Department of Genetics and Pathology, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden.
Nucleic Acids Res. 2009 Dec;37(22):7498-508. doi: 10.1093/nar/gkp823.
Gene expression is regulated by combinations of transcription factors, which can be mapped to regulatory elements on a genome-wide scale using ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here, we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. Distal elements with USF2 signal was frequently bound also by HNF4a and FOXA2. GABP peaks were found at transcription start sites, whereas 94% of FOXA2 and 90% of HNF4a peaks were located at other positions. We developed a method to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An interaction between HNF4a and GABP was seen at TSS, with one-third of the HNF4a positive promoters being bound also by GABP, and this interaction was verified by co-immunoprecipitations.
基因表达受转录因子组合的调控，这些转录因子可以通过 ChIP 实验在全基因组范围内被映射到调控元件上。在我们之前的 USF1 和 USF2 的 ChIP-chip 研究中，我们还发现了 GABP、FOXA2 和 HNF4a 在富集区域内结合的证据。在这里，我们应用了这些转录因子的 ChIP-seq，鉴定到了 GABP 的 3064 个富集峰、FOXA2 的 7266 个富集峰和 HNF4a 的 18783 个富集峰。具有 USF2 信号的远端元件也经常被 HNF4a 和 FOXA2 结合。GABP 峰出现在转录起始位点，而 94%的 FOXA2 峰和 90%的 HNF4a 峰位于其他位置。我们开发了一种在峰内准确定义 TFBS 的方法，发现预测的位点与峰中心相比具有更高的保守水平；然而，大多数结合并不具有进化保守性。在 TSS 处观察到 HNF4a 和 GABP 之间的相互作用，三分之一的 HNF4a 阳性启动子也被 GABP 结合，这种相互作用通过共免疫沉淀得到了验证。
