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Effect of NKX2-5 or ETS1 on GATA4 pioneer activity [fibroblast]

ABSTRACT: Effect of NKX2-5 or ETS1 on GATA4 pioneer activity [fibroblast]

PROVIDER: PRJNA655132 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12383400.fastq.gz	Fastqsanger.gz
	SRR12383401.fastq.gz	Fastqsanger.gz
	SRR12383402.fastq.gz	Fastqsanger.gz
	SRR12383403.fastq.gz	Fastqsanger.gz
	SRR12383404.fastq.gz	Fastqsanger.gz

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Effect of NKX2-5 or ETS1 on GATA4 pioneer activity [fibroblast]

Project description:GATA4 is a pioneer transcription factor. The mechanisms by which pioneer factors select and occupy specific loci, open chromatin, and activate enhancers is not well understood. To address the influence of partner, non-pioneer factors on pioneer factor activity, we analyzed the effect of NKX2-5 or ETS1 on GATA4 pioneer activity. NIH3T3 cells were transduced with lentivirus to obtain stable cell lines that express GFP (control), GATA4 (G), NKX2-5 (N), ETS1 (E), GATA4+NKX2-5 (GN), and GATA4+ETS1 (GE). We measured chromatin accessibility using ATAC-seq, and enhancer activation using H3K27ac. From these measurements we determined GATA4, GATA4+ETS, and GATA4+NKX2-5 pioneer binding, pioneer opening, and pioneer enhancer activation. Our results show that ETS1 or NKX2-5 alter GATA4 pioneer binding, opening, and enhancer activation.

2021-07-01 | GSE155652 | GEO

Transcription profiling of mouse second field myocardium Gata4flox/+ Nkx2-5+/+ (control, n=3), Gata4flox/+ Nkx2-5Cre/+ (Gata4 Nkx2-5 double heterozygous animals reveals GATA4 is a direct activator of Cyclin D2 and is required for proliferation in 2nd heart field-derived myocardium

Project description:The second heart field (SHF) comprises a population of mesodermal progenitor cells that are added to the nascent linear heart to give rise to the majority of the right ventricle, interventricular septum, and outflow tract of mammals and birds. The zinc finger transcription factor GATA4 functions as an integral member of the cardiac transcription factor network in the SHF and its derivatives. In addition to its role in cardiac differentiation, GATA4 is also required for cardiomyocyte replication, although the transcriptional targets of GATA4 required for proliferation have not been previously identified. In the present study, we disrupted Gata4 function exclusively in the SHF and its derivatives. Gata4 SHF knockout mice die by embryonic day 13.5 and exhibit hypoplasia of the right ventricular myocardium and interventricular septum and display profound ventricular septal defects. Loss of Gata4 function in the SHF results in decreased myocyte proliferation in the right ventricle, and we identify numerous cell cycle genes that are dependent on Gata4 by microarray analysis. We show that Gata4 is required for Cyclin D2 expression in the right ventricle and that the Cyclin D2 promoter is bound and activated by GATA4 via three consensus GATA binding sites. These findings establish Cyclin D2 as a direct transcriptional target of GATA4 and support a model in which GATA4 controls cardiomyocyte proliferation by coordinately regulating numerous cell cycle genes. Experiment Overall Design: Onewat ANOVA with post-hoc was done with 3 genotypes with replicates. Three genetypes are Gata4flox/+; Nkx2-5+/+ (control, n=3), Gata4flox/+; Nkx2-5Cre/+ (Gata4; Nkx2-5 double heterozygous, Experiment Overall Design: 170 n=3), and Gata4flox/flox; Nkx2-5Cre/+ (Gata4 CKONkx, n=5).

2008-10-20 | E-GEOD-9652 | biostudies-arrayexpress

Genome-wide occupancy profile of Tbx3, Gata4, Nkx2-5 and p300 in adult mouse whole heart

Project description:The contraction pattern of the heart relies on the activation and conduction of the electrical impulse. Perturbations of cardiac conduction have been associated with congenital and acquired arrhythmias as well as cardiac arrest. The pattern of conduction depends on the regulation of heterogeneous gene expression by key transcription factors and transcriptional enhancers. Here, we assessed the genome-wide occupation of conduction system–regulating transcription factors TBX3, NKX2-5, and GATA4 and of enhancer-associated coactivator p300 in the mouse heart, uncovering cardiac enhancers throughout the genome. Examination of 3 cardiac transcription factors and p300 in adult mouse heart

2012-06-22 | E-GEOD-35151 | biostudies-arrayexpress

Genome-wide occupancy profile of Tbx3, Gata4, Nkx2-5 and p300 in adult mouse whole heart

2012-06-22 | GSE35151 | GEO

Fibroblast Gata4 and Gata6 promote myocardial adaptation to pressure overload by enhancing cardiac angiogenesis

Project description:Here, we show that adult cardiac fibroblasts express the cardiomyocyte transcription factors GATA-4 and GATA-6 to promote adaptive remodeling in pressure overload induced cardiac hypertrophy. Using a mouse model with specific single or double deletion of Gata4 and Gata6 in stress activated fibroblasts, we found a reduced myocardial capillarization in mice with Gata4/6 double deletion following pressure overload, while single deletion of Gata4 or Gata6 had no effect. Importantly, we confirmed the reduced angiogenic response using an in vitro co-culture system with Gata4/6 deleted cardiac fibroblast and endothelial cells. A comprehensive RNA-sequencing analysis revealed an upregulation of anti-angiogenic genes upon Gata4/6 deletion in fibroblasts, and siRNA mediated downregulation of these genes restored endothelial cell growth. In conclusion, we identified a novel role for the cardiac transcription factors GATA4 and GATA6 in heart fibroblasts, where both proteins act in concert to promote myocardial capillarization and heart function by directing intercellular crosstalk.

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Project description:Synovial fibroblasts critically contribute to the pathogenesis of rheumatoid arthritis (RA) by acquiring either a pro-inflammatory or tissue-destructive phenotype. To explore the molecular mechanisms underlying the tissue-destructive fibroblast phenotype in arthritis, we performed bulk RNA-sequencing analysis on the synovial fibroblasts which were isolated from Col6a1-Cre-Ets1-flox/flox (Ets1ΔFib) and Ets1-flox/flox (Ets1flox) mice.

2022-07-06 | GSE201310 | GEO

Expression data of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors

Project description:Expression profiling of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors, WT T cells, and WT Pro B cells WT Hematopoietic progenitors, CD4 T cells, Pro B cells, and WT and Ets1-deficient NK cells were FACs sorted. RNA was subsequently extracted, labelled, and hybridized to Affymetrix microarrays. The goal if this experiment was to identify Ets1 dependent genes in NK cells

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Using Mouse Embryonic Fibroblast to test the pioneer factor activity of POU4F3

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ETS1 and ETS2

Project description:ETS1 and ETS2

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Effect of Ets1 knockdown in the P5424 thymic cell line

Project description:We performed ChIP-Seq for Ets1 and histone modifications in P5424 thymic cells, without and with Ets1 knockdown via shRNA. Overall, we find that loss of Ets1 results in specific, higher occupancy of H3K4me1-marked nucleosomes at the Ets1 binding site, but not H3K4me3 nucleosomes. We verified the specificity of this mechanism as Ets1-dependent by also computing H3K4me1 and 3 nucleosome occupancy in hypersensitive, Ets1-depleted sites. This effect was also found in primary WT DN+DP Ets1 sites. Overall, this suggests that Ets1 induces chromatin remodeling and that its loss increases H3K4me1 nucleosome occupancy in bound sites, with levels of H3K4me3 comparatively unchanged, thus reducing the activation status of these enhancers Genome-wide analysis via ChIP-Seq for Ets1, H3K4me1 and H3K4me3 in WT, sh-scramble and sh-Ets1 the P5424 thymic cell line

2015-12-19 | E-GEOD-74042 | biostudies-arrayexpress

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