Molecular Underpinnings in the Establishment of an Oncogenic 3D Genome in Response to Environmental Arsenic Exposure

Establishing the influence of pollutants on genome function is essential in defining their impact on human health. 24% of the diseases caused by environmental exposures might have been avoided by disease prevention, diagnosis and the development of safer metal-based therapeutic agents. In order to understand how these pollutants cause disease, we need to understand how pollutants change gene expression. Chromatin plays an integral role in gene regulation. At the one-dimensional (1D) level, chromatin is found as nucleosomes and at the three dimensional level (3D), chromatin is found in loops and topological domains, both of which regulate gene expression by allowing accessibility to the DNA wrapped up as chromatin. Inorganic arsenic (iAs) is a ubiquitous metal that impacts gene regulation through modulating the epigenome. We recently provided the epigenetic landscape (DNA methylation, histone PTMs and histone variants) mediated by inorganic arsenic. This landscape though important, makes it difficult to decipher effects due to local epigenetic environments’ modulation, or effects caused by remote changes several kilobases away, such as the activity of enhancer(s). Additionally, the effect of the 3D chromatin structure supersedes that at the 1D chromatin level. This 3D information is mediated by CTCF, known as ‘genome’s master weaver’, and any dysregulation of the CTCF binding alters this 3D structure, resulting in gene dysregulation. We recently showed that iAs selectively inhibits CTCF from binding to some of its target sites and instigating oncogenic expression patterns. Interestingly, carcinogenesis is not a linear process but involves a hybrid of in-between stages till final transformation. We therefore hypothesize that by inhibiting CTCF binding, iAs reorganizes the genome to maintain specific topologically-activated domains at the 3D chromatin structure to drive specific oncogenic potentials. To test this hypothesis, we will map CTCF binding (Aim 1), chromatin 3D (Aim 2), ChIP-seq of histone marks and chromatin structure (targeting CTCF insulator property) (Aim 3) as cells undergo iAs-mediated carcinogenesis. The knowledge derived from the proposed studies will allow us to characterize the resulting gene regulatory network mediated by iAs exposure, and allow us to unambiguously anchor iAs exposure to changes in the CTCF interactome in the process of iAs-mediated disease pathogenesis.