Transcriptional Mechanisms of Hormone Action and Metabolic Adaptation: Genome Organization and Cis-Regulatory Circuits

Abstract

Metabolic homeostasis is highly maintained through dynamic gene regulation in response to hormonal signals and metabolic transitions. Although many key signaling pathways and transcription factors involved in this process have been identified, the fundamental transcriptional mechanisms that enable these metabolic signals to rapidly control gene expression are unclear. This dissertation investigates the transcriptional mechanisms underlying hormone actions and metabolic adaptation in liver. The first part of this dissertation explores how metabolic hormones control the spatial organization of the genome, and how this process supports rapid gene regulation in vivo. We performed high-resolution 3D genome mapping and nascent transcription profiling in liver following insulin treatment. Insulin-induced gene regulation repositions gene bodies within the active compartment, while TSSs remain relatively static. Testing deductions from potential biophysical models demonstrates that this sub-genic reorganization is primarily driven by DNA mobilization associated with transcription elongation. Furthermore, super-resolution imaging shows inhibition of transcription elongation impairs recruitment of DNA into active compartments. These results demonstrate reversible hormone signaling repositions genes within active chromatin compartments by transcription elongation to enact rapid and precise transcriptional programs. The second part of this dissertation investigates how transcription itself can function as a cis-regulatory mechanism coordinating gene expression. Focusing on metabolically regulated bidirectional gene pairs, we identify a transcription-dependent regulatory circuit between the bidirectional long non-coding RNA (lncRNA) and its adjacent protein-coding gene (PCG). Rather than acting through the RNA transcripts, transcription process per se at the lncRNA locus promotes activation of the neighboring gene through maintaining the activity of enhancers embedded in the lncRNA. Conversely, transcription of the PCG reciprocally represses the lncRNA, which is also independent of RNA transcripts. This mutual regulation forms a closed-loop cis-regulatory circuit that coordinates gene expression within bidirectional gene pairs, revealing a general mechanism through which transcriptional activity itself can act as a regulatory signal in metabolic adaptation and hormone actions. The third part of this dissertation investigates how cellular redox states control transcriptional programs and hepatic metabolism. By manipulating hepatic glutathione levels through expression of the glutathione-degrading enzyme, Chac1, we demonstrate that glutathione depletion unexpectedly protects against metabolic dysfunction–associated steatotic liver disease (MASLD). Mechanistically, glutathione depletion induces selective protein oxidation and suppresses transcriptional programs driving hepatic lipogenesis. In addition, the transcription of Chac1 is highly regulated by fasting-feeding transition and insulin signaling. Chac1 is also suppressed in livers of MASLD patients. Thus, this chapter reveals a redox-dependent mechanism through which cellular metabolism directly modulates transcriptional and translational regulation of metabolic pathways. Together, these studies demonstrate that rapid transcriptional responses to hormones and metabolic transitions are coordinated through genome organization, cis-regulatory circuits, and redox signaling. By uncovering these interconnected molecular mechanisms, this dissertation provides new insights into how organisms rapidly adapt gene expression to maintain metabolic homeostasis and identifies potential molecular targets for the treatment of metabolic diseases.