Non-homologous end joining induced alterations in DNA methylation: A source of permanent epigenetic change

// Brittany Allen 1 , Antonio Pezone 2 , Antonio Porcellini 3 , Mark T. Muller 4 and Michal M. Masternak 1, 5 1 College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA 2 Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, Napoli, Italy 3 Dipartimento di Biologia, Università Federico II, Napoli, Italy 4 Epigenetics Division, TopoGEN, Inc., Buena Vista, CO, USA 5 Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan, Poland, Europe Correspondence to: Mark T. Muller, email: [email protected] Michal M. Masternak, email: [email protected] Keywords: DNA damage, NHEJ repair, DNA repair, DNA methylation Received: December 21, 2016 Accepted: February 07, 2017 Published: March 11, 2017 ABSTRACT In addition to genetic mutations, epigenetic revision plays a major role in the development and progression of cancer; specifically, inappropriate DNA methylation or demethylation of CpG residues may alter the expression of genes that promote tumorigenesis. We hypothesize that DNA repair, specifically the repair of DNA double strand breaks (DSB) by Non-Homologous End Joining (NHEJ) may play a role in this process. Using a GFP reporter system inserted into the genome of HeLa cells, we are able to induce targeted DNA damage that enables the cells, after successfully undergoing NHEJ repair, to express WT GFP. These GFP+ cells were segregated into two expression classes, one with robust expression (Bright) and the other with reduced expression (Dim). Using a DNA hypomethylating drug (AzadC) we demonstrated that the different GFP expression levels was due to differential methylation statuses of CpGs in regions on either side of the break site. Deep sequencing analysis of this area in sorted Bright and Dim populations revealed a collection of different epi-alleles that display patterns of DNA methylation following repair by NHEJ. These patterns differ between Bright and Dim cells which are hypo- and hypermethylated, respectively, and between the post-repair populations and the original, uncut cells. These data suggest that NHEJ repair facilitates a rewrite of the methylation landscape in repaired genes, elucidating a potential source for the altered methylation patterns seen in cancer cells, and understanding the mechanism by which this occurs could provide new therapeutic targets for preventing this process from contributing to tumorigenesis.