Supplementary Figure 5: HDAC3 is recruited to promoters of transcribed genes.
From: Histone deacetylase 3 associates with MeCP2 to regulate FOXO and social behavior
(a) Enrichment of HDAC3 binding peaks at annotated regions of the genome analyzed using Homer (enrichment over genome). TTS, transcriptional termination site; UTR, untranslated region. (b) Enrichment of HDAC3 binding peaks at genomic regions analyzed using chromatin state profiling of the hippocampus. TSS, transcriptional start site. (c) Aggregate plots of average HDAC3 ChIP-seq intensity signal in 3-month wild-type hippocampus. Aggregate plots were generated at the TSS of genes upregulated (green) and downregulated (blue) in the CA1 of Hdac3 cKO mice. HDAC3 ChIP-seq intensity signal at the TSS of genes with FPKM expression values below 0.1 (black; negative control). TSS, transcriptional start site. (d) UCSC genome browser view of Tle1 and Klf10 loci showing RNA-seq coverage from control and Hdac3 cKO hippocampus, and HDAC3 ChIP-seq coverage and peak calling from wild-type hippocampus. (e) ChIP of HDAC3 and IgG followed by qPCR analysis at the promoters of Arrdc2, Dusp4, Klf10, Tle1, Bdnf, and Nr4a1 in hippocampus of wild-type mice (% input); two-tailed t test; Arrdc2, t(4) = 6.944, ** P = 0.0023; Dusp4, t(4) = 5.074, ** P = 0.0071; Klf10, t(4) = 7.636, ** P = 0.0016; Tle1, t(4) = 2.917, * P = 0.0434; Bdnf, t(4) = 3.350, * P = 0.0286; Nr4a1, t(3) = 6.237, ** P = 0.0083; n = 3, 3 mice. (f) ChIP of HDAC3 and IgG followed by qPCR analysis at the promoters of Arrdc2, Dusp4, Klf10, Tle1, Bdnf, and Nr4a1 in hippocampal CA1 region of control and Hdac3 cKO mice (% input); One-way ANOVA; Arrdc2, F(2,6) = 9.653, * P = 0.0133; Dusp4, F(2,6) = 20.38, ** P = 0.0021; Klf10, F(2,6) = 77.61, **** P < 0.0001; Tle1, F(2,6) = 19.07, ** P = 0.0025; Bdnf, F(2,6) = 15.94, ** P = 0.0040; Nr4a1, F(2,6) = 54.27, *** P = 0.0001. Bonferroni post hoc; control versus Hdac3 KO: Arrdc2, * P = 0.0472; Dusp4, * P = 0.0246; Klf10, *** P = 0.0006; Tle1, * P = 0.0368; Bdnf, * P = 0.0201; Nr4a1, *** P = 0.0006; control versus IgG: Arrdc2, * P = 0.0105; Dusp4, ** P = 0.0014; Klf10, **** P < 0.0001; Tle1, ** P = 0.0017; Bdnf, ** P = 0.0029; Nr4a1, *** P = 0.0001; n = 3, 3, 3 mice. e, f, report mean value ± s.e.m.
