Clock-dependent chromatin topology modulates circadian transcription and behavior.

Jérôme Mermet,Frédéric Gachon,Félix Naef,Kyle Gustafson,Damien Nicolas,Paul Franken,Cédric Gobet,Jake Yeung,Daniel Mauvoisin,Clémence Hurni,Céline Jouffe,Yann Emmenegger

doi:10.1101/gad.312397.118

Abstract

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.

Highlights

The circadian clock, encoded in a core genetic network, governs rhythms in behavior and physiology (Schibler et al 2015), such as nocturnal activity in mice and oscillations in carbohydrate and lipid metabolism in the liver (Bass and Lazar 2016)
These transcripts are rhythmically expressed in the liver at opposite times of day, Cryptochrome 1 (Cry1) peaking during the night at Zeitgeber time 20 (ZT20) and Glycogen Synthase 2 (Gys2) peaking during the day at ZT08 (Supplemental Fig. S1A)
Using circular chromosome conformation capture (4C) combined with sequencing (4C-seq) (Gheldof et al 2012), we estimated the interaction frequencies of DNA bait fragments placed near the transcription start sites (TSSs) of Cry1 and Gys2 versus the entire genome in livers of wild-type mice collected at ZT08 and ZT20 (n = 4 per time point). 4C-seq signals around the Cry1 and Gys2 TSSs decayed to background levels following a power law (Supplemental Fig. S1B,C; Supplemental Table S1; Sanborn et al 2015) and did not exceed background on trans chromosomes (Supplemental Fig. S1D,E; Supplemental Table S1)

Summary

Introduction

The circadian clock, encoded in a core genetic network, governs rhythms in behavior and physiology (Schibler et al 2015), such as nocturnal activity in mice and oscillations in carbohydrate and lipid metabolism in the liver (Bass and Lazar 2016) This clock orchestrates the daily rhythmic synthesis of thousands of transcripts by impinging on multiple gene regulatory layers (Zhang et al 2014). Moters and enhancer DNA elements through promoter– enhancer looping (Fulco et al 2016) The remodeling of such DNA contacts and the accompanying dynamics of transcriptional responses have been investigated in the context of signal-dependent gene induction, cell differentiation, and developmental transitions (Palstra et al 2003; Ghavi-Helm et al 2014; Kuznetsova et al 2015). Rhythmic transcription could be regulated over an established static promoter–enhancer network (Ghavi-Helm et al 2014; Xu et al 2016), or, the clock could drive dynamic promoter–enhancer looping for high-amplitude daily oscillations in transcription

Methods

Results

Conclusion