Identification of promoters and enhancers induced by carbon nanotube exposure

Usage of carbon nanotubes (CNTs) is increasing in industry due to their mechanical and electrical properties. However, pulmonary exposure to CNTs induces, an asbestos-like toxicological response characterized by persistent inflammation, granuloma formation and fibrosis with low no-effect levels. Little is known about the regulation of the response to CNTs. To this end, we have profiled transcription start sites and enhancers in mouse lung tissues following CNT exposure using Cap Analysis Gene Expression Assay (CAGE). This revealed a massive transcriptome response, with over 100-fold expression increases for key promoters, and a large change in transcription of enhancer regions linked to similarly responding genes. The response included key genes involved in inflammation, phagocytosis, cell and proliferation. We found a clear correlation between the overall CNT response strength and the number of alternative promoters in a given gene, but not the number of proximal enhancers. Upregulated genes after CNT exposure, where only the most annotated upstream promoter was upregulated, were associated to inflammation. Also NFkB binding sites were over-represented among these promoters. Conversely, upregulated genes where the upregulation could be attributed to promoters within the gene were not in particular linked to inflammation, and these promoters had distinct DNA motif enrichment patterns, not including the NFkB binding sites. Interestingly, NFkB binding sites were not over-represented in upregulated enhancer regions.