{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Koo AS"],"funding":["National Institutes of Health National Cancer Institute","NIA NIH HHS","NIAID NIH HHS","NHLBI NIH HHS","American Heart Association Inc","National Heart Lung and Blood Institute","National Institute of General Medical Sciences","National Institute on Aging","National Institute of Allergy and Infectious Diseases","University of Wisconsin Carbone Cancer Center","Yale School of Medicine","NCI NIH HHS","NIGMS NIH HHS"],"pagination":["110857"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12702018"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["301(12)"],"pubmed_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 RIF1-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<sub>2</sub> DNA damage checkpoint inhibition. These combined findings suggest DNA damage-dependent RIF1 alternative splicing contributes to RIF1 functional diversification in genome protection."],"journal":["The Journal of biological chemistry"],"pubmed_title":["DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation."],"pmcid":["PMC12702018"],"funding_grant_id":["EJ5-GFP","R01 AI079087","25PRE1374149","R35 GM126914","R01 HL130724","RF1 AG069483","R01 CA180765","P30 CA014520","P30CA014520"],"pubmed_authors":["Scalf M","Boos CE","Wang D","Koo AS","Tibbetts RS","Bajaj A","Keck JL","Guo L","Kim SH","Voter AF","Smith LM","Jia W","Chen Y","Bakkenist CJ"],"additional_accession":[]},"is_claimable":false,"name":"DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation.","description":"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 RIF1-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<sub>2</sub> DNA damage checkpoint inhibition. These combined findings suggest DNA damage-dependent RIF1 alternative splicing contributes to RIF1 functional diversification in genome protection.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Dec","modification":"2026-06-30T03:25:19.749Z","creation":"2026-06-30T03:20:40.35Z"},"accession":"S-EPMC12702018","cross_references":{"pubmed":["41489901"],"doi":["10.1016/j.jbc.2025.110857"]}}