Genome-wide profiling of histone modification H3K27ac and CTCF transcription factor binding following VPA treatment in HEK293 cells

Valproic acid (VPA), a histone deacetylase (HDAC) inhibitor induces epigenetic changes through histone hyperacetylation which lead to alteration to H3K27ac and CTCF binding in the genome. To determine the effects of VPA on 3D chromatin organization, we performed ChIP-seq on untreated and VPA-treated HEK293T cells. VPA treatment results in elevated H3K27ac marks and slightly reduced CTCF binding, which supports the evidence of active transcription triggered upon histone hyperacetylation induced by VPA. Overall design: We performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac and transcription factor CCCTC-binding factor (CTCF) in both untreated and VPA-treated HEK293T cells. The experiments were performed in triplicates. Peak calling and differential ChIP-seq peak analysis was performed to elucidate the genomic changes triggered by VPA.

丙戊酸（Valproic acid, VPA）作为组蛋白去乙酰化酶（histone deacetylase, HDAC）抑制剂，可通过组蛋白高度乙酰化诱导表观遗传改变，进而引发基因组中组蛋白H3赖氨酸27乙酰化（H3K27ac）修饰与CCCTC结合因子（CTCF）结合模式的改变。为明确VPA对三维染色质组织的调控效应，本研究对未处理及VPA处理的HEK293T细胞开展了染色质免疫共沉淀测序（ChIP-seq）实验。实验结果显示，VPA处理可提升H3K27ac修饰水平，并轻度降低CTCF的结合强度，这一发现佐证了VPA诱导组蛋白高度乙酰化后所触发的活跃转录过程。本研究的整体实验设计如下：针对未处理与VPA处理的HEK293T细胞，分别对组蛋白修饰H3K27ac与转录因子CCCTC结合因子（CTCF）开展染色质免疫共沉淀测序（ChIP-seq），所有实验均设置三次生物学重复。后续通过峰识别与差异ChIP-seq峰分析，阐明VPA诱导的基因组层面改变。