Similar Datasets
Project description:FoxA transcription factors are critical for liver development through their pioneering activity, which initiates a highly complex network thought to become resistant to the loss of any individual hepatic transcription factor via mutual redundancy. To investigate the dispensability of FoxA factors for this regulatory network, we ablated all FoxA genes in the adult liver. Remarkably, loss of FoxA caused a rapid and massive reduction in the expression of key liver genes back to the low levels of the fetal prehepatic endoderm stage, leading to necrosis and lethality within days. Mechanistically, we found FoxA proteins to be required for maintaining chromatin activity, nucleosome positioning and binding by other hepatic transcription factors. Thus, the hepatic gene regulatory network is dependent on the FoxA proteins throughout life.
2020-07-10 | GSE140423 | GEO
Project description:whole genome bisulfite sequencing of single control and Tet-TKD 2-cell embryos
2021-11-22 | GSE156006 | GEO
Project description:The tumorigenesis capacity of MLL-AF4 alone is insufficient for causing leukemia. Based on the finding that an Flt3 gene mutation in the tyrosine kinase domain (TKD) was observed in approximately 15% of MLL leukemia, we investigated synergistic leukemogenesis effects of the two genes in vitro. In a mouse IL3-dependent cell line, 32Dc, the expression of MLL-AF4 and Flt3 TKD was induced using a lentiviral vector. We performed gene expression profiling in the MLL-AF4 and the Flt3 TKD+MLL-AF4 expressing 32Dc cells. The enhancement of Hox genes expression was not identified. However, instead, the expression of S100A6, which was involved in the control of cell proliferation, was synergistically enhanced in the presence of both MLL-AF4 and Flt3 TKD genes. We performed gene expression profiling: 32Dc vs. MLL-AF4 expressing 32Dc, 32Dc vs. Flt3 TKD+MLL-AF4 expressing 32Dc, and MLL-AF4 expressing 32Dc vs. Flt3 TKD+MLL-AF4 expressing 32Dc. A single sample for each expressing cells was analyzed.
2009-03-31 | E-GEOD-14236 | biostudies-arrayexpress
Project description:Nucleosomes are the most basic units of chromatin and are regulators of genome integrity and gene expression. The fundamental mechanism how nucleosomes are dynamically regulated is one of the main questions in chromatin organization; most of the study has, however, focused on its positioning. Here we performed HiLo-MNase-seq, which involves limit and partial digestion of chromatin by micrococcal nuclease (MNase) to identify the positioning of nucleosome array along with the kinetics of MNase digestion. We identified a subset of unique nucleosomes with fast digestion kinetics at the transcription factor binding sites that have been characterized as nucleosome depleted regions (NDRs). By inhibiting RNA polymerase II, we also showed that those nucleosomes changed its sensitivity to MNase in a context-dependent manner. These findings implicated a self-reinforcing regulatory network involving nucleosomes, Pol II, and transcription factors for fine-tuning of gene expression.
2020-02-01 | GSE77526 | GEO
Project description:Foregut organogenesis is regulated by inductive interactions between the endoderm and the adjacent mesoderm. We identified genes induced in the foregut progenitors by the adjacent mesoderm. We used microarrays to detail the global programme of early foregut endoderm gene expression resulting from mesoderm induction and identified distinct classes of up-regulated genes during this process. Xenopus foregut endoderm explants cultured from Stages 15 to 23 either intact with mesoderm or as endoderm alone. Total RNA was isolated from the endoderm of these two culture conditions in quadruplicate and were subjected to Affymetrix microarray analysis.
2012-06-11 | E-GEOD-38654 | biostudies-arrayexpress
Project description:We utilized MNase-seq to profile nucleosome positions in wild type (Ax2) and ChdC null cells both in growing cells and a partially developed state (loose-mound) to study changes in nucleosome positioning and occupancy during development and the impact the deletion of ChdC an ATP-dependent chromatin remodeller has on nucleosome positioning and occupancy. As a control for MNase sequence bias we also digested naked DNA with MNase.
2017-02-26 | GSE70122 | GEO
Project description:The tumorigenesis capacity of MLL-AF4 alone is insufficient for causing leukemia. Based on the finding that an Flt3 gene mutation in the tyrosine kinase domain (TKD) was observed in approximately 15% of MLL leukemia, we investigated synergistic leukemogenesis effects of the two genes in vitro. In a mouse IL3-dependent cell line, 32Dc, the expression of MLL-AF4 and Flt3 TKD was induced using a lentiviral vector. We performed gene expression profiling in the MLL-AF4 and the Flt3 TKD+MLL-AF4 expressing 32Dc cells. The enhancement of Hox genes expression was not identified. However, instead, the expression of S100A6, which was involved in the control of cell proliferation, was synergistically enhanced in the presence of both MLL-AF4 and Flt3 TKD genes.
2009-03-31 | GSE14236 | GEO
Project description:We used the technology of MNase-seq and capture-based target enrichment to analyze nucleosome positioning on the HIV DNA.
2020-03-02 | GSE135551 | GEO
Project description:Foregut organogenesis is regulated by inductive interactions between the endoderm and the adjacent mesoderm. We identified genes induced in the foregut progenitors by the adjacent mesoderm. We used microarrays to detail the global programme of early foregut endoderm gene expression resulting from mesoderm induction and identified distinct classes of up-regulated genes during this process.
2012-06-12 | GSE38654 | GEO
Project description:Iron is a key nutrient for almost all living organisms and paradoxically poorly soluble and consequently poorly bioavailable. To get access to this metal, bacteria have developed many different strategies. One of the most common consists of the use of siderophores, small compounds chelating ferric iron with a very high affinity. Many bacteria are able to produce their own siderophores or use those produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin and is able to use a large panel of exosiderophores. We investigated the ability of P. aeruginosa to use nocardamine (NOCA) and ferrioxamine B (DFOB) as exosiderophores under iron-limited planktonic growth conditions. Proteomic and RT-qPCR approaches showed an induction of the transcription and expression of the outer membrane transporter FoxA in the presence of NOCA or DFO in the bacterial environment. Expression of the proteins of the heme or pyoverdine and pyochelin dependent iron uptake pathways were not affected in the presence of these two tris-hydroxamate siderophores. 55Fe uptake assays using foxA mutants demonstrated that ferri-NOCA was exclusively transported by FoxA, while ferri-DFO was transported by FoxA and at least one another unidentified transporter. The crystal structure of FoxA in complex with NOCA revealed very similar siderophore binding sites between NOCA and DFO. Iron uptake by hydroxamate exosiderophores in P. aeruginosa cells is discussed in the light of these results.
2021-04-29 | PXD020868 | Pride