Transcription Factors as Direct Mediators of Homeostasis and Defense

Daniel Jong-Woong Kim, Yale University Graduate School of Arts and Sciences


Metazoan signaling is typically conceived as a cascade of specialized proteins transducing environmental stimuli into differential expression of genes. In this thesis, we study two transcription factors that more directly mediate cellular responses involved in homeostasis and defense through somewhat less traditional mechanisms. First, we investigated the aryl hydrocarbon receptor (AhR) which is a transcription factor that both binds ligands containing aromatic hydrocarbon rings and directly induces a pleiotropic transcriptional repertoire. In addition to binding environmental toxins like TCDD, AhR also binds a variety of natural ligands generated by tryptophan catabolism originating from the host, microbiota, or diet. In our current understanding, the vast majority of natural AhR ligands are agonists, and the few antagonists that have been characterized are low in affinity and not present at physiologically relevant concentrations in humans. Yet, the vast majority of people do not exhibit symptoms of AhR hyperstimulation – which includes birth defects, anemia, and fatty liver – indicating that there may be a high affinity, physiological antagonist that has yet to be identified. Deficiencies of vitamin B12 and folic acid (FA) present with a similar clinical picture as AhR hyperstimulation, and each vitamin contains an aromatic hydrocarbon ring moiety that has not yet been functionally characterized. Given these observations, we assessed whether B12 and FA antagonize AhR to alleviate symptoms of vitamin deficiency. In Chapter 2, we report that B12 and FA bind competitively to the ligand binding domain (LBD) of AhR, suppress AhR nuclear localization, and decrease transcriptional activity at xenobiotic responsive elements (XREs) present in target gene promoters. In vivo, we found that B12, FA, and their aryl hydrocarbon moieties were able to rescue mice from cleft palates, anemia, and fatty liver induced by TCDD exposure. Furthermore, B12- and FA-deficient mice exhibited higher AhR transcriptional activity and accumulation of erythroid progenitors at baseline, and in the case of FA-deficient mice, both of these changes were dependent on functional AhR. Finally, by analyzing RNA-Seq data from The Cancer Genome Atlas (TCGA), we observed that samples with deficient B12 and FA uptake pathways have higher expression of AhR transcriptional targets and lower expression of developmental pathways whose deficiencies have already been linked with birth defects. In contrast, samples deficient in enzymes known to interact with B12 and FA (and are currently thought to mediate the symptoms of deficiency) did not show significant difference in expression of either of these gene sets. Alongside AhR, we also investigated RUNX transcription factors and their less conventional roles in binding and repressing viral genes. Mammalian RUNX1 and RUNX3 are lineage-defining transcription factors for nociceptive and proprioceptive sensory neurons, respectively, in the dorsal root ganglia (DRG). Given the role of RUNX1 in binding HIV-1 LTR and reinforcing viral latency in T cells, we hypothesized that RUNX transcription factors in DRG may also bind and transcriptionally repress the genomes of HSV1 and HSV2 – DNA viruses that classically establish latency in DRG neurons. In Chapter 3, we report that RUNX consensus binding sequences (CBSs) are uniquely enriched among genomes of herpesviruses, but not those of non-herpesviruses. Through in vitro infections, we verified that overexpressed RUNX1 binds to putative CBSs, represses viral gene expression, and decreases overall infection. These studies broaden our understanding of how AhR and RUNX1 directly mediate host homeostasis and defense. By further investigating the roles of AhR and RUNX1 in aging and latent states of other herpesviruses, respectively, future work can help reveal broader implications these transcription factors may have for human health.