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Structured 3' UTRs destabilize mRNAs in plants.

Tianru Zhang1,2, Changhao Li1, Jiaying Zhu3

  • 1Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Genome Biology
|February 23, 2024
PubMed
Summary
This summary is machine-generated.

Highly structured 3' untranslated regions (3' UTRs) reduce mRNA accumulation across species. Engineering RNA secondary structure in 3' UTRs offers a new strategy for modifying plant traits and mRNA stability.

Keywords:
3′ UTR3′ end target-specific DMS-MaPseqDIM-2P-seqRNA secondary structure (RSS)mRNA stability

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • RNA secondary structure (RSS) plays a crucial role in gene regulation, affecting transcription, RNA processing, and protein synthesis.
  • 3' untranslated regions (3' UTRs) of mRNA are key regulatory elements, but the role of RSS within them in gene expression remains debated across different organisms and contexts.

Purpose of the Study:

  • To investigate the impact of RNA secondary structure within 3' UTRs on mRNA accumulation and stability.
  • To explore the potential of engineering 3' UTR RSS for agricultural and biotechnological applications.

Main Methods:

  • Utilized pri-miR159a embedded in a 3' UTR to observe effects on mRNA accumulation.
  • Performed RNA decay assays and genome-wide DMS-MaPseq to analyze mRNA stability and RSS.
  • Investigated the role of specific exoribonucleases (SOV and XRN4) in degrading structured transcripts.
  • Engineered 3' UTR RSS in the FT gene to assess its effect on flowering time in Arabidopsis.

Main Results:

  • Poorly structured 3' UTRs promote mRNA stability and accumulation, while highly structured 3' UTRs destabilize mRNA in vivo.
  • A genome-wide inverse relationship between 3' UTR RSS and transcript accumulation was observed in Arabidopsis, rice, and human.
  • Highly structured 3' UTRs are preferentially degraded by 3'-5' exoribonuclease SOV and 5'-3' exoribonuclease XRN4, leading to reduced expression.
  • Engineering 3' UTR RSS in the FT gene altered FT-regulated flowering time in Arabidopsis.

Conclusions:

  • Highly structured 3' UTRs generally lead to reduced transcript accumulation in plants, a pattern also observed in rice and mammals.
  • Engineering 3' UTR RSS presents a novel strategy for modifying plant traits in agriculture and enhancing mRNA stability in biotechnology.