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Different Plant Species Have Common Sequence Features Related to mRNA Degradation Intermediates

Daishin Ueno1, Takafumi Mukuta1, Shotaro Yamasaki1

  • 1Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 Japan.

Plant & Cell Physiology
|September 11, 2019
PubMed

Insights

mRNA degradation is crucial for gene expression control. New research confirms G-rich sequences at the 5' ends of mRNA degradation intermediates across diverse plant species, revealing conserved mechanisms.

Area of Science:

  • Molecular Biology
  • Plant Science
  • Genetics

Background:

  • mRNA degradation is a key regulator of gene expression in eukaryotes.
  • Existing methods for profiling mRNA degradation often exhibit 3'-end bias due to reliance on poly (A) selection.
  • The Truncated RNA End Sequencing (TREseq) method was previously developed to overcome 3'-end bias and identify 5'-end features of degradation intermediates.

Purpose of the Study:

  • To validate the presence of G-rich sequences near the 5'-ends of mRNA degradation intermediates in diverse plant species.
  • To investigate the conservation of mRNA degradation mechanisms across different angiosperms.
  • To assess the involvement of the translation process in mRNA decay pathways.

Main Methods:

  • Application of the Truncated RNA End Sequencing (TREseq) method to analyze mRNA degradation intermediates.
  • Comparative genomic analyses across four diverse plant species: Arabidopsis thaliana, Lactuca sativa (lettuce), Oryza sativa (rice), and Rosa hybrida (rose).
  • Bioinformatic analysis to identify sequence features and functional associations of degradation intermediates.

Main Results:

  • TREseq analysis confirmed the presence of G-rich sequences near the 5'-ends of mRNA degradation intermediates in all four studied plant species.
  • Evidence suggests the involvement of the translation process in mRNA degradation across these species.
  • Homologous genes exhibited similar mRNA degradation efficiencies, indicating conserved mechanisms.

Conclusions:

  • The 5'-end G-rich sequence feature in mRNA degradation intermediates is conserved across diverse angiosperm species.
  • mRNA degradation pathways, including the involvement of translation, are conserved in plants.
  • TREseq is a valuable tool for unbiased analysis of mRNA degradation and its regulatory features.
Keywords:
Degradome sequencingPlant mRNAmRNA degradation

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