N-alpha-acetyltransferase 40 modulates ecdysteroid action through chromatin accessibility changes near the promoters of 20-hydroxyecdysone response genes in Tribolium Castaneum TcA cells

Changes in chromatin accessibility leading to altered gene expression play critical roles in cellular response to environmental signals. The function of N-alpha-acetyltransferase 40 (NAA40) in modulating chromatin accessibility and transcriptional regulation of 20-hydroxyecdysone (20E) response in Tribolium castaneum (TcA) cells was investigated. RNA interference (RNAi) was used to knockdown NAA40, and ATAC and RNA sequencing were used to examine changes in chromatin accessibility and gene expression in TcA cells exposed to 20E. ATAC-seq data revealed chromatin accessibility patterns between NAA40 knockdown and control cells exposed to 20E. Significant differences were detected in chromatin accessibility at transcription start sites (TSS) and promoter regions between dsNAA40 or dsGFP-treated cells exposed to 20E. Differential peak analysis identified many regions in the genome with altered chromatin accessibility upon NAA40 knockdown or 20E treatment, suggesting that NAA40 plays a critical role in 20E regulation of gene expression by modifying chromatin accessibility near the promoters of genes involved in 20E action. RNA sequence data analysis revealed changes in the expression of 20E response genes after NAA40 knockdown or 20E treatment. Comparison of ATAC-seq and RNA-seq data showed a correlation between chromatin accessibility and transcriptional changes of 20E response genes such as E74 and E75. Our results demonstrate that NAA40 affects chromatin dynamics and transcriptional regulation in modulating 20E response, increasing our understanding of the molecular mechanisms underlying the hormonal regulation of gene expression.