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<p>Abiotic stress significantly impacts plant productivity, leading to complex responses that involve various physiological, biochemical, and transcriptional mechanisms. Nuclear transcription factor Y emerges as a crucial candidate gene in managing these stress responses. Although several NF-Y genes have been identified in <i>Arabidopsis thaliana, Oryza sativa, Cicer arietinum</i> and <i>Sorghum bicolor</i>, comprehensive investigations remain limited. Therefore, genome-wide exploration of NF-Y gene members across four genera led to identification of thirty-six <i>AtNF-Ys</i>, thirty-four <i>OsNF-Ys</i>, forty <i>CaNF-Ys</i> and forty-two <i>SbNF-Ys</i>. Protein structure analysis of NF-YA subunits revealed the conserved CCAAT-binding factor domain across four genera, responsible for binding to the CCAAT-box within eukaryotic promoters. Additionally, the NF-YB and NF-YC sub-families exhibited conserved histone fold domains, serving as a structural scaffold facilitating NF-Ys trimerization. Cis-Acting Regulatory Elements identified in <i>OsNF-Ys</i> were found to be associated with either stress or hormone responsiveness. Meta-analysis revealed that NF-Y genes responded variably in different environmental stress consistent with the qRT-PCR experiments that were meticulously performed at seedling and tillering developmental stages, revealing significant upregulation of <i>OsNF-YA1, A4, A7, C1</i> and <i>C4</i> in response to drought and salinity across different time points in shoot and root tissues. Eventually, we investigated potential miRNAs targeting NF-Y genes to elucidate the plausible mechanism in <i>O. sativa</i>. <i>Osa-miR169a</i> was found to target 3′ UTR of <i>OsNF-YA1, OsNF-YA4</i> and <i>OsNF-YA10</i> while <i>Osa-miR2919</i> was found to target 3′ UTR of <i>OsNF-YC1</i> and <i>Osa-miR5075</i> was found to target 3′ UTR of <i>OsNF-YC4</i>. Exploring these interactions offered valuable insights into the molecular mechanisms of NF-Ys governing stress responses in plants.</p>

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Genome-wide analysis of NF-Y genes and assessing their potential as miRNA targets in rice

  • 期刊论文

  • 发表日期：

    2026年4月9日

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  • Arushi Jain,
  • Mujibur Rehman,
  • R. Rakhi,
  • Nazmir Binta Alam,
  • Ananda Mustafiz

摘要

Abiotic stress significantly impacts plant productivity, leading to complex responses that involve various physiological, biochemical, and transcriptional mechanisms. Nuclear transcription factor Y emerges as a crucial candidate gene in managing these stress responses. Although several NF-Y genes have been identified in Arabidopsis thaliana, Oryza sativa, Cicer arietinum and Sorghum bicolor, comprehensive investigations remain limited. Therefore, genome-wide exploration of NF-Y gene members across four genera led to identification of thirty-six AtNF-Ys, thirty-four OsNF-Ys, forty CaNF-Ys and forty-two SbNF-Ys. Protein structure analysis of NF-YA subunits revealed the conserved CCAAT-binding factor domain across four genera, responsible for binding to the CCAAT-box within eukaryotic promoters. Additionally, the NF-YB and NF-YC sub-families exhibited conserved histone fold domains, serving as a structural scaffold facilitating NF-Ys trimerization. Cis-Acting Regulatory Elements identified in OsNF-Ys were found to be associated with either stress or hormone responsiveness. Meta-analysis revealed that NF-Y genes responded variably in different environmental stress consistent with the qRT-PCR experiments that were meticulously performed at seedling and tillering developmental stages, revealing significant upregulation of OsNF-YA1, A4, A7, C1 and C4 in response to drought and salinity across different time points in shoot and root tissues. Eventually, we investigated potential miRNAs targeting NF-Y genes to elucidate the plausible mechanism in O. sativa. Osa-miR169a was found to target 3′ UTR of OsNF-YA1, OsNF-YA4 and OsNF-YA10 while Osa-miR2919 was found to target 3′ UTR of OsNF-YC1 and Osa-miR5075 was found to target 3′ UTR of OsNF-YC4. Exploring these interactions offered valuable insights into the molecular mechanisms of NF-Ys governing stress responses in plants.