements in the maize genome [J]. Nature Plants, 2019, 5(12): 1–13.
[51] Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok S O, Wicker T, Radchuk V, Dockter C, Hedley P E, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang X Q, Zhang Q, Barrero R A, Li L, Taudien S, Groth M, Felder M, Hastie A, ?imková H, Staňková H, Vrána J, Chan S, Mu?oz–Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva–Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, Mccooke J K, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland J A, Bellgard M I, Borisjuk L, Houben A, Dole?el J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer G J, Clark M D, Caccamo M, Schulman A H, Mayer K F X, Platzer M, Close T J, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. A chromosome conformation capture ordered sequence of the barley genome [J]. Nature, 2017, 544(7651): 427–433.
[52] Concia L, Veluchamy A, Ramirezprado J S, Martinramirez A, Huang Y, Perez M, Domenichini S, Rodriguez Granados N Y, Kim S K, Blein T. Wheat chromatin architecture is organized in genome territories and transcription factories [J]. Genome Biology, 2020, 21(1): 104.
[53] Louwers M, Bader R, Haring M, Driel R V, Stam L M. Tissue- and Expression level-specific chromatin looping at maize b1 epialleles [J]. Plant Cell, 2009, 21(3): 832–842.
[54] Crevillén P, Sonmez C, Wu Z, Dean C. A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization [J]. The EMBO Journal, 2013, 32(1): 140–148.
[55] Liu L, Adrian J, Pankin A, Hu J, Dong X, Von Korff M, Turck F. Induced and natural variation of promoter length modulates the photoperiodic response of FLOWERING LOCUS T [J]. Nature Communications, 2014, 5(1): 4558.
[56] Zhao L, Wang S, Cao Z, Ouyang W, Li X. Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation [J]. Nature Communications, 2019, 10(1): 3640.
[57] Zhao L, Xie L, Zhang Q, Ouyang W, Deng L, Guan P, Ma M, Li Y, Zhang Y, Xiao Q. Integrative analysis of reference epigenomes in 20 rice varieties [J]. Nature Communications, 2020, 11(1): 2658.
[58] Sun J, He N, Niu L, Huang Y, Shen W, Zhang Y, Li L, Hou C. Global quantitative mapping of enhancers in rice by STARR-seq [J]. Elsevier, 2019, 17 (2): 140–153.

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植物三维基因组学研究进展

Advances in Plant Three-Dimensional Genomics Research

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