Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
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DOI：
10.1101/gr.4887606
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发表时间：
2006-05-01
期刊：
影响因子：
7
通讯作者：
Farnham, PJ
中科院分区：
文献类型：
--
作者：
Bieda, M;Xu, XQ;Farnham, PJ
E2F转录因子家族调节基本的细胞过程。在这里，我们通过使用高密度寡核苷酸瓷砖阵列检查E2F1结合位点的定位来采用公正的方法来识别E2F1靶基因。首先，我们开发了一种基于统计的方法，用于分析从代表30 MB人类基因组的阵列获得的芯片芯片数据。使用此方法，我们确定了受E2F1，MYC和RNA聚合酶II（POLR2A）约束的区域。我们发现了所有三个因素的大量结合位点。外推表明可能有20,000-30,000 E2F1-和MYC结合位点，并且类似于HeLa细胞中的12,000-17,000个活跃启动子。与我们对MYC的结果相反，我们发现大多数E2F1结合位点（> 80％）位于核心启动子中，并且50％的站点重叠转录开始。只有一小部分E2F1位点具有规范结合基序。令人惊讶的是，我们发现在30-MB区域中，在核心启动子中具有E2F1结合位点的基因的30％相似，而E2F1的结合接近POLR2A结合位点的83％。为了确定这些结果是否代表了整个人类基因组，我们进行了类似于24,000个启动子的芯片芯片分析，并确认大于20％的启动子受E2F1绑定。我们的结果表明，E2F1是通过一种不同于对已知共识位点的识别的方法招募到启动子的，并指出对E2F1的新理解是有助于调节大量人类基因的因素。
The E2F family of transcription factors regulates basic cellular processes. Here, we take an unbiased approach towards identifying E2F1 target genes by examining localization of E2F1-binding sites using high-density oligonucleotide tiling arrays. To begin, we developed a statistically-based methodology for analysis of ChIP-chip data obtained from arrays that represent 30 Mb of the human genome. Using this methodology, we identified regions bound by E2F1, MYC, and RNA Polymerase II (POLR2A). We found a large number of binding sites for all three factors; extrapolation suggests there may be similar to 20,000-30,000 E2F1- and MYC-binding sites and similar to 12,000-17,000 active promoters in HeLa cells. In contrast to our results for MYC, we find that the majority of E2F1- binding sites (> 80%) are located in core promoters and that 50% of the sites overlap transcription starts. Only a small fraction of E2F1 sites possess the canonical binding motif. Surprisingly, we found that similar to 30% of genes in the 30-Mb region possessed an E2F1 binding site in a core promoter and E2F1 was bound near to 83% of POLR2A-bound sites. To determine if these results were representative of the entire human genome, we performed ChIP-chip analyses of similar to 24,000 promoters and confirmed that greater than 20% of the promoters were bound by E2F1. Our results suggest that E2F1 is recruited to promoters via a method distinct from recognition of the known consensus site and point toward a new understanding of E2F1 as a factor that contributes to the regulation of a large fraction of human genes.