The EC-HDA9 complex rhythmically regulates histone acetylation at the TOC1 promoter in Arabidopsis

Kyounghee Lee,Pil Joon Seo,Paloma Mas

doi:10.1038/s42003-019-0377-7

Kyounghee Lee, Pil Joon Seo + Show 1 more

Open Access

https://doi.org/10.1038/s42003-019-0377-7

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Abstract

Circadian clocks are conserved time-keeper mechanisms in some prokaryotes and higher eukaryotes. Chromatin modification is emerging as key regulatory mechanism for refining core clock gene expression. Rhythmic changes in histone marks are closely associated to the TIMING OF CAB EXPRESSION 1 (TOC1) Arabidopsis clock gene. However, the chromatin-related modifiers responsible for these marks remain largely unknown. Here, we uncover that the chromatin modifier HISTONE DEACETYLASE 9 (HDA9) and the Evening complex (EC) component EARLY FLOWERING 3 (ELF3) directly interact to regulate the declining phase of TOC1 after its peak expression. We found that HDA9 specifically binds to the TOC1 promoter through the interaction with ELF3. The EC-HDA9 complex promotes H3 deacetylation at the TOC1 locus, contributing to suppressing TOC1 expression during the night, the time of EC function. Therefore, we have identified the mechanism by which the circadian clock intertwines with chromatin-related components to shape the circadian waveforms of gene expression in Arabidopsis.

Highlights

Circadian clocks are conserved time-keeper mechanisms in some prokaryotes and higher eukaryotes
As pharmacological inhibition of the reduced potassium dependency 3 (RPD3)/ HDA1 family class I histone deacetylases (HDACs) activities[25] with TSA (Trichostatin A) affects the circadian oscillation[20,25], we investigated their possible function within the circadian clock
(RT-quantitative PCR (qPCR)) analysis revealed that the circadian expression of CLOCK–ASSOCIATED 1 (CCA1) was unaffected in hda[] mutant compared with wild type (Supplementary Fig. 1)

Summary

Introduction

Circadian clocks are conserved time-keeper mechanisms in some prokaryotes and higher eukaryotes. A transcriptional repressing wave includes additional members of the PRR family including PRR5, PRR7, and PRR9 and CCA1 and LHY3,4 Eveningexpressed clock components such as TOC1 and the EC contribute to the repression of the morning-expressed genes[5,6,7,8]. Histone acetyltransferases (HATs) catalyze the addition of acetyl groups to lysine residues at histones, neutralizing positive charges and decreasing the affinity of histones to DNA17 This facilitates the accessibility of transcriptional regulators and other chromatin modifiers[18]. HDA9 might facilitate a closed chromatin structure at the TOC1 promoter, contributing to its declining phase of expression during the night period These results provide an insight into how temporal regulation of histone acetylation is achieved in order to stably maintain circadian activity

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