A scheduler for rhythmic gene expression.

Area of Science:

• Developmental Biology
• Genetics
• Systems Biology

Background:

• Genetic oscillators are fundamental for precisely timed gene expression during development and physiological processes.
• Understanding the regulatory mechanisms governing large-scale gene expression scheduling is crucial for deciphering biological complexity.

Purpose of the Study:

• To investigate how genetic oscillators schedule the expression of thousands of genes using the C. elegans molting clock as a model.
• To identify the key regulatory factors and mechanisms underlying rhythmic gene expression and chromatin dynamics.

Main Methods:

• Single-cell RNA sequencing to analyze gene expression patterns across individual tissues.
• Time-resolved Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to map chromatin accessibility dynamics.
• Development of a linear model integrating transcription factor binding data to predict chromatin dynamics.

Main Results:

• Broad peak phase dispersion observed in individual tissues, correlating with rhythmic chromatin accessibility changes at thousands of regulatory elements.
• A linear model identified nine key transcription factors whose additive binding determines the phase and amplitude of regulatory elements.
• Demonstrated that these factors can also induce constitutive gene expression through destructive interference, as validated by GRH-1/Grainyhead perturbation experiments.

Conclusions:

• A conceptual framework was established for understanding how combinatorial, non-cooperative transcription factor binding schedules complex gene expression patterns.
• The findings provide insights into the regulatory logic of developmental timing and other dynamic biological processes.
• The developed model accurately predicts the impact of transcription factor perturbations on gene expression and chromatin accessibility.