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Detection of Alternative Splicing During Epithelial-Mesenchymal Transition
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Evolution of Alternative Splicing in Eudicots.

Zhihao Ling1, Thomas Brockmöller1, Ian T Baldwin1

  • 1Max Planck Institute for Chemical Ecology, Jena, Germany.

Frontiers in Plant Science
|June 28, 2019
PubMed
Summary

Alternative splicing (AS) in plants evolves through gene gains/losses and conserved PTC-containing transcripts, suggesting a role for nonsense-mediated decay. Key splice site features drive AS mechanisms and divergence.

Keywords:
alternative splicingdeep learningevolutionnonsense-mediated decaysplicing codetranscriptome

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Area of Science:

  • Plant molecular biology
  • Evolutionary genomics
  • Transcriptomics

Background:

  • Alternative pre-mRNA splicing (AS) is crucial for plant responses to environmental stresses.
  • Understanding the evolutionary patterns and mechanisms of AS in plants is essential but remains unclear.

Purpose of the Study:

  • To investigate the evolutionary divergence of alternative splicing (AS) in plants.
  • To identify the key determinants and conserved mechanisms of AS evolution.

Main Methods:

  • Comparative transcriptome analysis of four eudicot species.
  • Machine learning approach to identify key determinants of AS.
  • Analysis of AS events, including those generating premature termination codons (PTC).

Main Results:

  • AS divergence is primarily driven by the gain and loss of AS events in orthologous genes.
  • AS events producing PTC-containing transcripts are more conserved than non-PTC ones, implicating nonsense-mediated decay (NMD).
  • Splice site features like presence/absence of alternative sites, distance to authentic sites, and exon-exon junction size are major determinants of AS, indicating conserved mechanisms.

Conclusions:

  • AS evolution in plants involves both gains/losses of events and conserved mechanisms.
  • Nonsense-mediated decay (NMD) likely plays a significant role in post-transcriptional regulation via conserved AS.
  • Variations in AS determinants contribute to divergence, particularly in closely related species like Solanaceae and Brassicaceae.