Metabolic Regulation of Gene Expression by Histone Lysine ß-hydroxybutyrylation [ChIP-seq]

We identified a new type of histone mark-lysine ß-hydroxybutyrylation (Kbhb). This ketone body derived histone mark (Kbhb) was dramatically induced in livers during starvation. To charactize histopne Kbhb: 1) We mapped genomic distributions of histone Kbhb marks (H3K9bhb, H3K4bhb and H4K8bhb) by ChIP-seq in mouse liver. 2) We examined the response of histone Kbhb mark to starvation by carrying out ChIP-seq experiments for H3K9bhb in both "starved" and "fed" mouse liver. 3) We also examined differentially-expressed genes during starvation by carrying out RNA-seq experiments in both "starved" and "fed" mouse liver. By integrating analyses of ChIP-seq and RNA-seq data, we tried to get a correlation between H3K9bhb mark and gene expression in response to starvation. Sequencing was performed on the HiSeq2000 (Illumina). Overall design: ChIP-seq for histone Kbhb marks in both "starved (ST)" and "fed (AL)" mouse liver cells The anti-H3K4bhb, -H3K9bhb, and -H4K8bhb antibodies were generated from PTM biolabs. The process for generating antibodies were described similarly in Cell, 2011. 146: p. 1016-1028, Mol Cell, 2015. 58(2): p. 203-15, Nat Chem Biol, 2014. 10(5): p. 365-70, except for using different immunogens.