# CLOCK is an Epigenetic Integrator of Circadian Rhythm and T Cell Immunity

## TL;DR

This study shows how the CLOCK protein regulates T cell immunity and circadian rhythms through distinct epigenetic mechanisms.

## Contribution

The study reveals distinct roles of CLOCK in regulating circadian and immune gene programs in T cells.

## Key findings

- CLOCK-BMAL1 controls circadian and metabolic programs through promoter binding.
- CLOCK alone regulates immune genes and disrupts Th17 suppression in mutant models.
- CLOCKΔ19 leads to β-catenin stabilization and altered T cell differentiation.

## Abstract

The circadian clock imposes a critical yet incompletely understood layer of regulation on adaptive immunity. T helper 17 (Th17) antimicrobial immune responses including expression of IL-17A by lamina propria CD4+ T cells, exhibit diurnal variation and are sensitive to circadian disruption. While the core circadian regulators CLOCK and BMAL1 canonically function as a heterodimer to drive rhythmic gene expression, emerging evidence suggests they may have distinct regulatory roles. Here we integrated ChIP-seq, ATAC-seq, and RNA-seq analyses in naïve CD4+ T cells to reveal that the CLOCK-BMAL1 complex controls circadian and metabolic programs through promoter binding, whereas exclusive CLOCK binding at promoters, together with CLOCK-BMAL1 binding at enhancers, regulates immune-associated genes. Using the mutant CLOCKΔ19, which lacks the transactivation domain, we observed disrupted circadian transcription and globally reduced chromatin accessibility, alongside increased accessibility at Th17-associated loci and altered their temporal regulation. Functionally, CLOCKΔ19 produces β-catenin stabilization in T cells, pronounced expansion of RORγt+ CD4+ T cells and Treg cells, impaired Treg suppression of Th17 responses, heightened Th17 responses, and reduced IFN-γ production during viral infection. Collectively, these findings define BMAL1 dependent and independent CLOCK functions that program naïve CD4+ T cell fate, restrain Th17 differentiation, and preserve immune homeostasis.