Abstract：
We have developed a novel method for genomic footprinting of transcription factors (TFs) that detects potential gene regulatory relationships from DNase-seq data at the nucleotide level. We introduce an assay termed cross-link (XL)-DNase-seq, designed to capture chromatin interactions of dynamic TFs. A mild cross-linking step in XL-DNase-seq improves the detection of DNase-based footprints of dynamic TFs. The footprint strengths and detectability depend on an optimal cross-linking procedure. This method may help extract novel gene regulatory circuits involving previously undetectable TFs. The XL-DNase-seq method is illustrated here for activated mouse macrophage-like cells, which share several features with inflammatory macrophages.
摘要：
我们已经开发了一种用于转录因子（TF）的基因组足迹的新方法，该方法可以从核苷酸水平的DNase-seq数据中检测潜在的基因调控关系。我们引入了一种称为交联（XL）-DNase-seq的测定法，旨在捕获动态TFs的染色质相互作用。XL-DNase-seq中的温和交联步骤改善了动态TF的基于DNase的足迹的检测。足迹强度和可检测性取决于最佳的交联程序。这种方法可能有助于提取涉及以前无法检测的TFs的新基因调节回路。XL-DNase-seq方法在这里说明了激活的小鼠巨噬细胞样细胞，与炎性巨噬细胞有几个共同的特征。
