Gene expression profiles in multiple metabolic organs have revealed a circadian control of the transcriptome, which might be mediated by regulation of histone acetylation (11–13) that alters the structure of the epigenome. Regulation of histone acetylation is complex, involving multiple histone acetyltransferase (HATs) and histone deacetylases (HDACs)(14). Histone deacetylase 3 (HDAC3) functions in the regulation of circadian rhythm and glucose metabolism (15). Here we report diurnal recruitment of HDAC3 to the mouse liver genome detected by chromatin immunoprecipitation with an HDAC3-specific antibody (Supp. Fig. 1) and massively parallel DNA sequencing (ChIP-seq).

At ZT10, in the light period when mice are inactive, HDAC3 bound to over 14,000 sites in adult mouse liver (the HDAC3 ZT10 cistrome)(Supp. Fig. 2A); a majority of these binding sites were distant from transcription start sites (TSS) or present in introns (Supp. Figs. 2B and C). However, at ZT22, in the dark period when mice are active and feeding, the HDAC3 signal was dramatically reduced at ZT10 sites, with only 120 specific peaks (Fig. 1A; Supp. Figs. 2A, 2D, and 3). HDAC3 recruitment oscillated in a 24h cycle (Fig. 1B), and this rhythm was retained in constant darkness (Fig. 1C), suggesting that it was controlled by the circadian clock. The liver clock is entrained by food intake (16) and, indeed, the pattern of HDAC3 enrichment was reversed when food was provided only during the light period (Fig. 1D), further supporting the conclusion that the rhythm of HDAC3 genomic recruitment was controlled by the circadian clock.

Despite its known role in histone deacetylation and transcriptional repression, HDAC3 recruitment has been reported to be associated with high histone acetylation, RNA polymerase II (Pol II) recruitment, and gene expression in human primary T cells (17). In mouse liver, HDAC3 recruitment at ZT10 was also enriched around active genes (Supp. Fig. 4A), and many of these display circadian expression patterns (18)(Supp. Fig. 4B). Thus HDAC3 may have an important role in transient regulation of these active genes by the circadian clock. Consistent with this hypothesis, we observed decreases in acetylation of histone H3 lysine 9 (H3K9) at ZT10 compared with that at ZT22, the inverse of HDAC3 recruitment to these sites (Figs. 2A and B). Deletion of hepatic HDAC3 by tail vein injection of adeno-associated virus expressing cre-recombinase (AAV-Cre) into adult C57Bl/6 mice homozygous for a floxed HDAC3 allele (HDAC3^fl/fl)(Supp. Fig. 1A) led to H3K9 acetylation at ZT10 comparable to that of wild type (WT) mice at ZT22 (Figs. 2A and B). Accompanying the decreased H3K9 acetylation at ZT10 was a decrease in binding of RNA polymerase II (Pol II) at the TSS of genes with HDAC3 binding within 10kb, indicating that they were actively repressed (Fig. 2C). Indeed, the majority of genes whose transcripts were increased 1 week after HDAC3 deletion in liver displayed HDAC3 binding within 10 kb of their TSS in WT mice at ZT10 (Fig. 2D). Thus, genome-wide diurnal recruitment of HDAC3 directs a rhythm of epigenomic modification, Pol II recruitment, and gene expression.

Although HDAC3 recruitment to the genome is diurnal, the abundance of HDAC3 was constant throughout the light/dark cycle (Fig. 3A). HDAC3 enzyme activity requires interaction with nuclear receptor (NR) corepressors (19), and de novo motif analysis of the HDAC3 binding sites revealed the classical motif recognized by a number of NRs (Supp. Fig. 5). The NR Rev-erbα is a transcriptional repressor that is expressed in a circadian manner (20), and the abundance of Rev-erbα protein oscillated in phase with HDAC3 recruitment (Fig. 3A). We used a Rev-erbα-specific antibody (Supp. Fig. 6A) to determine the Rev-erbα binding sites (Supp. Figs. 6B and C). At ZT10, the Rev-erbα binding sites overlapped with the majority of HDAC3 binding sites (Fig. 3B). Furthermore, Rev-erbα bound to the majority of HDAC3 ZT10 sites at ZT10 but not ZT22 (Fig. 3C). The extent of overlap of HDAC3 with Rev-erbα was surprising given that other NRs can interact with corepressors and HDAC3 (21). However, HDAC3 recruitment was diminished at many sites in Rev-erbα KO mice (Fig. 3D), consistent with a critical role for Rev-erbα, although residual HDAC3 binding suggests that other factors also contribute to its recruitment. Rev-erbα recruits HDAC3 via the nuclear receptor corepressor (NCoR) (22, 23). NCoR was recruited to HDAC3 sites with a diurnal rhythm (Fig. 3C), which was attenuated in the Rev-erbα KO mice (Fig. 3E). Moreover, HDAC3 bound together with NCoR as well as Rev-erbα at the majority of ZT10 sites (Supp. Fig 7).

We addressed the biological role of the circadian genomic recruitment of HDAC3 in mouse liver. The set of genes bound by Rev-erbα and HDAC3, and upregulated in livers depleted of HDAC3, was enriched for genes encoding proteins that function in lipid metabolic processes (Fig. 4A). Indeed, in liver of chow fed mice in which HDAC3 was deleted for 2 weeks, Oil Red O staining for neutral lipid was dramatically increased (Fig. 4B) and liver triglyceride content was increased nearly 10-fold (Fig. 4C), with serum transaminase activity increasing only modestly (Supp. Fig. 8A). This was consistent with a fatty liver phenotype of mice depleted of hepatic HDAC3 in utero [(24) and Supp. Fig. 9].

The majority of genes upregulated in liver depleted of Rev-erbα (25) were bound by HDAC3 as well as Rev-erbα at ZT10 (Supp. Fig. 10). Indeed, chow-fed C57Bl/6 mice genetically lacking Rev-erbα (26) had normal serum transaminase activity (Supp. Fig. 8B), but Oil Red O staining of liver was increased (Fig. 4D) and hepatic triglyceride content was nearly double that of WT mice (Fig. 4E). The relatively modest hepatic steatosis in the Rev-erbα deleted mice likely reflects a role for HDAC3 in mediating effects of other NRs, including Rev-erbβ whose circadian expression pattern is similar to that of Rev-erbα (27), but could also reflect a compensatory effect of Rev-erbα knockout in other tissues. Nevertheless the finding that depletion of either Rev-erbα or HDAC3 led to a fatty liver phenotype supports the conclusion that circadian Rev-erbα recruitment of HDAC3 to lipid metabolic genes plays a critical physiological role.

Rev-erbα and HDAC3 colocalized at 130 lipid biosynthetic genes at ZT10 (Supp. Table 1), and Pol II recruitment increased from ZT10 to ZT22 at the TSS of many of these genes (Fig. 2C), including Fasn, Acaca, and Thrsp, suggesting that they were directly repressed. Assessment of palmitate synthesis after injection of deuterated water revealed increased de novo lipogenesis in mice lacking hepatic HDAC3 (Fig. 4F) or in Rev-erbα KO mice (Supp. Fig. 11), thus revealing a molecular mechanism underlying the observation that hepatic lipogenesis in mice follows a diurnal rhythm (28) that is antiphase to Rev-erbα and HDAC3 recruitment to the mouse genome.