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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 .

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