Characterization of the Molecular Mechanisms Associated with Circadian Clock Control of Transcription

Abstract

The mammalian circadian clock, found in virtually every cell, coordinates rhythmic expression to control the daily regulation of biological functions. These cell autonomous circadian clocks rely on a molecular feedback loop involving the heterodimeric transcription factor CLOCK:BMAL1 to activate the transcription of repressor elements Period (Per1/2) and Cryptochrome (Cry1/2). PER and CRY feedback to inhibit CLOCK:BMAL1’s transcriptional activation of this feedback loop, as well as expression of genes needed to regulate biological functions. However, recently a surprising disconnect has been found between CLOCK:BMAL1 genome-wide binding sites and CLOCK:BMAL1’s target genes expression. The goal of this research was to investigate the mechanisms of how the circadian clock controls transcription and how disruption of the circadian clock leads to diseases. To achieve this goal, we did a computational analysis of genome-wide sequencing datasets. We found that while CLOCK:BMAL1 promotes rhythmic nucleosome removal, this was not sufficient to activate these enhancers. Likely, these enhancers rely on cooperation of CLOCK:BMAL1 and the recruitment of ubiquitously expressed transcription factors, and not tissue-specific transcription factors to control transcription. These data were exemplified by analysis of how fasting effects the amplitude of rhythmically transcribed CLOCK:BMAL1 target genes, but not the expression of CLOCK:BMAL1. Altogether this suggest that CLOCK:BMAL1 creates transcriptionally permissive enhancers, priming their target genes for transcription activation and may provide a new framework of how disruption of the circadian clock leads to pathological conditions. To study disruption of the circadian clock we used a shift work model in rats to discover if this can emulate cardiovascular disease. Additionally, since temporal food consumption has been found to have preventive effect on shift work induced metabolic disorders, we restricted food intake to the night for a group of shift working rats. We found that five weeks of shift work in rats causes a significant increase in collagen deposition in the heart and that gene expression for shift work rats that had their food restricted, exhibited a significant up-regulation of profibrotic genes. Altogether, this suggests that five weeks of shift work in rats is capable of inducing cardiovascular disease through up-regulation of profibrotic collagen deposition in the heart.