Brain transcriptomic response of threespine sticklebacks to cues of a predator

Abstract

Predation pressure represents a strong selective force that influences the development and evolution of living organisms. An increasing number of studies have shown that both environmental and social factors, including exposure to predators, substantially shape the structure and function of the brain. However, our knowledge about the molecular mechanisms underlying the response of the brain to environmental stimuli is limited. In this study, we used whole-genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to cues of a predator in the threespine stickleback, Gasterosteus aculeatus. We found that repeated exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorrhynchus mykiss) for 6 days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to cues of a predator and the control group were related to antigen processing and presentation involving the major histocompatibility complex, transmission of synaptic signals, brain metabolic processes, gene regulation and visual perception. The top four identified pathways were synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction. Our study demonstrates that exposure of sticklebacks to cues of a predator results in the activation of a wide range of biological and molecular processes and lays the foundation for future investigations on the molecular factors that modulate the function and evolution of the brain in response to stressors.

Fig. 1.

Methods used in preprocessing and quality control of the arrays. a Histogram of standard deviations. Genes with very low standard deviations are more likely not to be differentially expressed and were removed from the data. The dotted line represents the peak of the distribution (shorth value). b Hierarchical clustering of the samples (arrays). Control group: CON_1–5; experimental group: EXP_1–EXP_5. c Principal components plots used as dimension reduction of the samples (arrays). d Volcano plot highlighting the top 30 differentially expressed genes (★) between sticklebacks exposed to predator cues and the control group.

Fig. 2.

Heat map of top 30 differentially expressed genes between control (CON_1–5) and experimental (EXP_1–5) group with gene names. The Z-score represents the number of standard deviation units a specific gene expression value is from the mean (defined as 0). Red color in the heat map indicates upregulated genes, in blue are downregulated genes and in white are genes that do not change between conditions. Color-coded bars represent the clustering of samples per treatment (horizontal bar) and clusters of differentially expressed genes (vertical bar).

Fig. 3.

qPCR validation of microarray gene expression in the brains of sticklebacks exposed to predator cues. The microarray results are plotted next to the qPCR results for the samples used in the microarray (n = 7 experimental and n = 7 control), and the qPCR results for the independent biological replicates not on the array (n = 2 experimental and n = 2 control).