Functions of BET proteins in GATA1-mediated transcription [expression array]
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE62709 | GEO | 2015/02/23
SECONDARY ACCESSION(S): PRJNA264844
REPOSITORIES: GEO
Similar Datasets
Project description:Role of bromodomain and extra-terminal motif (BET) proteins in GATA1-null erythrolbasts (G1E) and in differentiation induced by activation of conditional GATA1 tested by addition of BET inhibitor JQ1 (250nM) Array protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual by the University of Pennsylvania Molecular Profiling Core. Two-factor design (+/- JQ1, +/- GATA1). External RNA spike-in controls (ERCC controls, Ambion) added to each sample in proportion to cell number at the time of RNA harvest.
2015-02-23 | E-GEOD-62709 | biostudies-arrayexpress
Project description:Transcription factor GATA1 binding in erythroblasts in the presence and absence of BET inhibitor JQ1, and BET protein BRD3 and BRD4 binding in erythroblasts in the presence and absence of GATA1. Inhibitors of Bromodomain and Extra-Terminal motif proteins (BETs) are being evaluated for the treatment of cancer and other diseases yet their physiologic mechanisms remain largely unknown. We used genomic and genetic approaches to examine BET function in a hematopoietic maturation system driven by GATA1, an acetylated transcription factor previously shown to interact with BETs. We found that while BRD3 occupied the majority of GATA1 binding sites, BRD2 and BRD4 were also recruited to a subset of GATA1-occupied sites. Functionally, BET inhibition impaired GATA1-mediated transcriptional activation, but not repression, genome-wide. Co-activation by BETs was accomplished both by facilitating genomic occupancy of GATA1 and subsequently supporting transcription activation. Using a combination of CRISPR/CAS9-mediated genomic engineering and shRNA approaches we observed that depletion of either BRD2 or BRD4 alone blunted erythroid gene activation, while depletion of BRD3 only affected erythroid transcription in the setting of BRD2 deficiency. These results suggest that pharmacologic BET inhibition should be interpreted in the context of distinct steps in transcriptional activation and partially overlapping functions among BET family members. GATA1 null erythroblasts (G1E) conditionally expressing GATA1 as a GATA1-ER fusion protein were induced to express GATA1 by addition of 100nM estradiol for 24 hours. For GATA1 binding experiments this occurred in the absence or presence of 250nM JQ1. For BRD3 and BRD4 occupancy experiments G1E cells were compared to G1E cells with activated GATA1-ER fusion protein.
2015-02-23 | E-GEOD-62736 | biostudies-arrayexpress
Project description:Transcription factor GATA1 binding in erythroblasts in the presence and absence of BET inhibitor JQ1, and BET protein BRD3 and BRD4 binding in erythroblasts in the presence and absence of GATA1. Inhibitors of Bromodomain and Extra-Terminal motif proteins (BETs) are being evaluated for the treatment of cancer and other diseases yet their physiologic mechanisms remain largely unknown. We used genomic and genetic approaches to examine BET function in a hematopoietic maturation system driven by GATA1, an acetylated transcription factor previously shown to interact with BETs. We found that while BRD3 occupied the majority of GATA1 binding sites, BRD2 and BRD4 were also recruited to a subset of GATA1-occupied sites. Functionally, BET inhibition impaired GATA1-mediated transcriptional activation, but not repression, genome-wide. Co-activation by BETs was accomplished both by facilitating genomic occupancy of GATA1 and subsequently supporting transcription activation. Using a combination of CRISPR/CAS9-mediated genomic engineering and shRNA approaches we observed that depletion of either BRD2 or BRD4 alone blunted erythroid gene activation, while depletion of BRD3 only affected erythroid transcription in the setting of BRD2 deficiency. These results suggest that pharmacologic BET inhibition should be interpreted in the context of distinct steps in transcriptional activation and partially overlapping functions among BET family members.
2015-02-23 | GSE62736 | GEO
Project description:G1E cells infected with control (HMD empty vector), human GATA1, or human GATA1 mutant cDNA
2019-03-20 | GSE124830 | GEO
Project description:Missense mutations in transcription factor GATA1 underlie several distinct forms of anemia and thrombocytopenia. Clinical severity depends on the site and type of substitution, and distinct substiutions of the same residue produce disparate phenotypes. To investigate the effect of GATA1 missense mutations on erythroid differentiation we expressed conditionally activated wild type or mutant versions of GATA1 in GATA1-null G1E cells. We used gene expression microarrays to explore how GATA1 missense mutations affect erythroid transcription programs. GATA1-null G1E cells ectopically expressing conditionally activated versions of GATA1 (GATA1-ER, GATA1(R216Q)-ER, GATA1(R216W)-ER, GATA1(D218G)-ER, or GATA1(D218Y)-ER) were treated with estradiol for 24 hours to initiate erythroid differentiation. Total RNA from treated cells was extracted for Affymetrix microarray. All data were generated from three biological replicates. Transcript levels were compared in wild type vs. mutant lines.
2013-03-04 | E-GEOD-43356 | biostudies-arrayexpress
Project description:Missense mutations in transcription factor GATA1 underlie several distinct forms of anemia and thrombocytopenia. Clinical severity depends on the site and type of substitution, and distinct substiutions of the same residue produce disparate phenotypes. To investigate the effect of GATA1 missense mutations on erythroid differentiation we expressed conditionally activated wild type or mutant versions of GATA1 in GATA1-null G1E cells. We used gene expression microarrays to explore how GATA1 missense mutations affect erythroid transcription programs.
2013-03-04 | GSE43356 | GEO
Project description:Background: The present study investigated a role of proteins from BET family (epigenetic readers) in schizophrenia-like abnormalities in MAM-E17 model of schizophrenia. Methods: An inhibitor of BET proteins, JQ1, was given during adolescence in postnatal days (P) 23-P30, and behavioral response (sensorimotor gating, recognition memory) and prefrontal cortex (mPFC) function (long-term potentiation (LTP), molecular and proteomic studies) were performed in adult males and females. Results: Deficits in sensorimotor gating and recognition memory were observed only in MAM-treated males. However, adolescent JQ1 treatment affected control, but MAM-treated groups in both sexes. Electrophysiological study showed an LTP impairment only in male MAM-treated animals, and JQ1 did not have any effect on LTP in the mPFC. In contrast, MAM did not affect immediate early gene expression (markers of neuronal and synaptic activity), but JQ1 altered them in both sexes. Proteomic study revealed alterations in MAM-treated groups only in males, while JQ1 affected both sexes. Conclusions: Prenatal MAM administration induced schizophrenia-like abnormalities only in males. In contrast, adolescent JQ1 treatment affected both sexes and induced behavioral changes in control groups, altered a markers of neuronal and synaptic activity and proteomic landscape in the mPFC of both groups (VEH- and MAM-treated). Thus, adolescent inhibition of BET family might change neuroplasticity in the mPFC.
2021-09-07 | PXD027050 | Pride
Project description:Role of the bromodomain and extraterminal motif (BET) protein BRD2 in CTCF chromatin occupancy, tested by CRISPR/Cas9-mediated depletion of BRD2 in GATA1-null erythroblasts expressing an inducible GATA1-ER fusion (G1E-ER4). Pharmacologic inhibitors of the BET (bromodomain and extraterminal motif) family of proteins are being explored for the treatment of various diseases, including cancer, yet the individual functions of BET proteins remain unclear. Here we find that BRD2 co-localizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites, whereas BRD2 is dispensable for CTCF occupancy. Genome editing at a CTCF/BRD2 co-occupied site reveals a functional boundary element that upon perturbation results in transcriptional misregulation. Single-molecule RNA FISH reveals that either site-specific CTCF loss or BRD2 depletion increases the correlation in expression of two genes flanking the boundary. Together these findings indicate that BRD2 supports chromatin boundary activity in a CTCF-dependent manner and suggest that pharmacologic BET inhibitors influence gene expression in part by perturbing chromatin domain boundary function.
2017-03-31 | GSE80527 | GEO
Project description:We analyzed the transcriptional consequences of the BET bromodomain inhibitor JQ1 in the T-ALL cell line LOUCY by microarray analysis. Short-term exposure to a low dose of JQ1 (4h, 250nM) provided insights in the genes whose expression was immediately affected by BET bromodomain inhibition. Significantly downregulated genes upon short-term drug treatment included stem-cell associated genes and putative oncogenes such as BAALC, WT1, MN1, MEF2C, LMO1 and LMO2. Genes associated with the 500 highest ranked enhancer regions in LOUCY, were significantly enriched in genes downregulated after JQ1 treatment.
2016-12-15 | GSE81915 | GEO
Project description:Tissue-specific transcription patterns are preserved throughout cell divisions to maintain lineage fidelity. We investigated whether transcription factor GATA1 plays a role in transmitting hematopoietic gene expression programs through mitosis when transcription is transiently silenced. Live cell imaging revealed that a fraction of GATA1 is retained focally within mitotic chromatin. ChIP-seq of highly purified mitotic cells uncovered that key hematopoietic regulatory genes are occupied by GATA1 in mitosis. The GATA1 co- regulators FOG1 and TAL1 dissociate from mitotic chromatin, suggesting that GATA1 functions as platform for their postmitotic recruitment. Mitotic GATA1 target genes tend to re-activate more rapidly upon entry into G1 than genes from which GATA1 dissociates. A novel system designed to destroy GATA1 specifically during mitosis revealed that mitotic occupancy is required for rapid target gene reactivation. These studies suggest a requirement of mitotic “bookmarking” by GATA1 for the faithful propagation of cell type-specific transcription programs through cell division GATA1 occupancy profiles in mitotic G1E-ER4 +E2 cells generated by ChIP-sequencing. ChIP input DNA was sequenced as control. Previously reported (GSE18164) GATA1 occupancy in asynchrnous G1E-ER4 +E2 cells was analysed and compared with mitotic GATA1 occupancy.
2012-08-17 | E-GEOD-36589 | biostudies-arrayexpress