Intercalated Motifs Contribute to Transcription Regulation in an Acidosis Model

The formation and function of intercalated motifs (iMs) in cytosine-rich regions of the human genome have long been debated. While these pH-sensitive structures are unlikely to govern gene expression in normal tissues, their contribution to acidosis-specific transcriptional reprogramming cannot be ruled out. Here, we focused on previously reported iM-forming sequences from the regulatory regions of early response genes. We tested their impact on transcription via luciferase-based assays under normal conditions, as well as under conditions favoring or disfavoring iMs (acidic media or iM-destabilizing ligands, respectively). We verified and elucidated the effects of pH and ligands by optical methods and molecular modeling, respectively. Our data indicate that iMs tend to repress reporter gene expression in response to acidification, and this effect could be reversed by selective ligands, including an anticancer drug candidate. These results highlight the potential of targeting iMs to mitigate the pathogenic response to acidosis.