Histone Lysine ß-hydroxybutyrylation ChIP-seq and RNA-seq analysis of mouse liver during starvation
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE69617 | GEO | 2016/04/06
SECONDARY ACCESSION(S): PRJNA285986
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2016-04-06 | E-GEOD-69617 | biostudies-arrayexpress
Project description:Histone Lysine ß-hydroxybutyrylation ChIP-seq and RNA-seq analysis of mouse liver during starvation
| PRJNA285986 | ENA
Project description: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).
2016-04-06 | GSE69615 | GEO
Project description: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).
2016-04-06 | GSE69616 | GEO
Project description:β-hydroxybutyrate (β-OHB) is an essential metabolic energy source during fasting and functions as a chromatin regulator by lysine β-hydroxybutyrylation (Kbhb) modification of the core histones H3 and H4. We report that Kbhb on histone H3 (H3K9bhb) is enriched at proximal promoters of critical gene subsets associated with lipolytic and ketogenic metabolic pathways in small intestine (SI) crypts during fasting. Similar Kbhb enrichment is observed in Lgr5+ stem cell-enriched epithelial spheroids treated with β-OHB in vitro. Combinatorial chromatin state analysis reveals that H3K9bhb is associated with active chromatin states and that fasting enriches for an H3K9bhb-H3K27ac signature at active metabolic gene promoters and distal enhancer elements. Intestinal knockout of Hmgcs2 results in marked loss of H3K9bhb-associated loci, suggesting that local production of β-OHB is responsible for chromatin reprogramming within the SI crypt. We conclude that modulation of H3K9bhb in SI crypts is a key gene regulatory event in response to fasting.
2021-11-23 | GSE122896 | GEO
Project description:Here we report the identification and verification of a ?-hydroxybutyrate-derived protein modification, lysine ?-hydroxybutyrylation (Kbhb), as a new type of histone mark. Histone Kbhb marks are dramatically induced in response to elevated ?-hydroxybutyrate levels in cultured cells and in livers from mice subjected to prolonged fasting or streptozotocin-induced diabetic ketoacidosis. In total, we identified 44 histone Kbhb sites, a figure comparable to the known number of histone acetylation sites. By ChIP-seq and RNA-seq analysis, we demonstrate that histone Kbhb is a mark enriched in active gene promoters and that the increased H3K9bhb levels that occur during starvation are associated with genes upregulated in starvation-responsive metabolic pathways. Histone ?-hydroxybutyrylation thus represents a new epigenetic regulatory mark that couples metabolism to gene expression, offering a new avenue to study chromatin regulation and diverse functions of ?-hydroxybutyrate in the context of important human pathophysiological states, including diabetes, epilepsy, and neoplasia.
| S-EPMC5540445 | biostudies-literature
Project description:We identified a new type of histone mark-lysine Ã-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). 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.
2016-04-06 | E-GEOD-69615 | biostudies-arrayexpress
Project description:Ketone bodies are bioactive metabolites that function as energy substrates, signaling molecules, and regulators of histone modifications. β-hydroxybutyrate (β-OHB) is utilized in lysine β-hydroxybutyrylation (Kbhb) of histones, and associates with starvation-responsive genes, effectively coupling ketogenic metabolism with gene expression. The emerging diversity of the lysine acylation landscape prompted us to investigate the full proteomic impact of Kbhb. Global protein Kbhb is induced in a tissue-specific manner by a variety of interventions that evoke β-OHB. Mass spectrometry analysis of the β-hydroxybutyrylome in mouse liver revealed 891 sites of Kbhb within 267 proteins enriched for fatty acid, amino acid, detoxification, and one-carbon metabolic pathways. Kbhb inhibits S-adenosyl-L-homocysteine hydrolase (AHCY), a rate-limiting enzyme of the methionine cycle, in parallel with altered metabolite levels. Our results illuminate the role of Kbhb in hepatic metabolism under ketogenic conditions and demonstrate a functional consequence of this modification on a central metabolic enzyme.
| S-EPMC8372761 | biostudies-literature
Project description:Fasting enriched metabolic enhancers associate with histone lysine 9 ß-hydroxybutyrylation
| PRJNA506838 | ENA
Project description:We identified a new type of histone mark-lysine Ã-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). RNA-seq of mouse liver cells both in "starved" and "fed" conditions.
2016-04-06 | E-GEOD-69616 | biostudies-arrayexpress