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<p><i>Brachypodium distachyon</i> is a model plant for studying temperate grass cereals. Although the transcriptome of plant callus formation-related genes has been extensively studied, information on their regulation is largely unavailable. We conducted assays of callus morphology, the transcriptome, and open chromatin in seeds whose endosperm was removed (sheared seeds), revealing a significant improvement in callus formation. Genome-wide assays of DNase I-hypersensitive sites (DHSs) demonstrated that their landscapes were not substantially disturbed in the sheared seeds. By comparison, 256 and 422 sheared seed-specific DHSs were identified from the early (2d) and late (8d) stages of callus formation, respectively. Twenty-one and 43 binding motifs of transcription factors (TFs) were predicted by mining these sheared seed-specific DHSs. Functional annotation revealed that these TFs were well known to be involved in jasmonic acid, gibberellic acid, and abscisic acid signaling pathways, highlighting the potential roles of these hormones in promoting callus formation in <i>B. distachyon</i>. Transcriptional regulatory networks were developed by interaction assays on these TFs. Six TFs (MYC3, LRL1, BBM, RGA1, IDD2, and ABI5) showed strong causal connections, suggesting their possible roles in regulatory networks. Overall, we provided experimental annotations of 19,574 DHSs and 55 derived TF binding motifs related to callus formation in <i>B. distachyon</i>, which can serve as a valuable resource for elucidating the transcriptional networks that function in callus formation and other physiological processes.</p>

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Genome-wide identification of cis-regulatory elements and transcription factors associated with promoted callus formation in Brachypodium distachyon

  • 期刊论文

  • 发表日期：

    2025年1月22日

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  • Xin Zhang,
  • Yan Dai,
  • Qi Chen,
  • Xiaobing Kou,
  • Eid M. Mehareb,
  • Ghulam Raza,
  • Wei Wang,
  • Ruqin Zhou,
  • Robert Hasterok,
  • Jinlei Han,
  • Kai Wang

摘要

Brachypodium distachyon is a model plant for studying temperate grass cereals. Although the transcriptome of plant callus formation-related genes has been extensively studied, information on their regulation is largely unavailable. We conducted assays of callus morphology, the transcriptome, and open chromatin in seeds whose endosperm was removed (sheared seeds), revealing a significant improvement in callus formation. Genome-wide assays of DNase I-hypersensitive sites (DHSs) demonstrated that their landscapes were not substantially disturbed in the sheared seeds. By comparison, 256 and 422 sheared seed-specific DHSs were identified from the early (2d) and late (8d) stages of callus formation, respectively. Twenty-one and 43 binding motifs of transcription factors (TFs) were predicted by mining these sheared seed-specific DHSs. Functional annotation revealed that these TFs were well known to be involved in jasmonic acid, gibberellic acid, and abscisic acid signaling pathways, highlighting the potential roles of these hormones in promoting callus formation in B. distachyon. Transcriptional regulatory networks were developed by interaction assays on these TFs. Six TFs (MYC3, LRL1, BBM, RGA1, IDD2, and ABI5) showed strong causal connections, suggesting their possible roles in regulatory networks. Overall, we provided experimental annotations of 19,574 DHSs and 55 derived TF binding motifs related to callus formation in B. distachyon, which can serve as a valuable resource for elucidating the transcriptional networks that function in callus formation and other physiological processes.