PUBLICATION
Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio).
- Authors
- Renaud, L., da Silveira, W.A., Glen, W.B., Hazard, E.S., and, Hardiman, G.
- ID
- ZDB-PUB-181103-3
- Date
- 2018
- Source
- Current genomics 19: 615-629 (Journal)
- Registered Authors
- Keywords
- Bioinformatics, Homeostasis, MicroRNAs, Non-coding RNAs, Systems level analysis, Zebrafish, mRNAs
- Datasets
- GEO:GSE108437, GEO:GSE108436, GEO:GSE108435
- MeSH Terms
- none
- PubMed
- 30386173 Full text @ Curr. Genomics
Citation
Renaud, L., da Silveira, W.A., Glen, W.B., Hazard, E.S., and, Hardiman, G. (2018) Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio).. Current genomics. 19:615-629.
Abstract
Background Cellular homeostasis is regulated by the intricate interplay between a plethora of signaling pathways and "energetic sensors" in organs. In order to maintain energy balance, induction or repression of metabolic pathways must be regulated and act in concert with the energetic demands of the cell at a given point in time. A new class of small noncoding RNAs, the microRNAs (miRNAs), has added yet further complexity to the control of metabolic homeostasis.
Objective Understanding the damages induced by toxins in the liver and the intestine as well as the interplay between the miRNome and transcriptome first requires baseline characterization in these tissues in healthy animals under cellular homeostasis.
Methods The liver (main site for detoxification) and the gut (primary exposure routes for contaminant exposure) were dissected out (wildtype fish), total and small RNA extracted, mRNA and miRNA libraries constructed and subjected to high throughput sequencing. Differential Expression (DE) analysis was performed comparing liver with gut and an "miRNA matrix" that integrates the miRNA-seq and mRNA-seq data was constructed.
Results Both the miRNome and transcriptome of the liver and gut tissues were characterized and putative novel miRNAs were identified. Exploration of the "miRNA matrix" regulatory network revealed that miRNAs uniquely expressed in the liver or gut tissue regulated fundamental cellular processes important for both organs, and that commonly expressed miRNAs in both tissues regulated biological processes that were specific to either the liver or the gut.
Conclusion The result of our analyses revealed new insights into microRNA function in these tissues.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping