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Long-range interactions between proximal and distal regulatory regions in maize

Author

Listed:
  • En Li

    (China Agricultural University)

  • Han Liu

    (China Agricultural University)

  • Liangliang Huang

    (China Agricultural University)

  • Xiangbo Zhang

    (China Agricultural University)

  • Xiaomei Dong

    (China Agricultural University)

  • Weibin Song

    (China Agricultural University)

  • Haiming Zhao

    (China Agricultural University)

  • Jinsheng Lai

    (China Agricultural University
    China Agricultural University)

Abstract

Long-range chromatin interactions are important for transcriptional regulation of genes, many of which are related to complex agronomics traits. However, the pattern of three-dimensional chromatin interactions remains unclear in plants. Here we report the generation of chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data and the construction of extensive H3K4me3- and H3K27ac-centered chromatin interaction maps in maize. Results show that the interacting patterns between proximal and distal regulatory regions of genes are highly complex and dynamic. Genes with chromatin interactions have higher expression levels than those without interactions. Genes with proximal-proximal interactions prefer to be transcriptionally coordinated. Tissue-specific proximal–distal interactions are associated with tissue-specific expression of genes. Interactions between proximal and distal regulatory regions further interweave into organized network communities that are enriched in specific biological functions. The high-resolution chromatin interaction maps will help to understand the transcription regulation of genes associated with complex agronomic traits of maize.

Suggested Citation

  • En Li & Han Liu & Liangliang Huang & Xiangbo Zhang & Xiaomei Dong & Weibin Song & Haiming Zhao & Jinsheng Lai, 2019. "Long-range interactions between proximal and distal regulatory regions in maize," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10603-4
    DOI: 10.1038/s41467-019-10603-4
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    Cited by:

    1. Victoria L. Sork & Shawn J. Cokus & Sorel T. Fitz-Gibbon & Aleksey V. Zimin & Daniela Puiu & Jesse A. Garcia & Paul F. Gugger & Claudia L. Henriquez & Ying Zhen & Kirk E. Lohmueller & Matteo Pellegrin, 2022. "High-quality genome and methylomes illustrate features underlying evolutionary success of oaks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Yi Liao & Juntao Wang & Zhangsheng Zhu & Yuanlong Liu & Jinfeng Chen & Yongfeng Zhou & Feng Liu & Jianjun Lei & Brandon S. Gaut & Bihao Cao & J. J. Emerson & Changming Chen, 2022. "The 3D architecture of the pepper genome and its relationship to function and evolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    3. Linhua Sun & Jingru Zhou & Xiao Xu & Yi Liu & Ni Ma & Yutong Liu & Wenchao Nie & Ling Zou & Xing Wang Deng & Hang He, 2024. "Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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