ArticleEpigenetics & chromatin2019
XL-DNase-seq: improved footprinting of dynamic transcription factors.
Article in Epigenetics & chromatin, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- Systematic benchmarking of CUT&Tag improves the reliability and reproducibility of chromatin analysis.Cell reports methods · 2026Article
- DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants.Genome biology · 2024Article
- Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility.Nature genetics · 2024Article
- XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Single-cell mapping of DNA G-quadruplex structures in human cancer cells.Scientific reports · 2021Article
- Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo.Molecular cell · 2021Article
- Efficient low-cost chromatin profiling with CUT&Tag.Nature protocols · 2020Article
- Genomic methods in profiling DNA accessibility and factor localization.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAs 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.
resultsHere 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.
conclusionsXL-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.
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