HDGFR2 regulates osteogenic differentiation by balancing histone crotonoylation and acetylation modifications [RNA-Seq]
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ABSTRACT:
PROVIDER: PRJNA1100476 | ENA |
REPOSITORIES: ENA
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Project description:HDGFR2 regulates osteogenic differentiation by balancing histone crotonoylation and acetylation modifications [Cut & Tag]
| PRJNA1100470 | ENA
Project description:Epigenetics regulates the expression of osteogenic genes and mediates the osteogenic differentiation of MSCs. It was found that hepatoma-derived growth factor (HDGFR2) is a histone methylated reader protein, which can recognize histone methylation modification and play an important "switch" role in gene transcriptional regulation. It is unclear whether HDGFR2 is involved in bone formation studies. Our study aims to investigate the effect of HDGFR2 on osteogenic differentiation and provide evidence for BMSCs as seed cells for tissue regeneration. We found that compared with the wild-type (WT) mice, the bone mass of the femur and the root furcation bone in HDGFR2-KO mice was significantly elevated to attenuate age-related bone loss. Compared with the BMSCs in WT mice, the cloning and osteogenic differentiation of BMSCs in HDGFR2-KO mice were significantly accelerated, and vice versa when HDGFR2 was overexpressed. GO analysis suggested that differential genes were mainly involved in osteoblast differentiation, ossification, collagen fiber tissue and mineralization. The bone defect repair ability of HDGFR2-KO mice was significantly enhanced compared to the control group. Moreover, the depletion of HDGFR2 suppressed periodontal bone loss. The HDGFR2 interacts with the active regulator of SIRT1 (AROS) and sirtuin family deacetylases to form a chromatin remodeling complex, and AROS regulated osteogenesis through combining with HDFGR2. The decreased ratio of H3K18 crotonylation to acetylation improved the transcription of osteogenic genes in HDGFR2 knockout BMSCs. Taken together, these data demonstrated that the knockdown of HDGFR2 could promote osteogenic differentiation and bone repair, providing a new theoretical basis for bone tissue regeneration.
2024-04-19 | GSE263962 | GEO
Project description:Epigenetics regulates the expression of osteogenic genes and mediates the osteogenic differentiation of MSCs. It was found that hepatoma-derived growth factor (HDGFR2) is a histone methylated reader protein, which can recognize histone methylation modification and play an important "switch" role in gene transcriptional regulation. It is unclear whether HDGFR2 is involved in bone formation studies. Our study aims to investigate the effect of HDGFR2 on osteogenic differentiation and provide evidence for BMSCs as seed cells for tissue regeneration.
2024-04-19 | GSE263961 | GEO
Project description:In this study, full human genome promoter microarrays and expression microarrays were used to explore the roles of histone modifications (H3K9Ac and H3K9Me2) upon the induction of MSC osteogenic differentiation.
2009-04-14 | E-MEXP-2134 | biostudies-arrayexpress
Project description:We report the acetylation of lysine residues in the globular domain of H3 (H3K64ac and H3K122ac) marks active gene promoters and also a subset of active enhancers in mouse embryonic stem cells (mESCs), human erythroleukemic cell line (K562). Moreover, we find a novel class of active functional enhancers in ESCs that are marked by H3K122ac but which lack H3K27ac. This work suggests that a more complex analysis of histone acetylation is required to identify enhancers than was previously considered. Examination of histone modifications in mouse ESCs (2 biological replicates) and K562 cells
2016-03-12 | E-GEOD-66023 | biostudies-arrayexpress
Project description:Normal cell type specific histone H3 acetylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 acetylation affect miRNA expression. Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-acetylated histone H3 antibody (06-599, Millipore).
2011-04-05 | E-GEOD-28375 | biostudies-arrayexpress
Project description:The re-assembly of chromatin following DNA replication is a critical event in the maintenance of genome integrity. Histone H3 acetylation at K56 and phosphorylation at T45 are two important chromatin modifications that accompany chromatin assembly. Here we report a microarray expression study of the protein kinase Pkc1, histone acetyl transferase Rtt109 and histone H3 in Saccharomyces cerevisiae under conditions of replicative stress.
2015-12-04 | E-MTAB-3359 | biostudies-arrayexpress
Project description:Differences in global levels of histone acetylation occur in normal and cancer cells, although the reason cells regulate these levels has remained unclear. Here we demonstrate a role for histone acetylation in regulating intracellular pH (pHi). As pHi decreases, histones are globally deacetylated by histone deacetylases (HDACs) and the released acetate anions are co-exported with protons out of the cell by monocarboxylate transporters (MCTs), preventing further reductions in pHi. Conversely, global histone acetylation increases at more alkaline pHi, such as when resting cells are induced to proliferate. Inhibition of HDACs or MCTs decreases acetate export and lowers pHi, particularly compromising pHi maintenance in acidic environments. Global deacetylation at low pH is reflected at a genomic level by decreased abundance and extensive redistribution of acetylation at promoters and intergenic regions. Thus acetylation of chromatin functions as a rheostat to regulate pHi with important implications for therapeutic use of HDAC inhibitors. To investigate the redistribution of H4K16ac throughout the genome upon treatment at pH 6.5
2012-11-04 | E-GEOD-40114 | biostudies-arrayexpress
Project description:Specific histone modifications play important roles in chromatin functions such as activation or repression of gene transcription. These participation must occur as a dynamic process, however, most of histone modification state maps reported to date only provide static pictures linking certain modification with active or silenced states. This study focused on the global histone modification variation that occurs in response to transcriptional reprogramming produced by a physiological perturbation in yeast. We have performed genome-wide chromatin immunoprecipitation analysis for eight specific histone modifications before and after of a saline stress. The most striking change is a quick deacetylation of lysines 9 and 14 of H3 and lysine 8 of H4 associated to repression of genes. Genes that are activated increase the acetylation levels at these same sites, but this acetylation process of activated genes seems minor quantitatively to that of the deacetylation of repressed genes. The observed changes in tri-methylation of lysines 4, 36 and 79 of H3 and also di-methylation of lysine 79 of H3 are much more moderate than those of acetylation. Additionally, we have produced new genome-wide maps for six histone modifications at more than five times higher resolution of previous available data and analyzed for the first time in S. cerevisiae genome wide profiles of two more, acetylation of lysine 8 of H4 and di-methylation of lysine 79 of H3. In this research we have shown that dynamic of acetylation state of histones during activation or repression of transcription is a process much quicker than methylation and therefore the changes produced in the acetylation may affect methylation but the reverse path is not possible. The experiments described in this study compare ChIP with a histone modification antibody to a control ChIP with a core histone antibody. Budding yeast samples were analyzed in exponential growing conditions (YPD) or after 10 minutes of 0.4M NaCl stress. For each experiment 1 or 2 biological replicates were performed.
2014-04-06 | E-GEOD-41587 | biostudies-arrayexpress
Project description:Normal cell type specific histone H3 acetylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 acetylation affect miRNA expression.
2011-04-05 | GSE28375 | GEO