Genome wide analysis of FOXO3 transcription regulation through RNA pol II profiling. Homo sapiens

FOXO transcription factors are key players in diverse cellular processes affecting tumorigenesis, stem cell maintenance and lifespan. To gain insight into mechanisms of FOXO regulated target gene expression, we studied genome-wide effects of FOXO3 activation. Profiling RNA polymerase II changes shows FOXO3 regulates gene expression through transcription initiation. Correlative analysis of FOXO3 and RNA polymerase II ChIP-seq profiles demonstrates FOXO3 to act as a transcriptional activator. Furthermore, this analysis reveals a significant part of FOXO3 gene regulation proceeds through enhancer regions. FOXO3 binds to pre-existing enhancers and further activates these enhancers as shown by changes in histone acetylation and RNA polymerase II recruitment. In addition, FOXO3-mediated enhancer activation correlates with regulation of adjacent genes and pre-existence of chromatin loops between FOXO3 bound enhancers and target genes. Combined, our data elucidate how FOXOs regulate gene transcription and provide insight into mechanisms by which FOXOs can induce different gene expression programs depending on chromatin architecture. Paper with published gene expression: PMID 22139133. Overall design: Examination of FOXO3 binding and changes in RNAPII occupancy (0, 4, 24 hours after induction) in colorectal cell line

FOXO转录因子（FOXO transcription factors）是参与肿瘤发生、干细胞维持与寿命调控等多种细胞过程的关键调控因子。为深入解析FOXO家族调控靶基因表达的分子机制，本研究探究了FOXO3激活在全基因组层面的生物学效应。对RNA聚合酶II（RNA polymerase II）的变化进行谱型分析显示，FOXO3通过转录起始环节调控基因表达。对FOXO3与RNA聚合酶II的染色质免疫共沉淀测序（ChIP-seq）谱型进行关联分析，结果表明FOXO3作为转录激活因子发挥功能。此外，该分析揭示FOXO3的基因调控有相当一部分通过增强子区域完成。FOXO3可结合预先存在的增强子，并通过组蛋白乙酰化水平改变与RNA聚合酶II的招募情况，进一步激活这些增强子。不仅如此，FOXO3介导的增强子激活与邻近基因的调控，以及FOXO3结合的增强子与靶基因之间预先存在的染色质环密切相关。综上，本研究数据阐明了FOXO家族调控基因转录的具体方式，并揭示了FOXO家族可依赖染色质高级结构诱导不同基因表达程序的分子机制。相关基因表达数据已发表于论文：PubMed编号（PMID）22139133。实验整体设计：在结直肠细胞系中检测FOXO3的结合情况以及RNA聚合酶II（RNAPII）的占据量变化（诱导后0、4、24小时）。