The epigenetic landscapes of histone modifications on HSV-1 genome in human THP-1 cells [ChIP-seq]

To study the dynamic changes of histone modifications across HSV-1 genome during lytic infection in THP-1 cells. Totally 20 maps of HSV-1 epigenome were generated at 5 different time points after infection, together with their corresponding gene expression profiles.We found that histone modifications were detected on HSV-1 genome soon after infection; all four studied modifications, H3K9me3, H3K27me3, H3K4me3 and H3K27ac, change rapidly along with virus life cycle progression.The transcription repression marks, H3K9me3 and H3K27me3, tended to decrease along with infection process, and the transcription activation mark H3K27ac increased on viral genome, which were aligned with increased expression of viral genes. Moreover, treatment with C646, an inhibitor for H3K27ac transferase p300, inhibited expression of viral genes; and EPZ6438, an inhibitor for H3K27 methyltransferase EZH2, enhanced viral gene expression. To study the distribution of histone modifications on HSV-1 genome during lytic stage, as well as their dynamic changes, we used HSV-1 (1×108 / 10 cm dish) to infect THP-1 cells, and collected samples at 1 hr, 2 hr, 4 hr, 8 hr and 24 hr after infection. The cells were then subjected to RNA-Seq and ChIP-Seq with antibodies recognizing H3K27ac, H3K4me3, H3K9me3 and H3K27me3. Two biological replications were performed for each sequencing and data quality control was done before analysis.本研究旨在探究THP-1细胞发生单纯疱疹病毒1型（HSV-1）裂解性感染期间，病毒基因组上组蛋白修饰的动态变化。本研究在感染后5个不同时间点共生成20组HSV-1表观基因组图谱，并同步获取了对应样本的基因表达谱数据。研究发现，感染后不久即可在HSV-1基因组上检测到组蛋白修饰；所研究的四种修饰——H3K9me3、H3K27me3、H3K4me3及H3K27ac——均随病毒生命周期推进快速发生改变。其中，转录抑制标记H3K9me3与H3K27me3随感染进程逐渐降低，而转录激活标记H3K27ac在病毒基因组上的水平则逐步升高，这一变化与病毒基因表达量的上调趋势一致。此外，使用H3K27乙酰转移酶p300的抑制剂C646处理细胞可抑制病毒基因的表达；而H3K27甲基转移酶EZH2的抑制剂EPZ6438则可增强病毒基因的表达。为研究裂解感染阶段HSV-1基因组上组蛋白修饰的分布特征及其动态变化，本研究以1×10^8病毒粒子/10cm培养皿的剂量感染THP-1细胞，并分别于感染后1、2、4、8及24小时收集样本。随后对收集的样本进行RNA测序（RNA-Seq）以及针对H3K27ac、H3K4me3、H3K9me3和H3K27me3的染色质免疫共沉淀测序（ChIP-Seq）。所有测序实验均设置2次生物学重复，并在数据分析前完成数据质量控制。