IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-49721-z.html
   My bibliography  Save this article

Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa

Author

Listed:
  • Xiaoyun Xin

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Peirong Li

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Xiuyun Zhao

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Yangjun Yu

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Weihong Wang

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Guihua Jin

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science)

  • Jiao Wang

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science)

  • Liling Sun

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science)

  • Deshuang Zhang

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Fenglan Zhang

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Shuancang Yu

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

  • Tongbing Su

    (Beijing Academy of Agriculture and Forestry Science
    Beijing Academy of Agriculture and Forestry Science
    Beijing Key Laboratory of Vegetable Germplasms Improvement
    Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China))

Abstract

Global warming has a severe impact on the flowering time and yield of crops. Histone modifications have been well-documented for their roles in enabling plant plasticity in ambient temperature. However, the factor modulating histone modifications and their involvement in habitat adaptation have remained elusive. In this study, through genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we reveal that BrJMJ18 is a candidate gene for a QTL regulating thermotolerance in thermotolerant B. rapa subsp. chinensis var. parachinensis (or Caixin, abbreviated to Par). BrJMJ18 encodes an H3K36me2/3 Jumonji demethylase that remodels H3K36 methylation across the genome. We demonstrate that the BrJMJ18 allele from Par (BrJMJ18Par) influences flowering time and plant growth in a temperature-dependent manner via characterizing overexpression and CRISPR/Cas9 mutant plants. We further show that overexpression of BrJMJ18Par can modulate the expression of BrFLC3, one of the five BrFLC orthologs. Furthermore, ChIP-seq and transcriptome data reveal that BrJMJ18Par can regulate chlorophyll biosynthesis under high temperatures. We also demonstrate that three amino acid mutations may account for function differences in BrJMJ18 between subspecies. Based on these findings, we propose a working model in which an H3K36me2/3 demethylase, while not affecting agronomic traits under normal conditions, can enhance resilience under heat stress in Brassica rapa.

Suggested Citation

  • Xiaoyun Xin & Peirong Li & Xiuyun Zhao & Yangjun Yu & Weihong Wang & Guihua Jin & Jiao Wang & Liling Sun & Deshuang Zhang & Fenglan Zhang & Shuancang Yu & Tongbing Su, 2024. "Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49721-z
    DOI: 10.1038/s41467-024-49721-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-49721-z
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-49721-z?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Raphaël Margueron & Danny Reinberg, 2011. "The Polycomb complex PRC2 and its mark in life," Nature, Nature, vol. 469(7330), pages 343-349, January.
    2. Nobutoshi Yamaguchi & Satoshi Matsubara & Kaori Yoshimizu & Motohide Seki & Kouta Hamada & Mari Kamitani & Yuko Kurita & Yasuyuki Nomura & Kota Nagashima & Soichi Inagaki & Takamasa Suzuki & Eng-Seng , 2021. "H3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    3. Naibin Duan & Yang Bai & Honghe Sun & Nan Wang & Yumin Ma & Mingjun Li & Xin Wang & Chen Jiao & Noah Legall & Linyong Mao & Sibao Wan & Kun Wang & Tianming He & Shouqian Feng & Zongying Zhang & Zhiqua, 2017. "Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Xinyi Chen & Yiran Guo & Ting Zhao & Jiuwei Lu & Jian Fang & Yinsheng Wang & Gang Greg Wang & Jikui Song, 2024. "Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Thomas Davies & Sophie Watts & Kendra McClure & Zoë Migicovsky & Sean Myles, 2022. "Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)," PLOS ONE, Public Library of Science, vol. 17(3), pages 1-11, March.
    4. Allegra Angeloni & Skye Fissette & Deniz Kaya & Jillian M. Hammond & Hasindu Gamaarachchi & Ira W. Deveson & Robert J. Klose & Weiming Li & Xiaotian Zhang & Ozren Bogdanovic, 2024. "Extensive DNA methylome rearrangement during early lamprey embryogenesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Varadha Balaji Venkadakrishnan & Adam G. Presser & Richa Singh & Matthew A. Booker & Nicole A. Traphagen & Kenny Weng & Nathaniel C. E. Voss & Navin R. Mahadevan & Kei Mizuno & Loredana Puca & Osasena, 2024. "Lineage-specific canonical and non-canonical activity of EZH2 in advanced prostate cancer subtypes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Pedro L. Baldoni & Naim U. Rashid & Joseph G. Ibrahim, 2022. "Efficient detection and classification of epigenomic changes under multiple conditions," Biometrics, The International Biometric Society, vol. 78(3), pages 1141-1154, September.
    7. Zhaowei Yu & Qi Wang & Qichen Zhang & Yawen Tian & Guo Yan & Jidong Zhu & Guangya Zhu & Yong Zhang, 2024. "Decoding the genomic landscape of chromatin-associated biomolecular condensates," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    8. Rachel K. Lex & Weiqiang Zhou & Zhicheng Ji & Kristin N. Falkenstein & Kaleigh E. Schuler & Kathryn E. Windsor & Joseph D. Kim & Hongkai Ji & Steven A. Vokes, 2022. "GLI transcriptional repression is inert prior to Hedgehog pathway activation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    9. Lihu Gong & Xiuli Liu & Lianying Jiao & Xin Yang & Andrew Lemoff & Xin Liu, 2022. "CK2-mediated phosphorylation of SUZ12 promotes PRC2 function by stabilizing enzyme active site," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    10. Wen Hao Neo & Yiran Meng & Alba Rodriguez-Meira & Muhammad Z. H. Fadlullah & Christopher A. G. Booth & Emanuele Azzoni & Supat Thongjuea & Marella F. T. R. Bruijn & Sten Eirik W. Jacobsen & Adam J. Me, 2021. "Ezh2 is essential for the generation of functional yolk sac derived erythro-myeloid progenitors," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    11. Xiaozhen Zhao & Yiming Wang & Bingqin Yuan & Hanxi Zhao & Yujie Wang & Zheng Tan & Zhiyuan Wang & Huijun Wu & Gang Li & Wei Song & Ravi Gupta & Kenichi Tsuda & Zhonghua Ma & Xuewen Gao & Qin Gu, 2024. "Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    12. Nadia Khan & Barry Schoenike & Trina Basu & Heidi Grabenstatter & Genesis Rodriguez & Caleb Sindic & Margaret Johnson & Eli Wallace & Rama Maganti & Raymond Dingledine & Avtar Roopra, 2019. "A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-26, December.
    13. Qican Cheng & Yue Zeng & Sha Huang & Chuanwei Yang & Yu Xie & Wen-Hui Shen & Lin Li, 2024. "PHYTOCHROME-INTERACTING FACTOR 7 and RELATIVE OF EARLY FLOWERING 6 act in shade avoidance memory in Arabidopsis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    14. Yuki Furuta & Haruka Yamamoto & Takeshi Hirakawa & Akira Uemura & Margaret Anne Pelayo & Hideaki Iimura & Naoya Katagiri & Noriko Takeda-Kamiya & Kie Kumaishi & Makoto Shirakawa & Sumie Ishiguro & Yas, 2024. "Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    15. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    16. Reiko Akiyama & Takao Goto & Toshiaki Tameshige & Jiro Sugisaka & Ken Kuroki & Jianqiang Sun & Junichi Akita & Masaomi Hatakeyama & Hiroshi Kudoh & Tanaka Kenta & Aya Tonouchi & Yuki Shimahara & Jun S, 2023. "Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    17. Nikhil B. Ghate & Sungmin Kim & Yonghwan Shin & Jinman Kim & Michael Doche & Scott Valena & Alan Situ & Sangnam Kim & Suhn K. Rhie & Heinz-Josef Lenz & Tobias S. Ulmer & Shannon M. Mumenthaler & Wooji, 2023. "Phosphorylation and stabilization of EZH2 by DCAF1/VprBP trigger aberrant gene silencing in colon cancer," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    18. Noe E. Crespo & Alexandra Torres-Bracero & Jessicca Y. Renta & Robert J. Desnick & Carmen L. Cadilla, 2021. "Expression Profiling Identifies TWIST2 Target Genes in Setleis Syndrome Patient Fibroblast and Lymphoblast Cells," IJERPH, MDPI, vol. 18(4), pages 1-27, February.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49721-z. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.