Toxicoepigenetic alteration of the kidney injury molecule 1 gene in gentamicin-exposed rat kidney.

Chromatin modifications are now widely accepted as being essential steps involved in activation, repression, and poising of the expression of a large number of genes within the genome. Not only does understanding the role of such changes provide an opportunity to elucidate mechanisms controlling gene expression but in parallel offers the ability to develop novel indicative and predictive biomarkers of disease and toxicity. In the current study, we have applied the chromatin immunoprecipitation assay to investigate putative changes in the chromatin environment associated with the kidney injury molecule 1 (Kim1) gene upon exposure of rats to the nephrotoxicant, gentamicin. Chromatin was isolated from the kidneys of both control and gentamicin-treated animals and interrogated using specific antibodies recognizing two modifications of histone H3, acetylation of lysine 9, and trimethylation of lysine 4, along with RNA polymerase II. Enriched chromatin fractions were analyzed by quantitative PCR using tiled primer pairs covering 4 kb of the Kim1 gene (spanning -2 kb to + 2 kb, relative to the transcription start site). The results demonstrate a substantial increase in the presence of RNA polymerase II and both histone modifications following gentamicin treatment in regions downstream but not upstream of the transcriptional start site of the Kim1 gene. These changes were associated with a marked increase in messenger RNA coding for the Kim1 protein. Together these data suggest, for the first time, that the Kim1 gene is regulated in an epigenetic fashion under conditions of nephrotoxicity.