Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA.
Nucleic Acids Res. 2011 May;39(9):3558-73. doi: 10.1093/nar/gkq1313. Epub 2011 Jan 18.
The E2F family of transcription factors has important roles in cell cycle progression. E2F4 is an E2F family member that has been proposed to be primarily a repressor of transcription, but the scope of its binding activity and functions in transcriptional regulation is not fully known. We used ChIP sequencing (ChIP-seq) to identify around 16,000 E2F4 binding sites which potentially regulate 7346 downstream target genes with wide-ranging functions in DNA repair, cell cycle regulation, apoptosis, and other processes. While half of all E2F4 binding sites (56%) occurred near transcription start sites (TSSs), ∼20% of sites occurred more than 20 kb away from any annotated TSS. These distal sites showed histone modifications suggesting that E2F4 may function as a long-range regulator, which we confirmed by functional experimental assays on a subset. Overexpression of E2F4 and its transcriptional cofactors of the retinoblastoma (Rb) family and its binding partner DP-1 revealed that E2F4 acts as an activator as well as a repressor. E2F4 binding sites also occurred near regulatory elements for miRNAs such as let-7a and mir-17, suggestive of regulation of miRNAs by E2F4. Taken together, our genome-wide analysis provided evidence of versatile roles of E2F4 and insights into its functions.
E2F 转录因子家族在细胞周期进程中具有重要作用。E2F4 是 E2F 家族的一个成员，据推测其主要作为转录抑制剂发挥作用，但它在转录调控中的结合活性和功能的范围尚不完全清楚。我们使用 ChIP 测序（ChIP-seq）来鉴定约 16000 个 E2F4 结合位点，这些结合位点可能调节 7346 个下游靶基因，这些靶基因具有广泛的功能，包括 DNA 修复、细胞周期调控、细胞凋亡和其他过程。虽然所有 E2F4 结合位点的一半（56%）发生在转录起始位点（TSS）附近，但约 20%的位点发生在距离任何注释 TSS 超过 20kb 的位置。这些远端位点显示出组蛋白修饰，表明 E2F4 可能作为长距离调控因子发挥作用，我们通过对一部分位点的功能实验验证了这一点。E2F4 的过表达及其视网膜母细胞瘤（Rb）家族的转录共因子及其结合伴侣 DP-1 表明，E2F4 既可以作为激活剂，也可以作为抑制剂发挥作用。E2F4 结合位点也发生在 let-7a 和 mir-17 等 miRNA 的调控元件附近，提示 E2F4 可能调节 miRNA。总之，我们的全基因组分析为 E2F4 的多种作用提供了证据，并深入了解了其功能。
