Making Time Visible: A Circadian Window into Nuclear Organization Driving Gene Expression

Objective

Almost all life on Earth has a circadian clock to anticipate and adapt to daily environmental cycles by rhythmically regulating gene expression, protein levels, metabolism, and physiology. Disruptions to these rhythms in humans, like shift workers and frequent flyers, increase the risks of diabetes, cancer, and neurodegenerative diseases. While the transcriptional-translational feedback loop that regulates rhythmic expression has been extensively studied, far less is known about how nuclear architecture and gene expression machinery are dynamically reorganized over the circadian cycle. The green alga Chlamydomonas reinhardtii offers a powerful model to address this gap, as it exhibits a strong, self-sustained circadian clock, is genetically tractable, and is well-suited for structural biology. This project will investigate how circadian timing shapes both global gene expression outputs and nuclear architecture. In Aim 1, I will define clock-dependent rhythms in RNA and protein abundance by performing transcriptomic and proteomic analyses on entrained (12 h light/12 h dark) and free-running (constant light) cultures. This will provide a systems-level view of how circadian control reshapes cellular function beyond transcription. In Aim 2, I will apply time-resolved cryo-electron tomography (cryo-ET) to visualize nuclei in situ at defined phases across the circadian cycle under light-dark entrainment. By mapping the organization of nucleosomes, nucleoli, and pre-ribosomes over 24 hs, I will uncover how nuclear architecture is dynamically remodeled under circadian control. Together, these complementary approaches will provide the first multi-scale picture of circadian control of nuclear organization and gene expression machinery in a eukaryotic cell. This work will establish new paradigms for how biological clocks orchestrate cellular architecture and function, with broad implications for circadian biology, systems regulation, and structural cell biology.