Interplay between circadian and other transcription factors—Implications for cycling transcriptome reprogramming

2025/11/28 by Xinyu Y. Nie, Jérôme S. Menet · 1 voice
Neuroscience · Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Circadian rhythm and melatonin #Plant Molecular Biology Research #Genomics and Chromatin Dynamics

paper · doi:10.1002/1873-3468.70232

openalex publication_date 2025/11/28 · openalex created_date 2025/11/28 · openalex updated_date 2026/06/14

Abstract

Circadian transcription factors (TFs) orchestrate daily rhythms in gene expression to drive rhythmic biological functions. In mammals, this system relies on the TF CLOCK:BMAL1, which binds E-boxes to initiate rhythmic transcription. While traditionally viewed as a master activator, CLOCK:BMAL1 is now recognized to engage in additional regulatory functions that are essential for its activity. This perspective focuses on the mammalian circadian clock and integrates genomic, structural, and single-molecule footprinting data to highlight emerging insights into how CLOCK:BMAL1 regulates chromatin architecture, cooperates with other TFs, and coordinates complex enhancer dynamics. We propose an updated framework for how circadian TFs operate within dynamic and multifactorial chromatin landscapes, and prime cis-regulatory elements for rhythmic transcriptional bursts. We also discuss how this framework underlies circadian reprogramming and transcriptional plasticity.

Citations

• Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
• Genome access is transcription factor-specific and defined by nucleosome position
• Molecular architecture of the mammalian circadian clock

Discussions

• ⌛This perspective on the mammalian circadian clock integrates genomic, structural, and single-molecule data showing that CLOCK:BMAL1 isn’t just a master switch—it shapes #Chromatin, teams with other T [bsky, 1 points, 0 comments]

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