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.

组蛋白修饰引发的染色质可及性改变可调控基因转录。然而，针对组蛋白修饰介导的基因表达变化与病毒感染之间的关联，目前仍知之甚少。本研究以感染家蚕胞质型多角体病毒（Bombyx mori cypovirus，BmCPV）后48小时、96小时的家蚕中肠（分别记为CPV48、CPV96），以及同期未感染的家蚕中肠（分别记为GUT48、GUT96）为研究对象，采用CUT&Tag测序（CUT&Tag-seq）与RNA测序（RNA-seq）技术开展分析。我们在全基因组水平上解析了H3K9me3、H3K9ac及基因表达谱随BmCPV感染发生的动态变化。差异H3K9me3峰相关基因主要富集于丝裂原活化蛋白激酶（Mitogen-Activated Protein Kinase，MAPK）、Wnt及Hippo信号通路；差异H3K9ac峰相关基因主要富集于Hippo信号通路、细胞凋亡及三羧酸循环通路；差异表达基因（differentially expressed genes，DEGs）则主要富集于碳代谢、内质网蛋白质加工及糖酵解/糖异生通路。对H3K9me3/H3K9ac峰与基因表达的整合分析显示，基因表达谱的变化与启动子区域H3K9me3/H3K9ac的改变密切相关；基因本体区的H3K9me3信号与对应基因表达呈负相关，而转录起始位点处的H3K9ac信号则与基因表达呈正相关。我们筛选得到CUT&Tag-seq峰与RNA-seq的每百万片段数每千碱基（Fragments Per Kilobase of transcript per Million mapped reads，FPKM）的log₂倍数变化均大于1的交集基因并进行注释。差异H3K9me3峰相关基因与DEGs的共有基因富集于昆虫激素生物合成、MAPK信号通路及转化生长因子β（Transforming Growth Factor-beta，TGF-β）信号通路；差异H3K9ac峰相关基因与DEGs的共有基因则富集于糖酵解/糖异生、TGF-β信号通路及线粒体自噬通路。上述结果表明，BmCPV可通过调控H3K9me3与H3K9ac的修饰水平来介导基因表达的改变。