Genome-wide analysis of 8-oxoguanine DNA glycosylase-1

We report the application of ChIP-Sequencing for profiling genome-wide distribution of 8-oxoguanine DNA glycosylase (OGG1) which is a DNA base excision repair protein, after TNF exposure of cells. By obtaining an average of over 18 million of total reads per sample and over 19.5 million of unique reads per sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HEK293 cells. We performed gene ontology and functional pathway analysis of genes associate with peaks, and identify regions of the genomes (e.g. promoter, introns, etc) where the peaks tend to occur. The results show that OGG1 is primarily associated with promoter regions in vicinity of transcription factor binding sites 5' of transcription start sites (TSS). This pattern of distribution occurs in spite of genome-wide oxidative modifications of guanine (primarily 8-oxoG). OGG1 increased highly significant (1e-09 to 1e-517) enrichment of 57 transcription factor binding sites including those for Sox(2, 3, 6, 10), RUNX, RUNX(1, 2), HOX(C, D), STAT(1, 3, 6), IRF(1 to 4), NF-κB. In controls, the DNA was chromatin immunoprecipitated using antibody to NF-κB/RelA. These and other data derived from further analysis, suggest that OGG1 modulates binding of transcription factors and gene expression. FLAG-tagged OGG1 expressing HEK293 cells were stimulated with TNF (20 ng/ml) for 0, 15, 30 and 60 min. After TNF exposure, protein-DNA complexes crosslinked using formalin according to standard Millipore® protocol. DNA was sheared with 10-sec pulses using a Cole-Parmer GEX 130 ultrasonic processor (average 300 bp) and chromatin was immunoprecipitated (IP) with antibody to FLAG or anti-RelA/p65 antibody using G-agarose beads (Millipore Corporation). After extraction, the DNA was subjected to high-throughput sequencing using Solexa/Illumina genome analyzer (Ambry Genetics)