{"doi":"10.1101/pdb.prot5384","title":"DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells","abstract":"<jats:title>INTRODUCTION</jats:title><jats:p>Identification of active gene regulatory elements is a key to understanding transcriptional control governing biological processes such as cell-type specificity, differentiation, development, proliferation, and response to the environment. Mapping DNase I hypersensitive (HS) sites has historically been a valuable tool for identifying all different types of regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. This method utilizes DNase I to selectively digest nucleosome-depleted DNA (presumably by transcription factors), whereas DNA regions tightly wrapped in nucleosome and higher-order structures are more resistant. The traditional low-throughput method for identifying DNase I HS sites uses Southern blots. Here, we describe the complete and improved protocol for DNase-seq, a high-throughput method that identifies DNase I HS sites across the whole genome by capturing DNase-digested fragments and sequencing them by high-throughput, next-generation sequencing. In a single experiment, DNase-seq can identify most active regulatory regions from potentially any cell type, from any species with a sequenced genome.</jats:p>","journal":"Cold Spring Harbor Protocols","year":2010,"id":8133,"datarank":0.9745162485278795,"base_score":6.4967749901858625,"endowment":6.4967749901858625,"self_citation_contribution":0.9745162485278795,"citation_network_contribution":0.0,"self_endowment_contribution":0.9745162485278795,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":662,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.058,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2010-02-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":5210,"name":"Gregory E. Crawford","orcid":"0000-0001-6106-2772","position":1,"is_corresponding":false},{"id":11660,"name":"Lingyun Song","orcid":"0000-0003-2271-8067","position":0,"is_corresponding":true}],"reference_count":12,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}