BackgroundΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help us to fully understand the site-specific recognition function by ΦC31 integrase. The present study was aimed to uncover the global map of ΦC31 integrase binding sites in bovine cells and analysis the features of these binding sites by comprehensive bioinformatics methods.ResultsIn this study, we constructed a ChIP-seq method that can be used to uncover the global binding sites by phiC31 integrase. 6740 potential ΦC31 integrase binding sites were identified. A sequence motif was found that contains inverted repeats and has similarities to wild-type attP site. Using REPEATMASKER, we identified a total of 20,183 repeat-regions distributed in 50 repeat types for the 6740 binding sites. These sites enriched in “regulation of GTPase activity” of in the GO category of biological process and KEGG pathway of signal transmembrane transporter activity.ConclusionThis study is the first time to uncover the global map of binding sites for ΦC31 integrase using ChIP-sequencing method and analysis the features of these binding sites. This method will help us to fully understand the mechanism of the site-specific integration function by phiC31 integrase and will potentially boost its genetic manipulations in both gene therapy and generation of transgenic animals.

中文翻译：

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使用 ChIP-seq 绘制转基因马登达比牛肾细胞中 phic31 整合酶结合位点的全局图谱

背景ΦC31整合酶是一种位点特异性重组酶，可以有效地将携带attB的转基因靶向哺乳动物基因组中的内源性假attP位点。内源结合位点的序列特征将有助于我们全面了解ΦC31整合酶的位点特异性识别功能。本研究旨在揭示牛细胞中ΦC31整合酶结合位点的全局图谱，并通过综合生物信息学方法分析这些结合位点的特征。 phiC31 整合酶的结合位点。鉴定了 6740 个潜在的 ΦC31 整合酶结合位点。发现了一个包含反向重复序列的序列基序，并且与野生型 attP 位点具有相似性。使用 REPEATMASKER，我们一共确定了 20 个，183 个重复区域分布在 6740 个结合位点的 50 种重复类型中。这些位点富含 GO 类生物过程的“GTPase 活性调节”和信号跨膜转运蛋白活性的 KEGG 途径。分析这些结合位点的特征。该方法将帮助我们充分了解 phiC31 整合酶的位点特异性整合功能的机制，并有可能促进其在基因治疗和转基因动物产生中的基因操作。这些位点富含 GO 类生物过程的“GTPase 活性调节”和信号跨膜转运蛋白活性的 KEGG 途径。分析这些结合位点的特征。该方法将帮助我们充分了解 phiC31 整合酶的位点特异性整合功能的机制，并有可能促进其在基因治疗和转基因动物产生中的基因操作。这些位点富含 GO 类生物过程的“GTPase 活性调节”和信号跨膜转运蛋白活性的 KEGG 途径。分析这些结合位点的特征。该方法将帮助我们充分了解 phiC31 整合酶的位点特异性整合功能的机制，并有可能促进其在基因治疗和转基因动物产生中的基因操作。