Scaffold attachment factor A (SAF-A) and Ku temporally regulate repair of radiation-induced clustered genome lesions

// Muralidhar L. Hegde 1,2,3,* , Arijit Dutta 1,4,* , Chunying Yang 1,* , Anil K. Mantha 4,8 , Pavana M. Hegde 1 , Arvind Pandey 1 , Shiladitya Sengupta 1,3 , Yaping Yu 5 , Patrick Calsou 6 , David Chen 7 , Susan P. Lees-Miller 5 and Sankar Mitra 1,3,4 1 Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA 2 Houston Methodist Neurological Institute, Houston, TX, USA 3 Weill Medical College of Cornell University, Ithaca, NY, USA 4 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX , USA 5 Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada 6 Institut de Pharmacologie et de Biologie Structurale, CNRS, Universite de Toulouse-Universite  Paul Sabatier, Equipe Labellisee Ligue contre le Cancer, Toulouse, France 7 UT Southwestern Medical Center, Dallas, TX, USA 8 Center for Animal Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India * These authors have contributed equally to this work Correspondence to: Sankar Mitra, email: // Muralidhar L. Hegde, email: // Keywords : SAF-A/hnRNP-U, Ku, DNA-PK, BER, DSB repair Received : May 17, 2016 Accepted : May 26, 2016 Published : June 09, 2016 Abstract Ionizing radiation (IR) induces highly cytotoxic double-strand breaks (DSBs) and also clustered oxidized bases in mammalian genomes. Base excision repair (BER) of bi-stranded oxidized bases could generate additional DSBs as repair intermediates in the vicinity of direct DSBs, leading to loss of DNA fragments. This could be avoided if DSB repair via DNA-PK-mediated nonhomologous end joining (NHEJ) precedes BER initiated by NEIL1 and other DNA glycosylases (DGs). Here we show that DNA-PK subunit Ku inhibits DGs via direct interaction. The scaffold attachment factor (SAF)-A, (also called hnRNP-U), phosphorylated at Ser59 by DNA-PK early after IR treatment, is linked to transient release of chromatin-bound NEIL1, thus preventing BER. SAF-A is subsequently dephosphorylated. Ku inhibition of DGs in vitro is relieved by unphosphorylated SAF-A, but not by the phosphomimetic Asp59 mutant. We thus propose that SAF-A, in concert with Ku, temporally regulates base damage repair in irradiated cell genome.