The genome-wide landscape of histone modifications dynamics in non-heading Chinese cabbage root tips under salt stress

doi:10.1016/j.jia.2026.02.026

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Hao Liang^1*, Qifan Wang^1*, Haijiao He^1*, Xiaonan Zhang^1*, Zishuo Wang¹, Yingshuo Zhi¹, Baishen Zhang¹, Wei Ma¹, Zhaokun Liu³, Fuyan Liu^2#, Qing Liu^1#, Jianjun Zhao^1#

¹State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R&D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, College of Life Sciences, Hebei Agricultural University, Baoding 071000, China

²OmicsGang Biotechnology Corporation, 18 Yuan Street, Beijing, 101318, China

³Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China

Highlights

l This study constructed a genome-wide modification map of H3K27ac and H3K27me3 in the root tips of NHCC under salt stress.

l We found that the root tips of NHCC might respond to salt stress by regulating the cell wall pathway through H3K27ac. We identified the key gene BcPMEI4 (pectin methylesterase inhibitor 4) of the cell wall pathway with upregulated H3K27ac modification levels in the promoter region under salt stress, and preliminarily verified the positive regulatory effect of BcPMEI4 on salt tolerance of NHCC through VIGS.

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摘要

不结球白菜（NHCC, Brassica campestris （syn. Brassica rapa） ssp.chinensis）是中国最重要的叶菜类蔬菜之一。随着土壤盐渍化日益严重，盐胁迫限制了其生长发育，导致产量和品质下降。先前研究表明，组蛋白修饰通过调控关键基因的表达，在植物盐胁迫应答中发挥重要作用，但该修饰在 NHCC 中的作用尚不清楚。本研究利用 CUT&Tag-seq 和 RNA-seq 技术，全面分析了NHCC 根尖在盐胁迫 12 小时和 24 小时后，全基因组范围内的 H3K27ac 与H3K27me3修饰及其转录组变化。结果表明，盐胁迫下，抑制性染色质标记H3K27me3的全基因组水平升高，而活性标记H3K27ac的水平则降低。H3K27ac和 H3K27me3 水平发生响应的基因，主要参与海藻糖合成、转录调控、膜运输、防御反应及细胞壁结构等生物学过程。其中，在盐胁迫下 H3K27ac 水平升高且表达上调的细胞壁相关基因中，鉴定出一个拟南芥果胶甲基酯酶抑制剂 4 的同源基因 BcPMEI4。病毒诱导的基因沉默（VIGS）实验证实，沉默 BcPMEI4 会显著降低 NHCC 的耐盐性，具体表现为叶面积和根面积减少、过氧化氢含量升高。这表明 H3K27ac 介导的 BcPMEI4 转录激活可能通过调控细胞壁通路来增强耐盐性。总之，我们的研究揭示了盐胁迫下 NHCC 中活性与抑制性染色质标记的动态变化图谱，为理解 NHCC 及其他芸薹属作物盐胁迫应答的表观遗传机制提供了新的见解。

Abstract

Non-heading Chinese cabbage (NHCC, Brassica campestris [syn. Brassica rapa] ssp. chinensis) is one of the most important leafy vegetables in China. As soil salinization becomes increasingly serious, salt stress limits the growth and development of NHCC, reducing its yield and quality. Previous studies have shown that histone modifications play an important role in plant salt-stress responses by regulating the expression of key genes, but little is known about such modifications in NHCC. Here, we used CUT&Tag-seq and RNA-seq to profile genome-wide H3K27ac and H3K27me3 modifications and transcriptome changes in NHCC root tips subjected to salt stress at 12 and 24 hours. Genome-wide levels of the repressive chromatin mark H3K27me3 increased under salt stress, whereas those of the active chromatin mark H3K27ac decreased. Genes whose H3K27ac and H3K27me3 levels responded to salt stress were associated with processes such as trehalose synthesis, transcription, membrane transport, defense responses, and cell wall structure. Among the cell wall-related genes with increased H3K27ac levels and expression under salt stress, there is a homologous gene of Arabidopsis pectin methylesterase inhibitor 4 (BcPMEI4). The virus-induced gene silencing (VIGS) assay confirmed that silencing BcPMEI4 significantly reduced the salt tolerance of NHCC, as reflected by decreased leaf area, reduced root area, and increased hydrogen peroxide levels. This suggests that the H3K27ac-mediated transcriptional activation of BcPMEI4 may enhance salt tolerance by regulating the cell wall pathway. In summary, our findings provide the comprehensive picture of changes in active and repressive chromatin marks in NHCC under salt stress, offering insight into epigenetic mechanisms of salt-stress response in NHCC and other Brassica crops.

Keywords: Histone modifications Salt stress Cell wall Non-heading Chinese cabbage

Online: 17 February 2026

Fund:

This work was financially supported by the National Natural Science Foundation of China (32330096, U24A20417), Hebei Natural Science Foundation (C2024204246) and Science Research Project of Hebei Education Department (YJZ202400).

About author: Hao Liang, E-mail: joylh0319@163.com; #Correspondence Jianjun Zhao, E-mail: jjz1971@aliyun.com; Qing Liu, E-mail: liuqing12151118@163.com; Fuyan Liu, E-mail:1058443021@qq.com *These authors contributed equally to this study.

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Hao Liang, Qifan Wang, Haijiao He, Xiaonan Zhang, Zishuo Wang, Yingshuo Zhi, Baishen Zhang, Wei Ma, Zhaokun Liu, Fuyan Liu, Qing Liu, Jianjun Zhao. 2026. The genome-wide landscape of histone modifications dynamics in non-heading Chinese cabbage root tips under salt stress. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.02.026

Banerjee A, Wani S H, Roychoudhury A. 2017. Epigenetic Control of Plant Cold Responses. Front Plant Sci, 8, 1643. doi,10.3389/fpls.2017.01643.

Beauzamy L, Derr J, Boudaoud A. 2015. Quantifying hydrostatic pressure in plant cells by using indentation with an atomic force microscope. Biophys J, 108, 2448-2456. doi,10.1016/j.bpj.2015.03.035.

Chen C, Li C, Wang Y, Renaud J, Tian G, Kambhampati S, Saatian B, Nguyen V, Hannoufa A, Marsolais F, Yuan Z C, Yu K, Austin R S, Liu J, Kohalmi S E, Wu K, Huang S, Cui Y. 2017. Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis. Nat Plants, 3, 814-824. doi,10.1038/s41477-017-0023-7.

Colin L, Ruhnow F, Zhu J K, Zhao C, Zhao Y, Persson S. 2023. The cell biology of primary cell walls during salt stress. Plant Cell, 35, 201-217. doi,10.1093/plcell/koac292.

Du J, Anderson C T, Xiao C. 2022. Dynamics of pectic homogalacturonan in cellular morphogenesis and adhesion, wall integrity sensing and plant development. Nat Plants, 8, 332-340. doi,10.1038/s41477-022-01120-2.

Endler A, Kesten C, Schneider R, Zhang Y, Ivakov A, Froehlich A, Funke N, Persson S. 2015. A Mechanism for Sustained Cellulose Synthesis during Salt Stress. Cell, 162, 1353-1364. doi,10.1016/j.cell.2015.08.028.

Feng W, Kita D, Peaucelle A, Cartwright H N, Doan V, Duan Q, Liu M C, Maman J, Steinhorst L, Schmitz-Thom I, Yvon R, Kudla J, Wu H M, Cheung A Y, Dinneny J R. 2018. The FERONIA Receptor Kinase Maintains Cell-Wall Integrity during Salt Stress through Ca²⁺ Signaling. Curr Biol, 28, 666-675 e665. doi,10.1016/j.cub.2018.01.023.

Foroozani M, Vandal M P, Smith A P. 2021. H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants. Planta, 253, 4. doi,10.1007/s00425-020-03520-0.

Gigli-Bisceglia N, van Zelm E, Huo W, Lamers J, Testerink C. 2022. Arabidopsis root responses to salinity depend on pectin modification and cell wall sensing. Development, 149. doi,10.1242/dev.200363.

Hocq L, Senechal F, Lefebvre V, Lehner A, Domon J M, Mollet J C, Dehors J, Pageau K, Marcelo P, Guerineau F, Kolsek K, Mercadante D, Pelloux J. 2017. Combined Experimental and Computational Approaches Reveal Distinct pH Dependence of Pectin Methylesterase Inhibitors. Plant Physiol, 173, 1075-1093. doi,10.1104/pp.16.01790.

Li Y, Liu G F, Ma L M, Liu T K, Zhang C W, Xiao D, Zheng H K, Chen F, Hou X L. 2020. A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Hortic Res, 7, 212. doi,10.1038/s41438-020-00449-z.

Liang H, Shi Q, Li X, Gao P, Feng D, Zhang X, Lu Y, Yan J, Shen S, Zhao J, Ma W. 2024. Synergistic effects of carbon cycle metabolism and photosynthesis in Chinese cabbage under salt stress. Horticultural Plant Journal, 10, 461-472. doi,10.1016/j.hpj.2022.09.003.

Liu M J, Yeh F J, Yvon R, Simpson K, Jordan S, Chambers J, Wu H M, Cheung A Y. 2024. Extracellular pectin-RALF phase separation mediates FERONIA global signaling function. Cell, 187, 312-330 e322. doi,10.1016/j.cell.2023.11.038.

Liu X, Bie X M, Lin X, Li M, Wang H, Zhang X, Yang Y, Zhang C, Zhang X S, Xiao J. 2023. Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation. Nat Plants, 9, 908-925. doi,10.1038/s41477-023-01406-z.

Love M I, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15, 550. doi,10.1186/s13059-014-0550-8.

Manunza B, Deiana S, Pintore M, Gessa C. 1998. Interaction of Ca²⁺ and Na⁺ ions with polygalacturonate chains: a molecular dynamics study. Glycoconj J, 15, 297-300. doi,10.1023/a:1006905314435.

Munns R, Tester M. 2008. Mechanisms of salinity tolerance. Annu Rev Plant Biol, 59, 651-681. doi,10.1146/annurev.arplant.59.032607.092911.

Pan J, Zhang H, Zhan Z, Zhao T, Jiang D. 2023. A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis. J Genet Genomics, 50, 178-191. doi,10.1016/j.jgg.2022.09.001.

Raiola A, Camardella L, Giovane A, Mattei B, De Lorenzo G, Cervone F, Bellincampi D. 2004. Two Arabidopsis thaliana genes encode functional pectin methylesterase inhibitors. FEBS Lett, 557, 199-203. doi,10.1016/s0014-5793(03)01491-1.

Reca I B, Lionetti V, Camardella L, D'Avino R, Giardina T, Cervone F, Bellincampi D. 2012. A functional pectin methylesterase inhibitor protein (SolyPMEI) is expressed during tomato fruit ripening and interacts with PME-1. Plant Mol Biol, 79, 429-442. doi,10.1007/s11103-012-9921-2.

Ren Y, Wang W, He J, Zhang L, Wei Y, Yang M. 2020. Nitric oxide alleviates salt stress in seed germination and early seedling growth of pakchoi (Brassica chinensis L.) by enhancing physiological and biochemical parameters. Ecotoxicol Environ Saf, 187, 109785. doi,10.1016/j.ecoenv.2019.109785.

Sun L, Song G, Guo W, Wang W, Zhao H, Gao T, Lv Q, Yang X, Xu F, Dong Y, Pu L. 2019. Dynamic Changes in Genome-Wide Histone3 Lysine27 Trimethylation and Gene Expression of Soybean Roots in Response to Salt Stress. Front Plant Sci, 10, 1031. doi,10.3389/fpls.2019.01031.

Wang H, Li Z, Ren H, Zhang C, Xiao D, Li Y, Hou X, Liu T. 2022. Regulatory interaction of BcWRKY33A and BcHSFA4A promotes salt tolerance in non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Hortic Res, 9, uhac113. doi,10.1093/hr/uhac113.

Wolf S, Grsic-Rausch S, Rausch T, Greiner S. 2003. Identification of pollen-expressed pectin methylesterase inhibitors in Arabidopsis. FEBS Lett, 555, 551-555. doi,10.1016/s0014-5793(03)01344-9.

Yang Y, Guo Y. 2018. Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytol, 217, 523-539. doi,10.1111/nph.14920.

Yu G, Wang L G, He Q Y. 2015. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics, 31, 2382-2383. doi,10.1093/bioinformatics/btv145.

Zhang L, Cai X, Wu J, Liu M, Grob S, Cheng F, Liang J, Cai C, Liu Z, Liu B, Wang F, Li S, Liu F, Li X, Cheng L, Yang W, Li M H, Grossniklaus U, Zheng H, Wang X. 2018. Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Hortic Res, 5, 50. doi,10.1038/s41438-018-0071-9.

Zhang Y, Liu T, Meyer C A, Eeckhoute J, Johnson D S, Bernstein B E, Nusbaum C, Myers R M, Brown M, Li W, Liu X S. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol, 9, R137. doi,10.1186/gb-2008-9-9-r137.

Zhang Y Z, Yuan J, Zhang L, Chen C, Wang Y, Zhang G, Peng L, Xie S S, Jiang J, Zhu J K, Du J, Duan C G. 2020. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis. Nat Commun, 11, 6212. doi,10.1038/s41467-020-20089-0.

Zhao B, Shao Z, Wang L, Zhang F, Chakravarty D, Zong W, Dong J, Song L, Qiao H. 2022. MYB44-ENAP1/2 restricts HDT4 to regulate drought tolerance in Arabidopsis. PLoS Genet, 18, e1010473. doi,10.1371/journal.pgen.1010473.

Zhao C, Zayed O, Zeng F, Liu C, Zhang L, Zhu P, Hsu C C, Tuncil Y E, Tao W A, Carpita N C, Zhu J K. 2019. Arabinose biosynthesis is critical for salt stress tolerance in Arabidopsis. New Phytol, 224, 274-290. doi,10.1111/nph.15867.

Zheng D, Wang L, Chen L, Pan X, Lin K, Fang Y, Wang X E, Zhang W. 2019. Salt-Responsive Genes are Differentially Regulated at the Chromatin Levels Between Seedlings and Roots in Rice. Plant Cell Physiol, 60, 1790-1803. doi,10.1093/pcp/pcz095.

Zhou T, Wu P J, Chen J F, Du X Q, Feng Y N, Hua Y P. 2024. Pectin demethylation-mediated cell wall Na⁺ retention positively regulates salt stress tolerance in oilseed rape. Theor Appl Genet, 137, 54. doi,10.1007/s00122-024-04560-w.

Zhu Z, Li Q, Gichuki D K, Hou Y, Liu Y, Zhou H, Xu C, Fang L, Gong L, Zheng B, Duan W, Fan P, Wang Q, Xin H. 2023. Genome-wide profiling of histone H3 lysine 27 trimethylation and its modification in response to chilling stress in grapevine leaves. Horticultural Plant Journal, 9, 496-508. doi,10.1016/j.hpj.2023.03.002.

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