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The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

Author

Listed:
  • Mary Galli

    (Rutgers University)

  • Arjun Khakhar

    (University of Washington)

  • Zefu Lu

    (The University of Georgia)

  • Zongliang Chen

    (Rutgers University)

  • Sidharth Sen

    (University of Missouri)

  • Trupti Joshi

    (University of Missouri
    University of Missouri)

  • Jennifer L. Nemhauser

    (University of Washington)

  • Robert J. Schmitz

    (The University of Georgia)

  • Andrea Gallavotti

    (Rutgers University
    Rutgers University)

Abstract

AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes. We use DAP-seq to generate genome-wide in vitro TF:DNA interaction maps for fourteen maize ARFs from the evolutionarily conserved A and B clades. Comparative analysis reveal a high degree of binding site overlap for ARFs of the same clade, but largely distinct clade A and B binding. Many sites are however co-occupied by ARFs from both clades, suggesting transcriptional coordination for many genes. Among these, we investigate known QTLs and use machine learning to predict the impact of cis-regulatory variation. Overall, large-scale comparative analysis of ARF binding suggests that auxin response specificity may be determined by factors other than individual ARF binding site selection.

Suggested Citation

  • Mary Galli & Arjun Khakhar & Zefu Lu & Zongliang Chen & Sidharth Sen & Trupti Joshi & Jennifer L. Nemhauser & Robert J. Schmitz & Andrea Gallavotti, 2018. "The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06977-6
    DOI: 10.1038/s41467-018-06977-6
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    Cited by:

    1. Yue Yuan & Qiang Huo & Ziru Zhang & Qun Wang & Juanxia Wang & Shuaikang Chang & Peng Cai & Karen M. Song & David W. Galbraith & Weixiao Zhang & Long Huang & Rentao Song & Zeyang Ma, 2024. "Decoding the gene regulatory network of endosperm differentiation in maize," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    2. Liang-Yu Fu & Tao Zhu & Xinkai Zhou & Ranran Yu & Zhaohui He & Peijing Zhang & Zhigui Wu & Ming Chen & Kerstin Kaufmann & Dijun Chen, 2022. "ChIP-Hub provides an integrative platform for exploring plant regulome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Cunmin Qu & Meichen Zhu & Ran Hu & Yongchao Niu & Si Chen & Huiyan Zhao & Chengxiang Li & Zhen Wang & Nengwen Yin & Fujun Sun & Zhiyou Chen & Shulin Shen & Guoxia Shang & Yan Zhou & Xingying Yan & Lij, 2023. "Comparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Dawei Dai & Janaki S. Mudunkothge & Mary Galli & Si Nian Char & Ruth Davenport & Xiaojin Zhou & Jeffery L. Gustin & Gertraud Spielbauer & Junya Zhang & W. Brad Barbazuk & Bing Yang & Andrea Gallavotti, 2022. "Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Haihai Wang & Yongcai Huang & Yujie Li & Yahui Cui & Xiaoli Xiang & Yidong Zhu & Qiong Wang & Xiaoqing Wang & Guangjin Ma & Qiao Xiao & Xing Huang & Xiaoyan Gao & Jiechen Wang & Xiaoduo Lu & Brian A. , 2024. "An ARF gene mutation creates flint kernel architecture in dent maize," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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