APLF and long non-coding RNA NIHCOLE promote stable DNA synapsis in non-homologous end joining
Sara De Bragança,
Clara Aicart-Ramos,
Raquel Arribas-Bosacoma,
Angel Rivera-Calzada,
Juan Pablo Unfried,
Laura Prats-Mari,
Mikel Marin-Baquero,
Puri Fortes,
Oscar Llorca,
Fernando Moreno-Herrero
Affiliations
Sara De Bragança
Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
Clara Aicart-Ramos
Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
Raquel Arribas-Bosacoma
Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
Angel Rivera-Calzada
Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
Juan Pablo Unfried
Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel; Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
Laura Prats-Mari
Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
Mikel Marin-Baquero
Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
Puri Fortes
Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
Oscar Llorca
Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain; Corresponding author
Fernando Moreno-Herrero
Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain; Corresponding author
Summary: The synapsis of DNA ends is a critical step for the repair of double-strand breaks by non-homologous end joining (NHEJ). This is performed by a multicomponent protein complex assembled around Ku70-Ku80 heterodimers and regulated by accessory factors, including long non-coding RNAs, through poorly understood mechanisms. Here, we use magnetic tweezers to investigate the contributions of core NHEJ proteins and APLF and lncRNA NIHCOLE to DNA synapsis. APLF stabilizes DNA end bridging and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis for several minutes under piconewton forces. We find the C-terminal acidic region of APLF to be critical for bridging. NIHCOLE increases the dwell time of the synapses by Ku70-Ku80 and APLF. This effect is further enhanced by a small and structured RNA domain within NIHCOLE. We propose a model where Ku70-Ku80 can simultaneously bind DNA, APLF, and structured RNAs to promote the stable joining of DNA ends.
