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Atypical RNAs in the coelacanth transcriptome.

Anne Nitsche1, Gero Doose, Hakim Tafer

  • 1Department of Computer Science, Bioinformatics Group, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
|November 1, 2013
PubMed
Summary
This summary is machine-generated.

Researchers discovered abundant circular and trans-spliced RNAs in coelacanth transcriptome data. These non-colinear RNA types, including thousands of novel junctions, significantly contribute to the transcriptome, with unique splice sites not found in typical RNA forms.

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Area of Science:

  • * Transcriptomics
  • * Molecular Biology
  • * Evolutionary Biology

Background:

  • * Circular RNAs (circRNAs) and trans-spliced RNAs are recognized as significant components of mammalian transcriptomes.
  • * Non-colinear RNA structures, including circRNAs and trans-spliced RNAs, have been identified in various species.

Purpose of the Study:

  • * To investigate the presence and abundance of circular and trans-spliced RNAs in coelacanth transcriptome data.
  • * To characterize the nature of these non-colinear RNA molecules in a deep-sea fish model.
  • * To compare the splice junctions of atypical RNAs with those of canonical RNA isoforms.

Main Methods:

  • * RNA sequencing (RNA-seq) was performed on different tissues from both African and Indonesian coelacanth species.
  • * Bioinformatic analysis was employed to identify and quantify circularized and trans-spliced RNA products.
  • * Comparative analysis of splice junctions was conducted between atypical and normal RNA isoforms.

Main Results:

  • * Thousands of circularized and trans-spliced RNA products were identified in coelacanth transcriptomes, alongside over 8,000 linear long non-coding RNAs (lincRNAs).
  • * These atypical RNA forms constitute a substantial portion of the overall transcriptome.
  • * A significant finding is that the majority of splice junctions involved in circularization and trans-splicing are unique to these non-colinear RNA types and are not utilized in standard RNA isoforms.

Conclusions:

  • * Coelacanths possess a rich repertoire of circular and trans-spliced RNAs, highlighting the prevalence of these non-colinear RNA structures across vertebrate evolution.
  • * The substantial abundance and unique splice junction usage of atypical RNAs suggest specialized regulatory roles or origins.
  • * This study expands our understanding of transcriptome complexity beyond canonical RNA species, particularly in ancient fish lineages.