Genome-wide methylome and transcriptome dynamics provide insights into epigenetic regulation of kidney functioning of large yellow croaker (Larimichthys crocea) during low-salinity adaption

Abstract

Owing to extreme precipitation and surface runoff, low-salinity stress has become a severe environmental concern restricting inshore cultivation of large yellow croaker (Larimichthys crocea). Thus, illuminating adaptive mechanisms and cultivating new varieties with higher adaptability is essential for ensuring future cultivation success. DNA methylation can affect adaptability by regulating gene expression; however, little is known about the regulation mechanism of DNA methylation in marine fish facing low-salinity stress. Thus, we systematically explored the methylation landscape in the kidney and the potential regulation mechanism under low-salinity stress. Compared to the controls (25‰ salinity), expression of renal DNA transmethylase genes (dnmt1, dnmt3bb) and demethylase genes (tet1, tet2 and tet3) was notably up-regulated, and the global genome DNA methylation level in kidney was increased in the low-salinity treatment (5‰ salinity). Transcriptome analysis identified 316 differentially expressed genes, and 3827 differentially methylated promoters were identified through whole genome bisulfite sequencing. Integrative analyses produced 41 differentially methylated genes (DMGs), the expression of which was negatively correlated with promoter methylation. These DMGs were significantly enriched with respect to ion exchange, energy metabolism, cytoskeleton system, signal transduction, and other biological processes. The present study provides new insights for understanding renal epigenetic regulation mechanism and the selection of potential DNA methylation markers correlated with low-salinity adaption, which is crucial for future selection of new varieties of large yellow croaker with better low-salinity adaptability.