Serum response factor binding sites differ in three human cell types
Serum response factor binding sites differ in three human cell types
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DOI：
10.1101/gr.5875007
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发表时间：
2007-02-01
期刊：
影响因子：
7
通讯作者：
Myers, Richard M.
中科院分区：
文献类型：
--
作者：
Cooper, Sara J.;Trinklein, Nathan D.;Myers, Richard M.
血清反应因子（SRF）是胚胎发育和维持肌肉细胞和神经元所必需的。该因子控制这些不同途径的机制尚不清楚。在这里，我们提出了一个全基因组范围内的视图占用的SRF在其结合位点的重点是那些不同的细胞类型。我们使用染色质免疫沉淀（ChIP）结合人类启动子微阵列，以确定216个假定的SRF结合位点在人类基因组中。我们在这些位点中的一半以上进行了独立的定量PCR验证，得到了146个位点，我们认为这些位点是真实的结合位点，置信度超过90%。近一半的位点仅在我们测试的三种细胞类型中的一种中被SRF结合，这为SRF在不同细胞类型中的不同作用提供了强有力的证据。我们还探讨了可能的机制控制差异结合的SRF在这些细胞类型的辅因子结合，DNA甲基化，组蛋白甲基化，组蛋白乙酰化在一个子集的网站结合优先在平滑肌细胞。虽然我们没有看到SRF结合和表观遗传学修饰之间的强相关性，在这些网站上，我们建议，SRF辅因子可能在确定细胞依赖性SRF结合位点中发挥重要作用。ELK 4（以前称为SAP-1 [SRF相关蛋白-1]）广泛表达。因此，我们预计它会占据所有细胞类型中常见的SRF结合位点。事实上，90%的SRF位点也被ELK 4结合，这是所有三种细胞类型所共有的。总之，我们的数据提供了对SRF控制的监管网络的更全面的了解。
The serum response factor (SRF) is essential for embryonic development and maintenance of muscle cells and neurons. The mechanism by which this factor controls these divergent pathways is unclear. Here we present a genome-wide view of occupancy of SRF at its binding sites with a focus on those that vary with cell type. We used chromatin immunoprecipitation (ChIP) in combination with human promoter microarrays to identify 216 putative SRF binding sites in the human genome. We performed independent quantitative PCR validation at over half of these sites that resulted in 146 sites we assert to be true binding sites at over 90% confidence. Nearly half of the sites are bound by SRF in only one of the three cell types we tested, providing strong evidence for the diverse roles for SRF in different cell types. We also explore possible mechanisms controlling differential binding of SRF in these cell types by assaying cofactor binding, DNA methylation, histone methylation, and histone acetylation at a subset of sites bound preferentially in smooth muscle cells. Although we did not see a strong correlation between SRF binding and epigenetics modifications, at these sites, we propose that SRF cofactors may play an important role in determining cell-dependent SRF binding sites. ELK4 (previously known as SAP-1 [SRF-associated protein-1]) is ubiquitously expressed. Therefore, we expected it to occupy sites where SRF binding is common in all cell types. Indeed, 90% of SRF sites also bound by ELK4 were common to all three cell types. Together, our data provide a more complete understanding of the regulatory network controlled by SRF.