{"doi":"10.1016/j.celrep.2024.114178","title":"Improved detection of DNA replication fork-associated proteins","abstract":"Innovative methods to retrieve proteins associated with actively replicating DNA have provided a glimpse into the molecular dynamics of replication fork stalling. We report that a combination of density-based replisome enrichment by isolating proteins on nascent DNA (iPOND2) and label-free quantitative mass spectrometry (iPOND2-DRIPPER) substantially increases both replication factor yields and the dynamic range of protein quantification. Replication protein abundance in retrieved nascent DNA is elevated up to 300-fold over post-replicative controls, and recruitment of replication stress factors upon fork stalling is observed at similar levels. The increased sensitivity of iPOND2-DRIPPER permits direct measurement of ubiquitination events without intervening retrieval of diglycine tryptic fragments of ubiquitin. Using this approach, we find that stalled replisomes stimulate the recruitment of a diverse cohort of DNA repair factors, including those associated with poly-K63-ubiquitination. Finally, we uncover the temporally controlled association of stalled replisomes with nuclear pore complex components and nuclear cytoskeleton networks.","journal":"Cell Reports","year":2024,"id":433978,"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":13,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.949,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":653654,"name":"Ya‐Chu Chang","orcid":"0000-0002-2058-3827","position":1,"is_corresponding":false},{"id":216253,"name":"Ryan L. Ragland","orcid":null,"position":2,"is_corresponding":false},{"id":1239757,"name":"Yee Mon Thu","orcid":"0000-0002-9608-7336","position":3,"is_corresponding":false},{"id":333143,"name":"Muzaffer Ahmad Kassab","orcid":null,"position":4,"is_corresponding":false},{"id":1107484,"name":"Rahul Shubhra Mandal","orcid":"0000-0001-8939-3362","position":5,"is_corresponding":false},{"id":1240148,"name":"Susan K. Van Riper","orcid":null,"position":6,"is_corresponding":false},{"id":355124,"name":"Katarzyna Kulej","orcid":"0000-0002-4125-2533","position":7,"is_corresponding":false},{"id":296490,"name":"LeeAnn Higgins","orcid":null,"position":8,"is_corresponding":false},{"id":1240149,"name":"Todd M. Markowski","orcid":null,"position":9,"is_corresponding":false},{"id":1240150,"name":"David Shang","orcid":null,"position":10,"is_corresponding":false},{"id":683937,"name":"Jack Hedberg","orcid":"0000-0002-0914-9480","position":11,"is_corresponding":false},{"id":278183,"name":"Luke Erber","orcid":"0000-0001-5527-5501","position":12,"is_corresponding":false},{"id":227837,"name":"Benjamin A. García","orcid":"0000-0002-2306-1207","position":13,"is_corresponding":false},{"id":382599,"name":"Yue Chen","orcid":"0000-0002-0153-9927","position":14,"is_corresponding":false},{"id":263507,"name":"Anja‐Katrin Bielinsky","orcid":"0000-0003-1783-619X","position":15,"is_corresponding":false},{"id":231037,"name":"Eric J. Brown","orcid":"0000-0001-6562-6512","position":16,"is_corresponding":false},{"id":1239756,"name":"Rebecca S. Rivard","orcid":"0009-0004-3371-7283","position":0,"is_corresponding":true}],"reference_count":97,"raw_metadata":null,"created_at":"2026-07-19T01:59:49.434790Z","pmid":"38703364","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":[]}