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Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (BeadChip)

ABSTRACT: Suberoylanilidehydroxamic acid (SAHA) significantly increased the expression levels of 127 transcripts and suppressed expression of 130 genes by more than 2-fold within 3 standard deviations of the mean in differentiating MC3T3 sc4 osteoblasts

ORGANISM(S): Mus musculus

PROVIDER: GSE50549 | GEO | 2013/09/04

SECONDARY ACCESSION(S): PRJNA217928

REPOSITORIES: GEO

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Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (BeadChip)

Project description:Suberoylanilidehydroxamic acid (SAHA) significantly increased the expression levels of 127 transcripts and suppressed expression of 130 genes by more than 2-fold within 3 standard deviations of the mean in differentiating MC3T3 sc4 osteoblasts Total RNA was obtained from differentiating MC3T3 sc4 cells treated with SAHA or vehicle (DMSO).

2013-09-04 | E-GEOD-50549 | biostudies-arrayexpress

Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (ChIP-Seq)

Project description:ChIP-Seq analysis revealed that suberoylanilidehydroxamic acid (SAHA) increases genome-wide H4 acetylation in differentially regulated genes, except for the 500 bp upstream of transcription start sites (TSS). Chromatin immunoprecipitation (ChIP) with massively parallel high throughput sequencing (Seq) was used to map genome-wide histone H4 acetylation (K4/7/11/15) in the presence or absence of SAHA in differentiating MC3T3 sc4 osteoblasts.

2013-09-04 | E-GEOD-50551 | biostudies-arrayexpress

Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (ChIP-Seq)

2013-09-04 | GSE50551 | GEO

Histone deacetylase inhibition promotes osteoblast maturation by altering the histone H4 epigenome and reduces Akt phosphorylation.

Project description:Bone has remarkable regenerative capacity, but this ability diminishes during aging. Histone deacetylase inhibitors (HDIs) promote terminal osteoblast differentiation and extracellular matrix production in culture. The epigenetic events altered by HDIs in osteoblasts may hold clues for the development of new anabolic treatments for osteoporosis and other conditions of low bone mass. To assess how HDIs affect the epigenome of committed osteoblasts, MC3T3 cells were treated with suberoylanilide hydroxamic acid (SAHA) and subjected to microarray gene expression profiling and high-throughput ChIP-Seq analysis. As expected, SAHA induced differentiation and matrix calcification of osteoblasts in vitro. ChIP-Seq analysis revealed that SAHA increased histone H4 acetylation genome-wide and in differentially regulated genes, except for the 500 bp upstream of transcriptional start sites. Pathway analysis indicated that SAHA increased the expression of insulin signaling modulators, including Slc9a3r1. SAHA decreased phosphorylation of insulin receptor ?, Akt, and the Akt substrate FoxO1, resulting in FoxO1 stabilization. Thus, SAHA induces genome-wide H4 acetylation and modulates the insulin/Akt/FoxO1 signaling axis, whereas it promotes terminal osteoblast differentiation in vitro.

| S-EPMC3789974 | biostudies-literature

Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-04 | E-GEOD-50552 | biostudies-arrayexpress

Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-09-04 | GSE50552 | GEO

Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome.

Project description:The structural unit of eukaryotic chromatin is a nucleosome, comprising two histone H2A-H2B heterodimers and one histone (H3-H4)2 tetramer, wrapped around by ∼146 bp of DNA. The N-terminal flexible histone tails stick out from the histone core and have extensive posttranslational modifications, causing epigenetic changes of chromatin. Although crystal and cryogenic electron microscopy structures of nucleosomes are available, the flexible tail structures remain elusive. Using NMR, we have examined the dynamics of histone H3 tails in nucleosomes containing unmodified and tetra-acetylated H4 tails. In unmodified nucleosome, the H3 tail adopts a dynamic equilibrium structure between DNA-contact and reduced-contact states. In acetylated H4 nucleosome, however, the H3 tail equilibrium shifts to a mainly DNA-contact state with a minor reduced-contact state. The acetylated H4 tail is dynamically released from its own DNA-contact state to a reduced-contact state, while the H3 tail DNA-contact state becomes major. Notably, H3 K14 in the acetylated H4 nucleosome is much more accessible to acetyltransferase Gcn5 relative to unmodified nucleosome, possibly due to the formation of a favorable H3 tail conformation for Gcn5. In summary, each histone tail adopts a characteristic dynamic state but regulates one other, probably creating a histone tail network even on a nucleosome.

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Altering cancer transcriptomes using epigenomic inhibitors [Illumina beadchip]

Project description:We have compared the genome-wide effects on the transcriptome after treatment with ICG-001 (the specific CBP inhibitor) versus C646, a compound that competes with acetyl-coA for the Lys-coA binding pocket of both CBP and p300. We found that both drugs cause large-scale changes in the transcriptome of HCT116 colon cancer cells and PANC1 pancreatic cancer cells, and reverse some tumor-specific changes in gene expression. Interestingly, although the epigenetic inhibitors affect cell cycle pathways in both the colon and pancreatic cancer cell lines, the WNT signaling pathway was affected only in the colon cancer cells. Notably, WNT target genes were similarly down-regulated after treatment of HCT116 with C646 as with ICG-001. Total RNA obtained from isolated HCT116 or PANC1 cell lines were treated with 10uM ICG-001, 10uM C646, or 0.05% DMSO and collected after 12 or 96 hours.

| S-ECPF-GEOD-64038 | biostudies-other

Inhibition of Osteoblast Proliferation by Formaldehyde

Project description:RNA-seq analysis was performed to identify key signaling responding to formaldehyde in MC3T3-E1.

2023-05-22 | GSE151037 | GEO

Human histone acetyltransferase 1 protein preferentially acetylates H4 histone molecules in H3.1-H4 over H3.3-H4.

Project description:In mammalian cells, canonical histone H3 (H3.1) and H3 variant (H3.3) differ by five amino acids and are assembled, along with histone H4, into nucleosomes via distinct nucleosome assembly pathways. H3.1-H4 molecules are assembled by histone chaperone CAF-1 in a replication-coupled process, whereas H3.3-H4 are assembled via HIRA in a replication-independent pathway. Newly synthesized histone H4 is acetylated at lysine 5 and 12 (H4K5,12) by histone acetyltransferase 1 (HAT1). However, it remains unclear whether HAT1 and H4K5,12ac differentially regulate these two nucleosome assembly processes. Here, we show that HAT1 binds and acetylates H4 in H3.1-H4 molecules preferentially over H4 in H3.3-H4. Depletion of Hat1, the catalytic subunit of HAT1 complex, results in reduced H3.1 occupancy at H3.1-enriched genes and reduced association of Importin 4 with H3.1, but not H3.3. Finally, depletion of Hat1 or CAF-1p150 leads to changes in expression of a H3.1-enriched gene. These results indicate that HAT1 differentially impacts nucleosome assembly of H3.1-H4 and H3.3-H4.

| S-EPMC3307289 | biostudies-literature

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