Genome dimensions control biological and toxicological functions; myth or reality?

Abstract

The multidimensional genome offers a new perspective to understand molecular mechanisms of genotoxicity and provide deeper knowledge of how genome organization and reorganization in dimensions can alter cell sensitivity, tolerance, resistance, or toxicity to drugs, whether drugs per se can influence the 3D architecture of the genome directly or indirectly through transcriptional factors, and how we can improve cell sensitivity to drugs through the reorganization of genome and regulation of gene expression. We address roles of 3D genome organization and reorganization in the pathogenesis and progression of disease by evaluating various methodologies of studying the 3D genome, and in the genome integrity and stability susceptible to chemicals as mechanisms of genotoxicity. We discuss the value of imaging, visualizing, and nuclear proximity ligation-based methods of 3D genome organization to measure spatial proximity and visualize spatial distances between genomic loci. We also list a number of dynamic genome changes during genome function and call for further investigations on the interaction of drugs with genome-specific regulators, key enzymes, or spliceosome.