{Reference Type}: Journal Article
{Title}: XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.
{Author}: Oh KS;Aqdas M;Sung MH;
{Journal}: Methods Mol Biol
{Volume}: 2846
{Issue}: 0
{Year}: 2024
暂无{DOI}: 10.1007/978-1-0716-4071-5_15
{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.