De novo profiling of long non-coding RNAs involved in MC-LR–induced liver injury in whitefish: discovery and perspectives
| Autor: | Maciej Woźny, Maciej Florczyk, Paweł Brzuzan |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Untranslated region
de novo HULC Microcystins ceRNAs lncRNAs autonomous 3′UTRs Computational biology Biology Genome Catalysis Article lcsh:Chemistry Inorganic Chemistry Transcriptome Fish Diseases Animals RNA Messenger Physical and Theoretical Chemistry MALAT1 lcsh:QH301-705.5 Molecular Biology Spectroscopy Competing endogenous RNA Sequence Analysis RNA Organic Chemistry RNA HOTAIR Molecular Sequence Annotation General Medicine Computer Science Applications MicroRNAs lcsh:Biology (General) lcsh:QD1-999 Liver Chemical and Drug Induced Liver Injury Chronic non-coding RNAs biomarker Marine Toxins RNA Long Noncoding liver transcriptome drug-induced liver injury Salmonidae |
| Zdroj: | International Journal of Molecular Sciences International Journal of Molecular Sciences, Vol 22, Iss 941, p 941 (2021) Volume 22 Issue 2 |
| DOI: | 10.21203/rs.3.rs-62335/v1 |
| Popis: | Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, our knowledge concerning the role of lncRNAs in liver injury is limited. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq) data, we de novo assembled a high-quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC, and 4429 DE putative novel whitefish lncRNAs, which differed from annotated protein-coding transcripts (PCTs) in terms of minimum free energy, guanine-cytosine (GC) base-pair content and length. Additionally, we identified DE non-coding transcripts that might be 3&prime autonomous untranslated regions (3&prime UTRs) of mRNAs. We found both evolutionary conserved lncRNAs as well as novel whitefish lncRNAs that could serve as biomarkers of liver injury. |
| Databáze: | OpenAIRE |
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