Changes in gene expression levels caused by H3K9me3/H3K9ac modifications are associated with BmCPV infection in Bombyx mori.

Changes in chromatin accessibility caused by histone modifications regulate gene transcription. However, little is known about associations between gene expression changes caused by histone modifications and viral infections. We investigate the midguts of silkworms infected with Bombyx mori cypovirus (BmCPV) at 48 h and 96 h post infection (CPV48 and CPV96), and corresponding midguts of uninfected silkworms (GUT48 and GUT96) using CUT&Tag-seq and RNA-seq. We report H3K9me3, H3K9ac, and gene expression profiles at the genome-wide level to change with BmCPV infection. Differential H3K9me3 peak-related genes were mainly enriched in MAPK, Wnt, and Hippo signalling pathways; Differential H3K9ac peaks-related genes were mainly enriched in the Hippo signalling, apoptosis, and citrate cycle pathways; and differentially expressed genes (DEGs) were mainly enriched in carbon metabolism, protein processing in endoplasmic reticulum, and glycolysis/gluconeogenesis pathways. Integration analysis between H3K9me3/H3K9ac peaks and gene expression revealed changes in gene expression profiles to be associated with alteration of H3K9me3/H3K9ac at promoters; gene expression correlates negatively with corresponding H3K9me3 signals in gene bodies, and positively with corresponding H3K9ac signals at the transcription start site. Intersection genes with log₂foldchange of both CUT&Tag-seq peak and RNA-seq FPKM > 1 were screened and annotated. Genes shared by differential H3K9me3 peak-related genes and DEGs were enriched in insect hormone biosynthesis, MAPK signalling, and TGF-beta signalling pathways, and genes shared by differential H3K9ac peak-related genes and DEGs were enriched in glycolysis/gluconeogenesis, TGF-beta signalling, and mitophagy pathways. These results indicate that BmCPV regulates gene expression through H3K9me3/H3K9ac.