Long non-coding RNAs mediate fish gene expression in response to ocean acidification.

Area of Science:

• Marine Biology
• Genomics
• Environmental Science

Background:

• Non-coding transcripts, including long non-coding RNAs (lncRNAs), play vital regulatory roles in gene expression.
• Understanding lncRNA function is critical for predicting organismal responses to environmental changes like ocean acidification (OA).
• The specific roles of lncRNAs in fish facing OA remain largely unknown.

Purpose of the Study:

• To investigate the potential role of lncRNAs in fish brain responses to ocean acidification (OA).
• To identify and characterize lncRNAs, particularly intergenic lncRNAs (lincRNAs), in the coral reef fish Acanthochromis polyacanthus exposed to elevated CO₂.

Main Methods:

• Analysis of publicly available brain RNA-sequencing data from A. polyacanthus.
• Genome-wide annotation of lncRNAs and examination of differential expression of lincRNAs between fish from a natural CO₂ seep and a control site.
• Identification of species-specific lincRNAs and analysis of their potential regulatory relationships with protein-coding genes.

Main Results:

• 4728 lncRNAs, including 3272 lincRNAs, were identified; 93.03% of lincRNAs were species-specific.
• 125 highly expressed and 403 differentially expressed lincRNAs were found in response to elevated CO₂.
• Differentially expressed lincRNAs were associated with protein-coding genes involved in pH regulation, neural signal transduction, and ion transport.

Conclusions:

• lncRNAs likely play a significant role in mediating fish responses to ocean acidification (OA).
• These lncRNAs may facilitate fish acclimation to OA by modulating the expression of critical coding genes.
• This study provides insights into the regulatory mechanisms underlying fish adaptation to environmental change.