Genes Dev.: co-auth.: group Franken

 2018 Mar 1;32(5-6):347-358. doi: 10.1101/gad.312397.118. Epub 2018 Mar 23.

Clock-dependent chromatin topology modulates circadian transcription and behavior.

Author information

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
Nestle Institute of Health Sciences, CH-1015 Lausanne, Switzerland.
Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.


The circadian clock in animals orchestrates widespread oscillatory gene expression programs, which underlie 24-h rhythms in behavior and physiology. Several studies have shown the possible roles of transcription factors and chromatin marks in controlling cyclic gene expression. However, how daily active enhancers modulate rhythmic gene transcription in mammalian tissues is not known. Using circular chromosome conformation capture (4C) combined with sequencing (4C-seq), we discovered oscillatory promoter-enhancer interactions along the 24-h cycle in the mouse liver and kidney. Rhythms in chromatin interactions were abolished in arrhythmic Bmal1 knockout mice. Deleting a contacted intronic enhancer element in the Cryptochrome 1 (Cry1) gene was sufficient to compromise the rhythmic chromatin contacts in tissues. Moreover, the deletion reduced the daily dynamics of Cry1 transcriptional burst frequency and, remarkably, shortened the circadian period of locomotor activity rhythms. Our results establish oscillating and clock-controlled promoter-enhancer looping as a regulatory layer underlying circadian transcription and behavior.


DNA regulatory elements; chromatin topology; circadian rhythms; promoter–enhancer loops; transcriptional bursting

PMID: 29572261