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Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and
Magdalena Winklhofer1,2, Göran Erik Nilsson1, Sjannie Lefevre1
1Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
RNA Biology
|March 10, 2026
Summary
Long non-coding RNAs (lncRNAs) were identified in crucian carp brain during oxygen deprivation. These lncRNAs show potential cis-regulatory roles in the adaptive transcriptomic response to anoxia and reoxygenation.
Area of Science:
- Molecular Biology
- Genomics
- Transcriptomics
Background:
- Long non-coding RNAs (lncRNAs) are crucial regulators of cellular processes.
- Crucian carp exhibit remarkable tolerance to prolonged anoxia (oxygen deprivation).
- The role of lncRNAs in crucian carp's anoxic adaptation is largely unknown.
Purpose of the Study:
- To annotate lncRNAs in crucian carp.
- To investigate lncRNA involvement in transcriptomic changes during anoxia and reoxygenation.
- To characterize differentially expressed lncRNAs and their interaction partners.
Main Methods:
- Reference-guided assembly of RNA sequencing data from crucian carp brain under normoxia, anoxia, and reoxygenation.
- Identification of lncRNAs using multiple computational tools (CPC2, CNCI, CPAT, FEELnc).
- Differential expression analysis of transcripts and lncRNAs, and prediction of cis-acting interactions.
Main Results:
- 6072 lncRNAs were identified in the crucian carp brain.
- Anoxia triggered a significant transcriptomic response, with 1321 differentially expressed lncRNAs.
- Co-expression analysis revealed positive correlations between differentially expressed lncRNAs and their predicted interaction partners, suggesting cis-regulatory roles.
Conclusions:
- This study provides a comprehensive lncRNA annotation for crucian carp.
- lncRNAs are extensively co-expressed with nearby genes during anoxia and reoxygenation.
- lncRNAs likely play a cis-regulatory role in crucian carp's adaptive response to oxygen deprivation.
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