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Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat

Author

Listed:
  • Chao He

    (Huazhong Agricultural University)

  • Siteng Bi

    (Huazhong Agricultural University)

  • Yuqi Li

    (Huazhong Agricultural University)

  • Chengxiang Song

    (Huazhong Agricultural University)

  • Heping Zhang

    (Huazhong Agricultural University)

  • Xintong Xu

    (Huazhong Agricultural University)

  • Qiang Li

    (Huazhong Agricultural University)

  • Sulaiman Saeed

    (Huazhong Agricultural University)

  • Wei Chen

    (Huazhong Agricultural University)

  • Chunjie Zhao

    (Huazhong Agricultural University)

  • Caixia Lan

    (Huazhong Agricultural University)

  • Handong Su

    (Huazhong Agricultural University)

  • Hailiang Mao

    (Huazhong Agricultural University)

  • Wenhao Yan

    (Huazhong Agricultural University)

Abstract

Dissecting the genetic basis of seed traits in wheat is impeded by limited genetic polymorphisms and significant variations caused by environmental conditions and seed position in a spikelet. Seed performance is largely determined by endosperm development controlled by spatiotemporal variation in gene activities, which is greatly affected by chromatin status. Here, we map genome-wide dynamic distributions of H3K27me3, H3K4me3 and H3K9ac modifications and profile gene transcription across wheat endosperm development. The combinatorial effects of active and repressive marks ensure spatiotemporal dynamic gene expression, especially for starch biosynthesis. By scanning the transcription factor binding motifs in the ATAC-seq peaks, hub regulators are identified from the regulatory network. In addition, we observe significant correlations between sequence polymorphisms of hub regulators and variations in seed traits in a germplasm population. Thus, the analysis of genomic regulatory activities together with genetic variation provides a robust approach to dissect seed traits in bread wheat.

Suggested Citation

  • Chao He & Siteng Bi & Yuqi Li & Chengxiang Song & Heping Zhang & Xintong Xu & Qiang Li & Sulaiman Saeed & Wei Chen & Chunjie Zhao & Caixia Lan & Handong Su & Hailiang Mao & Wenhao Yan, 2024. "Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53300-7
    DOI: 10.1038/s41467-024-53300-7
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    References listed on IDEAS

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    1. Andrew Angel & Jie Song & Caroline Dean & Martin Howard, 2011. "A Polycomb-based switch underlying quantitative epigenetic memory," Nature, Nature, vol. 476(7358), pages 105-108, August.
    2. Yuyun Zhang & Zijuan Li & Jinyi Liu & Yu’e Zhang & Luhuan Ye & Yuan Peng & Haoyu Wang & Huishan Diao & Yu Ma & Meiyue Wang & Yilin Xie & Tengfei Tang & Yili Zhuang & Wan Teng & Yiping Tong & Wenli Zha, 2022. "Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Bates, Douglas & Mächler, Martin & Bolker, Ben & Walker, Steve, 2015. "Fitting Linear Mixed-Effects Models Using lme4," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 67(i01).
    4. Sang-Dong Yoo & Young-Hee Cho & Guillaume Tena & Yan Xiong & Jen Sheen, 2008. "Dual control of nuclear EIN3 by bifurcate MAPK cascades in C2H4 signalling," Nature, Nature, vol. 451(7180), pages 789-795, February.
    5. Mette Bentsen & Philipp Goymann & Hendrik Schultheis & Kathrin Klee & Anastasiia Petrova & René Wiegandt & Annika Fust & Jens Preussner & Carsten Kuenne & Thomas Braun & Johnny Kim & Mario Looso, 2020. "ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    6. Shelley L. Berger, 2007. "The complex language of chromatin regulation during transcription," Nature, Nature, vol. 447(7143), pages 407-412, May.
    7. Lun Zhao & Liang Xie & Qing Zhang & Weizhi Ouyang & Li Deng & Pengpeng Guan & Meng Ma & Yue Li & Ying Zhang & Qin Xiao & Jingwen Zhang & Hongmeijuan Li & Shunyao Wang & Jiangwei Man & Zhilin Cao & Qin, 2020. "Integrative analysis of reference epigenomes in 20 rice varieties," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    Full references (including those not matched with items on IDEAS)

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