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A Scheduler for Rhythmic Gene Expression

ABSTRACT: Genetic oscillators drive precisely timed gene expression, crucial for development and physiology. Using the C. elegans molting clock as a model, we investigate how oscillators can schedule the orderly expression of thousands of genes. Single cell RNA sequencing reveals a broad peak phase dispersion in individual issues, mirrored by rhythmic changes in chromatin accessibility at thousands of regulatory elements identified by time-resolved ATAC-seq. We develop a linear model to predict chromatin dynamics based on the binding of >200 transcription factors. This identifies nine key regulators acting additively to determine the peak phase and amplitude of each regulatory element. Strikingly, these factors can also generate constitutive, non-rhythmic activity through destructive interference. The model accurately predicts the impact of GRH-1/Grainyhead perturbation on both chromatin and transcript dynamics, validating its power. This work provides a powerful framework for understanding how combinatorial, non-cooperative transcription factor binding schedules complex gene expression patterns in development and other dynamic biological processes.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE288914 | GEO | 2025/09/17

REPOSITORIES: GEO

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