MER41 repeat sequences contain inducible STAT1 binding sites.
MER41 repeat sequences contain inducible STAT1 binding sites.
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DOI：
10.1371/journal.pone.0011425
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发表时间：
2010-07-06
期刊：
影响因子：
3.7
通讯作者：
Bucher P
中科院分区：
文献类型：
--
作者：
Schmid CD;Bucher P
染色质免疫沉淀结合大规模平行测序方法（ChIP-seq）正在成为研究转录因子（TF）与基因组序列相互作用的标准方法。以公共STAT 1 ChIP-seq数据集为例，我们提出了解释ChIP-seq数据的新方法。我们比较了最近开发的方法，以确定STAT 1结合位点的ChIP-seq数据。评估STAT 1结合位点的既定共有序列的内容，我们发现使用“阴性对照”ChIP-seq数据未能提供实质性优势。我们从这些ChIP-seq数据中推导出STAT 1结合序列的单一精确概率模型。与先前的声明相反，我们没有发现证据表明STAT 1在体内干扰素-γ刺激后与多个不同的基序结合。虽然大多数具有高ChIP-seq信号的基因组位点与代表STAT 1结合位点的核苷酸序列相关，但ChIP-seq数据仅涵盖人类基因组中超过500万个潜在STAT 1结合位点中的一小部分。此外，令人惊讶的是，ChIP-seq信号的大部分（5%）被重复序列的小家族（MER 41）吸收。 活化的STAT 1蛋白与特定重复元件结合的观察支持了关于p53和其他TF的类似报道，并加强了重复序列参与基因调控的概念。顺便说一句，MER 41对灵长类动物是特异性的，因此，IFN-STAT途径中的调节机制在灵长类动物和啮齿类动物之间可能根本不同。 在方法学方面，重复序列中存在大量几乎相同的结合位点可能导致关于TF内在结合偏好的错误结论，如间隔分析STAT 1串联基序所示。因此，ChIP-seq数据应在重复和非重复序列中独立分析。
Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we present novel approaches for the interpretation of ChIP-seq data. We compare recently developed approaches to determine STAT1 binding sites from ChIP-seq data. Assessing the content of the established consensus sequence for STAT1 binding sites, we find that the usage of “negative control” ChIP-seq data fails to provide substantial advantages. We derive a single refined probabilistic model of STAT1 binding sequences from these ChIP-seq data. Contrary to previous claims, we find no evidence that STAT1 binds to multiple distinct motifs upon interferon-gamma stimulation in vivo. While a large majority of genomic sites with high ChIP-seq signal is associated with a nucleotide sequence ressembling a STAT1 binding site, only a very small subset of the over 5 million potential STAT1 binding sites in the human genome is covered by ChIP-seq data. Furthermore a surprisingly large fraction of the ChIP-seq signal (5%) is absorbed by a small family of repetitive sequences (MER41). The observation of the binding of activated STAT1 protein to a specific repetitive element bolsters similar reports concerning p53 and other TFs, and strengthens the notion of an involvement of repeats in gene regulation. Incidentally MER41 are specific to primates, consequently, regulatory mechanisms in the IFN-STAT pathway might fundamentally differ between primates and rodents. On a methodological aspect, the presence of large numbers of nearly identical binding sites in repetitive sequences may lead to wrong conclusions about intrinsic binding preferences of TF as illustrated by the spacing analysis STAT1 tandem motifs. Therefore, ChIP-seq data should be analyzed independently within repetitive and non-repetitive sequences.