Project description:Global gene expression analysis was performed to investigate the changes of the fibroblast phenotype after four-week inductions toward adipocytic, osteoblastic and chondrocytic lineages. Human cells. Differential gene regulation, interpreted through Gene Set Enrichment Analysis, highlight important similarities and differences of induced fibroblasts compared to control cultures of human fibroblasts, adipocytes, osteoblasts and articular chondrocytes.
Project description:Global gene expression analysis was performed to investigate the changes of the fibroblast phenotype after four-week inductions toward adipocytic, osteoblastic and chondrocytic lineages. Human cells. Differential gene regulation, interpreted through Gene Set Enrichment Analysis, highlight important similarities and differences of induced fibroblasts compared to control cultures of human fibroblasts, adipocytes, osteoblasts and articular chondrocytes. Fibroblast controls were compared to Adipogenic induced fibroblasts and adipocytes. Gene sets were analysed with GSEA (webgestalt). Repeated for each lineage.
Project description:Sp7/Osterix is a master regulator of osteoblast specification. To identify transcripts profile in Sp7 positive osteoblast, we performed RNA-seq on primary mouse calvarial cells obtained from Sp7-GFP reporter mice at P1. By hierarchical clustering using transcriptional profiles for chondrocytes and mouse embryonic fibroblasts (MEFs) together with the osteoblast data, we identified cell-type enriched gene expression signatures in osteoblasts, chondrocytes and MEFs. In conjunction with Sp7 ChIP-seq in osteoblast, we identified putative Sp7 targets which underlie the osteoblast regulatory program.
Project description:We report that the winged helix transcription factor FOXA1 is unexpectedly associated with components of single and double stranded-DNA repair complexes. Biochemical studies and high-throughput approaches validated the hierarchical composition of this FOXA1-nucleated machinery and revealed the dependency on FOXA1 for global targeting of the key repair polymerase POLB. Genome-wide DNA methylomes at single-base resolution demonstrated that FOXA1-DNA repair complex is functionally linked to DNA demethylation in a lineage specific fashion. Loss-of-function studies indicate that a significant portion of FOXA1-bound regions display localized reestablishment of methylation and that the subsets with most consistent hypermethylation are represented by active promoters and enhancers that also exhibit the greatest depletion of POLB following FOXA1 removal. Consistently, forced expression of FOXA1 commits its binding sites to an active DNA demethylation in a POLB dependent manner. Finally, we showed that FOXA1-associated DNA demethylation is tightly coupled with genomic targeting of estrogen receptor and estrogen responsiveness. Together, our results link FOXA1-associated DNA demethylation to its transcriptional pioneering.
Project description:LCM-RNA-Seq data obtained from Xenopus tropicalis chondrocytes and osteoblasts at different stages of differentiation -immature chondrocytes and mature (hypertrophic) chondrocytes- isolated from the ceratohyal. Osteoblasts isolated from the mandible (dentary bone).
Project description:DNA methylation can contribute to the stable transcriptional silencing of mammalian genes. Oftentimes, these genes are important developmental regulators, and their silencing in cell types where they are not supposed to be active is important for the phenotypic stability of the cells. To identify key developmental regulator genes whose expression in terminally differentiated cells may be inhibited by DNA methylation, mouse dermal fibroblasts were demethylated with 5-aza-2-deoxycytidine, and changes in gene expression monitored by microarray analysis. Three biological replicates for both control and 5-aza-2'-deoxycytidine treatment were derived. Cells were primary mouse dermal fibroblasts, primary mouse chondrocytes, and primary mouse osteoblasts derived separately for each biological replicate. Treated cells were exposed to 5uM 5-aza-2'-deoxycytidine for 96 hours with recovery in normal medium for 24 hours. Control cells were untreated.
Project description:The transcriptional regulator Runx2 has essential roles in chondrocytes and osteoblasts, central to the coordinated development of cartilage and bone. However, the regulatory mechanisms underlying Runx2’s roles in skeletal programming are not well understood. Here, we performed an integrative analysis of Runx2–DNA binding and chromatin accessibility in vivo and identified cell type-distinct chromatin accessibility underlying Runx2 roles in osteoblasts and chondrocytes.
Project description:The transcriptional regulator Runx2 has essential roles in chondrocytes and osteoblasts, central to the coordinated development of cartilage and bone. However, the regulatory mechanisms underlying Runx2’s roles in skeletal programming are not well understood. Here, we performed an integrative analysis of Runx2–DNA binding and chromatin accessibility in vivo and identified cell type-distinct chromatin accessibility underlying Runx2 roles in osteoblasts and chondrocytes.
