As the cost of high-throughput sequencing technologies decreases, genome-wide chromatin accessibility profiling methods such as the assay of transposase-accessible chromatin using sequencing (ATAC-seq) are employed widely, with data accumulating at an unprecedented rate. However, accurate inference of protein occupancy requires higher-resolution footprinting analysis where major hurdles exist, including the sequence bias of nucleases and the short-lived chromatin binding of many transcription factors (TFs) with consequent lack of footprints. Here we introduce an assay termed cross-link (XL)-DNase-seq, designed to capture chromatin interactions of dynamic TFs. Mild cross-linking improved the detection of DNase-based footprints of dynamic TFs but interfered with ATAC-based footprinting of the same TFs. XL-DNase-seq may help extract novel gene regulatory circuits involving previously undetectable TFs. The DNase-seq and ATAC-seq data generated in our systematic comparison of various cross-linking conditions also represent an unprecedented-scale resource derived from activated mouse macrophage-like cells which share many features of inflammatory macrophages.

中文翻译：

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XL-DNase-seq：改善了动态转录因子的足迹。

随着高通量测序技术成本的下降，广泛使用了全基因组染色质可及性分析方法，例如使用测序法测定转座酶可利用的染色质（ATAC-seq），数据以前所未有的速度积累。但是，要准确推断蛋白质的占有率，就需要进行高分辨率的足迹分析，该分析存在主要障碍，包括核酸酶的序列偏倚和许多转录因子（TF）的短寿命染色质结合，因而缺乏足迹。在这里，我们介绍了一种称为交联（XL）-DNase-seq的检测方法，旨在捕获动态TF的染色质相互作用。温和的交联改善了动态TF基于DNase的足迹的检测，但干扰了相同TF的基于ATAC的足迹。XL-DNase-seq可能有助于提取涉及先前无法检测到的TF的新型基因调控电路。在我们对各种交联条件的系统比较中生成的DNase-seq和ATAC-seq数据也代表了一种空前规模的资源，其来源是活化的小鼠巨噬细胞样细胞，其具有炎性巨噬细胞的许多特征。