Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA125807 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Early B cell factor 1 (EBF1) is one of the key transcription factors required for orchestrating B-cell lineage development. Although studies have shown that Ebf1 haploinsufficiency is involved in the development of leukemia, no study has been conducted that characterizes the global effect of Ebf1 heterozygosity on the proteome of pro-B lymphocytes. Here, we employ both DIA (Data Independent Acquisition) and shotgun DDA (Data Dependent Acquisition) workflows for profiling proteins that are differently expressed between Ebf1+/+ and Ebf1+/- cells. Both DDA and DIA were able to reveal the downregulation of the EBF1 transcription factor in Ebf1+/- pro-B lymphocytes. Further examination of differentially expressed proteins by DIA revealed that, similar to EBF1, the expression of other B-cell lineage regulators, such as TCF3 and Pax5, is also down-regulated in Ebf1 heterozygous cells. Functional DIA analysis of differentially expressed proteins showed that EBF1 heterozygosity resulted in the deregulation of at least 8 transcription factors involved in lymphopoiesis, and to the deregulation of key proteins playing crucial roles in survival, development and differentiation of pro-B lymphocytes.
2017-12-20 | PXD008396 | Pride
Project description:Sex differences in liver gene expression are dictated by sex-differences in circulating growth hormone (GH) profiles. Presently, the pituitary hormone dependence of mouse liver gene expression was investigated on a global scale to discover sex-specific early GH response genes that might contribute to sex-specific regulation of downstream GH targets and to ascertain whether intrinsic sex-differences characterize hepatic responses to plasma GH stimulation. RNA expression analysis using 41,000-feature microarrays revealed two distinct classes of sex-specific mouse liver genes: genes subject to positive regulation (class-I) and genes subject to negative regulation by pituitary hormones (class-II). Genes activated or repressed in hypophysectomized (Hypox) mouse liver within 30-90min of GH pulse treatment at a physiological dose were identified as direct targets of GH action (early response genes). Intrinsic sex-differences in the GH responsiveness of a subset of these early response genes were observed. Notably, 45 male-specific genes, including five encoding transcriptional regulators that may mediate downstream sex-specific transcriptional responses, were rapidly induced by GH (within 30min) in Hypox male but not Hypox female mouse liver. The early GH response genes were enriched in 29 male-specific targets of the transcription factor Mef2, whose activation in hepatic stellate cells is associated with liver fibrosis leading to hepatocellular carcinoma, a male-predominant disease. Thus, the rapid activation by GH pulses of certain sex-specific genes is modulated by intrinsic sex-specific factors, which may be associated with prior hormone exposure (epigenetic mechanisms) or genetic factors that are pituitary-independent, and could contribute to sex-differences in predisposition to liver cancer or other hepatic pathophysiologies.
2010-01-27 | GSE17644 | GEO
Project description:The transcription factor EBF1 is essential for lineage specification in early B cell development. Here we demonstrate by conditional mutagenesis that EBF1 was required for B cell commitment, pro-B cell development and subsequent transition to pre-B cells. Later in B cell development, EBF1 was essential for the generation and maintenance of distinct mature B cell types. Marginal zone and B-1 B cells were lost, whereas follicular and germinal center B cells were reduced in the absence of EBF1. Activation of the B cell receptor resulted in impaired intracellular signaling, proliferation and survival of EBF1-deficient follicular B cells. Immune responses were severely reduced upon Ebf1 inactivation, as germinal centers were formed but not maintained. ChIP- and RNA-sequencing of follicular B cells identified EBF1-activated genes that code for receptors, signal transducers and transcriptional regulators implicated in B cell signaling. Notably, ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. These gain- and loss-of-function analyses uncovered novel important functions of EBF1 in controlling B cell immunity. 29 samples (4 ChIP-seq,16 input, 9 RNA-seq), All ChIP-seq in 2 biological replicates, but EBF1 ChIP-seq Pro-B in 2 technical replicates; All RNA-seq in 2 biological replicates but RNA-seq mature B_FO B_Cd23-Cre Ebf1(fl/–). WT and experimental samples are provided.
2012-03-20 | E-GEOD-35857 | biostudies-arrayexpress
Project description: Not available
| S-EPMC8784167 | biostudies-literature
Project description:Transcription factor Ebf1 is an important determinant of early B lymphopoiesis. To gain insight into differentiation stage-specific functions of Ebf1, we conditionally inactivated Ebf1. We found that Ebf1 is required for proliferation, survival and signaling of pro-B cells and peripheral B cell subsets. The proliferation defect of Ebf1-deficient pro-B cells, including the impaired expression of IL-7Ra and several cell cycle regulators, is overcome by transformation with v-Abl. The survival defect of transformed Ebf1fl/fl pro-B cells can be rescued by the forced expression of the Ebf1 targets c-Myb or Bcl-xL. In mature B cells, Ebf1 deficiency interferes with the BAFF-R and BCR-dependent Akt signaling pathways, as well as with germinal center formation and class switch recombination. Genome-wide analyses of Ebf1 binding and Ebf1-mediated gene expression in mature B cells and comparison with reported data sets in pro-B cells provide insight into the basis for lineage- and stage-specific functions of Ebf1. EBF1 binding in splenic B cells in mice
2012-04-02 | E-GEOD-35910 | biostudies-arrayexpress
Project description:SILAC based protein correlation profiling using size exclusion of protein complexes derived from Mus musculus tissues (Heart, Liver, Lung, Kidney, Skeletal Muscle, Thymus)
2021-05-05 | PXD022309 | Pride
Project description:SILAC based protein correlation profiling using size exclusion of protein complexes derived from seven Mus musculus tissues (Heart, Brain, Liver, Lung, Kidney, Skeletal Muscle, Thymus)
2018-04-24 | PXD007288 | Pride
Project description:Transcription factor Ebf1 is an important determinant of early B lymphopoiesis. To gain insight into differentiation stage-specific functions of Ebf1, we conditionally inactivated Ebf1. We found that Ebf1 is required for proliferation, survival and signaling of pro-B cells and peripheral B cell subsets. The proliferation defect of Ebf1-deficient pro-B cells, including the impaired expression of IL-7Ra and several cell cycle regulators, is overcome by transformation with v-Abl. The survival defect of transformed Ebf1fl/fl pro-B cells can be rescued by the forced expression of the Ebf1 targets c-Myb or Bcl-xL. In mature B cells, Ebf1 deficiency interferes with the BAFF-R and BCR-dependent Akt signaling pathways, as well as with germinal center formation and class switch recombination. Genome-wide analyses of Ebf1 binding and Ebf1-mediated gene expression in mature B cells and comparison with reported data sets in pro-B cells provide insight into the basis for lineage- and stage-specific functions of Ebf1. Localistaion of histone modification (H3K4me2 and H3K4me3) in splenic B cells in mice by ChIP-seq
2012-04-02 | E-GEOD-35914 | biostudies-arrayexpress
Project description:EBF1 is a transcription factor crucial for early B cell development. The phase separation ability of the EBF1 C-terminal domain (CTD) is essential for the transcription activation and pioneering function of EBF1. We identified the specific tyrosine residues in the CTD required for phase separation. We transduced pro-B cells with EBF1 wt, deletion of the entire CTD (dC), or mutation of these tyrosines (YmA). We performed ChIP-seq, ATAC-seq, and RNA-seq to see the effect of disrupting phase separation ability on DNA binding, chromatin opening, and target gene expression. Our findings confirm that phase separation is important for the EBF1 function.
2024-01-18 | GSE227615 | GEO
Project description:EBF1 is a transcription factor crucial for early B cell development. The phase separation ability of the EBF1 C-terminal domain (CTD) is essential for the transcription activation and pioneering function of EBF1. We identified the specific tyrosine residues in the CTD required for phase separation. We transduced pro-B cells with EBF1 wt, deletion of the entire CTD (dC), or mutation of these tyrosines (YmA). We performed ChIP-seq, ATAC-seq, and RNA-seq to see the effect of disrupting phase separation ability on DNA binding, chromatin opening, and target gene expression. Our findings confirm that phase separation is important for the EBF1 function.
2024-01-18 | GSE227613 | GEO