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Archaea express circular isoforms of IS200/IS605-associated ωRNAs.

Beatriz A Picinato1, Vinícius H Franceschini-Santos1, Lívia S Zaramela1

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Circular RNAs (circRNAs) are abundant in archaea, with novel circular ωRNAs linked to mobile elements. This study developed a computational pipeline, MonArch, to identify these circRNAs in archaeal RNA-Seq data.

Keywords:
IS200/IS605RNA-SeqarchaeacircRNArRNAtRNAωRNA

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Area of Science:

  • * Molecular Biology
  • * Genomics
  • * Bioinformatics

Background:

  • * Circular RNAs (circRNAs) are RNA molecules with ligated ends, known for regulatory roles in eukaryotes.
  • * circRNAs are understudied in prokaryotes, with limited identification in archaea.
  • * Previous studies primarily used eukaryotic-specific methods for circRNA identification.

Purpose of the Study:

  • * To develop a prokaryotic-specific computational pipeline (MonArch) for circRNA identification.
  • * To identify and characterize circRNAs in the archaeon *Halobacterium salinarum*.
  • * To investigate the prevalence and characteristics of circRNAs across diverse archaeal species.

Main Methods:

  • * Development of the MonArch computational pipeline for prokaryotic circRNA detection from RNA-Seq data.
  • * Application of MonArch to *Halobacterium salinarum* circRNA-Seq data and reanalysis of over 20 public archaeal RNA-Seq datasets.
  • * Validation of identified circRNAs using RT-PCR.

Main Results:

  • * Identification of 49 high-confidence circRNAs in *H. salinarum*, including novel circRNAs associated with ωRNAs and IS200/IS605 transposases.
  • * Discovery of growth-dependent expression patterns for circular ωRNAs, distinct from total ωRNAs.
  • * Detection of widespread circRNAs associated with rRNA and tRNA processing across major archaeal groups, indicating conserved mechanisms.
  • * Identification of circular ωRNAs in other haloarchaeal species, suggesting a conserved role in the IS200/IS605 system.

Conclusions:

  • * circRNAs are conserved and abundant in archaea, exceeding previous estimations.
  • * The MonArch pipeline effectively identifies prokaryotic circRNAs.
  • * Circular ωRNAs represent a novel class of archaeal circRNAs with potential roles in mobile element systems and conditional expression.