Profiling of chromatin accessibility and regulatory elements toward understanding the mechanisms underlying growth regulation in the Pacific oyster (Crassostrea gigas)

Abstract

Changes in phenotype are precisely controlled by transcriptional regulators, which depend on chromatin remodeling. Although artificial genetic breeding has significantly improved the growth performance of the Pacific oyster (Crassostrea gigas), the identification of gene regulatory elements and transcription factors related to growth is obscure. In this study, we performed a genome-wide characterization of chromatin accessibility using two strains of C. gigas that exhibit significant differences in growth. The results showed that accessible chromatin regions were mainly distributed in the noncoding regions of the genome, with a greater proportion of distal intergenic regions than that of promoters and introns. A total of 2044 differentially accessible regions and 2574 differentially expressed genes were identified through comparative analysis. Genes annotated from regions with differential chromatin accessibility were enriched in cell adhesion molecules, JAK-STAT, insulin resistance, HIF-1α, and platelet activation signaling pathways. Correlation analysis of ATAC-seq and RNA-seq data showed that differential gene expression was positively correlated with differential chromatin accessibility. Furthermore, motif screening and identification of accessible chromatin regions revealed a set of transcription factors, including LHX3, TCF7L2, and LEF1, that may play important roles in the growth of C. gigas. Integrated analysis with public Hi-C datasets allowed the identification of a differential peak located 47 kb upstream of angiopoietin-2, which may act as a potential enhancer that affects the growth of C. gigas. In summary, our work contributes to a better understanding of growth-related regulation in C. gigas and provides valuable information for deciphering the economic traits underlying growth, which is conducive to the development of the breeding industry of C. gigas in the future.