Comparative transcriptomic and epigenomic analyses to identify the cold resistance-associated genes and disclose the regulatory mechanisms in tilapias

Dissecting the genetic basis of cold resistance in fish has great theoretic and economic significance. Despite large numbers of cold-responsive genes have been identified from the tilapia tissues, the core cold resistance-associated genes (CRAGs) and their regulatory mechanisms remain to be explored. In this study, the blue tilapia (BT, Oreochromis aureus) and Nile tilapia (NT, O. niloticus) were exposed to a gradually intensified cold stress. Brain samples were collected from the fish during cold exposure and subjected to total RNA isolation. Isoform sequencing was performed using the pooled total RNA samples of each species to improve the transcriptome assemblies. Gene expression profiles upon cold exposure was characterized by RNA sequencing (RNA-seq). The core CRAGs were identified by a comparative analysis for the transcriptomic data represented here and that of zebrafish (Danio rerio) in one previous study. A total of 513 core CRAGs were identified, which demonstrated consistent cold-induced expression among BT, NT and zebrafish. The genes underwent cold-induced alternative splicing at each time point were also identified and compared with the corresponding differentially expressed genes. The samples matched to those for RNA-seq were subjected to assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to profile the chromatin accessibility dynamics. The genes associated with at least one open chromatin region (OCR) had significantly higher transcriptional abundance than those without an OCR. ATF3, FOS::JUN dimer and JDP2 were among the top transcription factors (TFs) that may play crucial roles in regulating the cold-elicited transcriptional responses. Furthermore, the genetic variations between BT and NT were mined from the RNA-seq and ATAC-seq reads and mapped to the TF binding sites and splicing regions. The function of a G/A variant in regulating the cold-induced alternative splicing of the dennd5a genes was confirmed by a minigene splicing assay. Our data provide new insights into the genetic mechanisms determining cold resistance of tilapias and are meaningful for the breeding of cold-tolerant tilapia varieties.