{"doi":"10.1016/j.xpro.2025.103695","title":"Protocol for chromatin immunoprecipitation of chromatin-binding proteins in Schizosaccharomyces pombe using a dual-crosslinking approach","abstract":"Single-crosslink chromatin immunoprecipitation (ChIP) is often ineffective at mapping the binding sites of chromatin-binding proteins that indirectly interact with DNA. Here, we present a protocol to map the genomic occupancy of different chromatin regulators and an RNA exosome adapter subunit in Schizosaccharomyces pombe using dual-crosslinking ChIP. We describe steps for cell growth, dual-crosslinking, cell lysis, sonification, and immunoprecipitation. We then detail procedures for washing, crosslink reversal, and DNA purification for downstream analysis using ChIP-qPCR and ChIP sequencing. For complete details on the use and execution of this protocol, please refer to Khanduja et al. 1 • Steps for lysing yeast cells by mechanical force using glass beads • Instructions for double crosslinking and chromatin preparation • Guidance on immunoprecipitation, washes, and DNA purification • Procedures for troubleshooting and improving efficiency Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Single-crosslink chromatin immunoprecipitation (ChIP) is often ineffective at mapping the binding sites of chromatin-binding proteins that indirectly interact with DNA. Here, we present a protocol to map the genomic occupancy of different chromatin regulators and an RNA exosome adapter subunit in Schizosaccharomyces pombe using dual-crosslinking ChIP. We describe steps for cell growth, dual-crosslinking, cell lysis, sonification, and immunoprecipitation. We then detail procedures for washing, crosslink reversal, and DNA purification for downstream analysis using ChIP-qPCR and ChIP sequencing.","journal":"STAR Protocols","year":2025,"id":539015,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9436,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":795232,"name":"Mo Motamedi","orcid":"0000-0002-2031-6155","position":1,"is_corresponding":false},{"id":1234931,"name":"Jasbeer Singh Khanduja","orcid":"0009-0000-6415-367X","position":0,"is_corresponding":true}],"reference_count":15,"raw_metadata":null,"created_at":"2026-07-19T02:52:25.799399Z","pmid":"40085649","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":[]}