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Area of Science:

  • Plant Biology
  • Molecular Biology
  • Genetics

Background:

  • Phosphorus is vital for plant growth, and plants adapt to low inorganic phosphate (Pi) availability by regulating gene expression.
  • RNA decay is a critical process in mRNA metabolism, alongside transcriptional regulation.
  • The roles of RNA modifications like N-methyladenosine (m6A) and N5-methylcytosine (m5C), and poly(A) tail length in mRNA decay under Pi stress were unclear.

Purpose of the Study:

  • To investigate the influence of RNA decay on mRNA stability in rice under varying phosphate conditions.
  • To determine the involvement of m6A and m5C modifications and poly(A) tails in regulating mRNA decay.
  • To elucidate how phosphate starvation remodels these factors to control gene expression.

Main Methods:

  • Development of a genome-wide mRNA decay assay in rice.
  • Utilizing Nanopore Direct RNA sequencing for precise detection of RNA modifications and poly(A) tails.
  • Analysis of gene expression changes in response to phosphate starvation, including phosphate-starvation-induced (PSI) and phosphate-starvation-downregulated (PSD) genes.

Main Results:

  • mRNA decay rates are influenced by 5' UTR G/C content, CDS G/C content and secondary structures, 3' UTR m6A and m5C modifications, intron number, and poly(A) tail length.
  • PSI and PSD genes exhibit faster decay than non-responsive genes, linked to higher CDS G/C content, fewer introns, and lower m6A rates.
  • Pi starvation accelerates PSI gene decay and slows PSD gene decay, with m6A modification and poly(A) tail length being central regulators, more so than m5C.
  • Overexpression of OsYTH10 enhanced Pi accumulation by protecting m6A-modified transcripts (OsPT2, OsPAP21b) from degradation.

Conclusions:

  • Phosphate starvation dynamically regulates mRNA stability in rice through modulation of m6A methylation and poly(A) tail length.
  • These regulatory mechanisms are crucial for adapting gene expression landscapes to nutrient availability.
  • Targeting RNA decay pathways, particularly m6A modification, presents a potential strategy for improving Pi uptake and utilization in crops.