{"doi":"10.1016/j.jbc.2025.110857","title":"DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation","abstract":"How RIF1 (RAP1 interacting factor 1) fulfills its diverse roles in DNA double-strand break repair, DNA replication, and nuclear organization remains elusive. Here, we show that alternative splicing of a cassette exon (Ex32) encoding a Ser/Lys-rich cassette in the RIF1 C-terminal domain (CTD) gives rise to RIF1-Long (RIF1-L) and RIF1-Short (RIF1-S) isoforms with different functional characteristics. We demonstrate that RIF 1 -Ex32 splice-in is mediated by an exonic splicing enhancer that is recognized by the serine and arginine rich splicing factor 1 (SRSF1) and antagonized by SRSF3 and SRSF7. Exposure to DNA damage inhibited Ex32 splice-in, potentiated the association of SRSF3 and SRSF7 with RIF1 pre-mRNA, and caused an increase in RIF1-S protein expression, which was also observed across a diverse set of primary cancers. Isoform-specific proteomic analyses revealed RIF1-L preferentially associated with mediator of DNA damage checkpoint 1 (MDC1) and sustained MDC1 focus formation to a greater extent than RIF1-S. We further show that the Ser/Lys-rich cassette stabilized a novel phase separation activity of the RIF1 CTD and enhanced RIF1-L chromatin retention, which was reversed by cyclin-dependent kinase 1–dependent phosphorylation of the RIF1 CTD in response to G 2 DNA damage checkpoint inhibition. These combined findings suggest DNA damage–dependent RIF1 alternative splicing contributes to RIF1 functional diversification in genome protection.","journal":"Journal of Biological Chemistry","year":2025,"id":535169,"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":0.9602,"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":722029,"name":"Weiyan Jia","orcid":"0000-0003-0899-0697","position":1,"is_corresponding":false},{"id":722030,"name":"Sang Hwa Kim","orcid":"0000-0002-9245-4514","position":2,"is_corresponding":false},{"id":691636,"name":"Mark Scalf","orcid":null,"position":3,"is_corresponding":false},{"id":1419283,"name":"Claire E. Boos","orcid":null,"position":4,"is_corresponding":false},{"id":1116305,"name":"Yuhong Chen","orcid":"0000-0001-6131-7595","position":5,"is_corresponding":false},{"id":295122,"name":"Demin Wang","orcid":"0000-0001-5549-3795","position":6,"is_corresponding":false},{"id":475673,"name":"Andrew F. Voter","orcid":"0000-0003-1691-0618","position":7,"is_corresponding":false},{"id":1418750,"name":"Aditya Bajaj","orcid":"0009-0005-8202-3744","position":8,"is_corresponding":false},{"id":267557,"name":"Lloyd M. Smith","orcid":"0000-0002-6652-8639","position":9,"is_corresponding":false},{"id":475676,"name":"James L. Keck","orcid":"0000-0002-5961-0220","position":10,"is_corresponding":false},{"id":576133,"name":"Christopher J. Bakkenist","orcid":"0000-0001-9672-0886","position":11,"is_corresponding":false},{"id":539723,"name":"Lin Guo","orcid":"0000-0002-2589-9513","position":12,"is_corresponding":false},{"id":722031,"name":"Randal S. Tibbetts","orcid":"0000-0003-2245-2297","position":13,"is_corresponding":false},{"id":1419282,"name":"Adenine Si-Hui Koo","orcid":null,"position":0,"is_corresponding":true}],"reference_count":99,"raw_metadata":null,"created_at":"2026-07-19T02:51:56.297114Z","pmid":"41489901","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":[]}