{"doi":"10.1101/2020.04.20.048470","title":"Affinity proteomic dissection of the human nuclear cap-binding complex interactome","abstract":"ABSTRACT A 5’, 7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). The CBC has come under renewed investigative interest in recent years due to its participation in RNA-fate decisions via interactions with RNA productive factors as well as with adapters of the degradative RNA exosome - including the proteins SRRT (a.k.a. ARS2) and ZC3H18, and macromolecular assemblies such as the nuclear exosome targeting (NEXT) complex and the poly(A) exosome targeting (PAXT) connection. A novel cap-binding protein, NCBP3, was recently proposed to form an alternative, non-canonical CBC together with NCBP1, and to interact with the canonical CBC along with the protein SRRT. The theme of post-transcriptional RNA fate, and how it relates to co-transcriptional ribonucleoprotein assembly is abundant with complicated, ambiguous, and likely incomplete models. In an effort to clarify the compositions of NCBP1-, 2-, and 3-related macromolecular assemblies, including their intersections and differences, we have applied an affinity capture-based interactome screening approach, where the experimental design and data processing have been modified and updated to identify interactome differences between targets under a range of experimental conditions, in the context of label-free quantitative mass spectrometry. This study generated a comprehensive view of NCBP-protein interactions in the ribonucleoprotein context and demonstrates the potential of our approach to benefit the interpretation of complex biological pathways.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":124799,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9489,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":484422,"name":"Svetlana Kalmykova","orcid":"0000-0001-5453-1884","position":1,"is_corresponding":false},{"id":485542,"name":"Maria Pashkova","orcid":null,"position":2,"is_corresponding":false},{"id":484423,"name":"Mehrnoosh Oghbaie","orcid":"0000-0002-8225-3436","position":3,"is_corresponding":false},{"id":463093,"name":"Hua Jiang","orcid":"0000-0002-7561-3085","position":4,"is_corresponding":false},{"id":321289,"name":"Kelly R. Molloy","orcid":"0009-0006-3142-4481","position":5,"is_corresponding":false},{"id":51698,"name":"Brian T. Chait","orcid":"0000-0003-3524-557X","position":6,"is_corresponding":false},{"id":321295,"name":"Michael P. Rout","orcid":"0000-0003-2010-706X","position":7,"is_corresponding":false},{"id":2222,"name":"David Fenyö","orcid":"0000-0001-5049-3825","position":8,"is_corresponding":false},{"id":463099,"name":"Torben Heick Jensen","orcid":"0000-0001-5127-1239","position":9,"is_corresponding":false},{"id":484424,"name":"Ilya Altukhov","orcid":"0000-0001-9821-1890","position":10,"is_corresponding":false},{"id":463098,"name":"John LaCava","orcid":"0000-0002-6307-7713","position":11,"is_corresponding":false},{"id":463091,"name":"Yuhui Dou","orcid":"0000-0003-4291-4671","position":0,"is_corresponding":true}],"reference_count":77,"raw_metadata":null,"created_at":"2026-07-18T23:15:11.632153Z","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":[]}