IRF4 genome wide binding and transciptomic profile in 501Mel melanoma cell line. IRF4 genome wide binding and transciptomic profile in 501Mel melanoma cell line

To map genome wide binding sites of IRF4, we performed ChIP-seq against eGFP tagged IRF4 in human melanoma cells. To assess whether IRF4 binding influences its target gene expression, RNA-seq was performed after siRNA mediated depletion of IRF4 in 501Mel cells. Subsequently, target genes of IRF4 obtained from ChIP-seq and RNA-seq studies were used to interrogate melanocyte meQTL and identified 131 candidate downstream target CpGs of IRF4, which were validated by cis-/trans-meQTL mediation analysis, suggesting transcription factor mediated expression changes reflected in methylation changes. Overall design: RNA-seq experiments were performed in triplicates respectively for siCTRL and siIRF4 in 501Mel cells. ChIP-seq experiments were performed in biological duplicates for eGFP tagged IRF4 in 501Mel cells.

为绘制干扰素调节因子4（IRF4）的全基因组结合位点，我们在人类黑色素瘤细胞中针对增强型绿色荧光蛋白（eGFP）标记的IRF4开展了染色质免疫共沉淀测序（ChIP-seq）。为评估IRF4结合是否会影响其靶基因的表达，我们在501Mel细胞中通过小干扰RNA（siRNA）介导敲低IRF4后，开展了RNA测序（RNA-seq）实验。随后，我们利用从ChIP-seq和RNA-seq研究中获取的IRF4靶基因，对黑色素细胞的甲基化数量性状位点（meQTL）进行解析，共鉴定出131个IRF4候选下游靶标CpG位点，并通过顺式/反式meQTL介导分析对其进行了验证，这表明转录因子介导的表达变化可反映在甲基化变化中。整体实验设计如下：在501Mel细胞中，针对阴性对照小干扰RNA（siCTRL）和靶向IRF4的小干扰RNA（siIRF4），分别设置3个生物学重复开展RNA-seq实验；在501Mel细胞中，针对eGFP标记的IRF4，设置2个生物学重复开展ChIP-seq实验。