Genome-wide maps of Nkx2-5 in E11.5 mouse embryonic heart
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE44574 | GEO | 2015/09/02
SECONDARY ACCESSION(S): PRJNA190090
REPOSITORIES: GEO
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Project description:We report the identification of genome-wide binding site of the cardiac transcription factor Nkx2-5 during mouse heart development. Examination of Nkx2-5 binding in wild-type mouse in duplicate.
2015-09-02 | E-GEOD-44574 | biostudies-arrayexpress
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
Project description:Differentiation of human pluripotent stem cells (hPSCs) can be used to model human heart development and, in turn, to analyze the developmental consequences of genetic abnormalities. Here, we deleted NKX2-5, a critical component of the cardiac gene regulatory network, in human embryonic stem cells (hESCs) and identified a novel genetic interaction between NKX2-5 and HEY2 that is required for heart development
2018-03-21 | GSE89443 | GEO
Project description:NKX2-5 is a homeodomain transcription factor that plays a central role in the cardiac gene regulatory network, and is commonly mutated in human congenital heart disease. Here, we take a functional genomics approach to congenital heart disease mechanism. We used DamID to establish a robust set of target genes for both wild type NKX2-5 and a mutation lacking the homeodomain (NKX2-5delHD), the latter to model loss-of-function in gene regulatory network. NKX2-5delHD bound hundreds of targets including NKX2-5 wild type targets and a unique set of “off-targets”, and retained partial functionality. We showed that NKX2-5delHD could heterodimerize with NKX2-5 wild type and cofactors, including ubiquitous ETS family members ELK1 and ELK4, through a tyrosine-rich homophilic interaction domain (YRD). NKX2-5delHD off-targets, but not those of an NKX2-5 YRD mutant, were enriched in ETS motifs and were occupied by ELK1/ELK4 proteins, as determined by DamID. Our study reveals unexpected activities for NKX2-5 mutations on chromatin, guided by interactions with their normal cardiac and general cofactors, and suggest potential for a novel type of gain-of-function in congenital heart disease. The supplementary bed file contains all binding regions detected for the N/C-terminal fusions reported in the manuscript, in addition to probe locations, ready to upload directly into UCSC browser (mm9).
2015-07-07 | GSE44902 | GEO
Project description:We comprehensively interrogate enhancers U1 and U2 in controlling Nkx2-5 transcription during heart development. Serial genomic deletions in mice reveal a functional hierarchy of U1 and U2 as evidenced by stage-dependent phenotypic variations. Specifically, U1 and U2 function redundantly to confer Nkx2-5 expression at early stages, but U2 instead of U1 supported its expression at later stages of heart chamber formation and maturation. Combined deletions markedly reduce Nkx2-5 dosage as early as E7.5, despite being largely reinstated two days later, displaying heart malformations with precocious differentiation of cardiac progenitors. Together, we propose a model that the temporal and partially compensatory regulatory function of two enhancers dictates a TF?s dosage and specificity during development.
2022-07-03 | GSE133760 | GEO
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.
2012-06-22 | GSE35151 | GEO
Project description:Mutations in Nkx2-5 are a main cause of cardiac congenital heart disease. Here we describe a new Nkx2-5 point-mutation murine model, akin to its human counterpart disease generating mutation. Our model fully reproduces the morphological and physiological clinical presentations of the disease and reveals an under-studied aspect of Nkx2-5 driven pathology, a primary right ventricular dysfunction. We further describe the molecular consequences of disrupting the transcriptional network regulated by Nkx2-5 in the heart and show that Nkx2-5 dependent perturbation of the Wnt signaling pathway promotes heart dysfunction through alteration of cardiomyocyte metabolism. Our data provide mechanistic insights on how Nkx2-5 regulates heart function and metabolism, a novel link in the study of congenital heart disease, and confirms that our models are the first murine genetic models to present all spectra of clinically relevant congenital heart disease phenotypes generated by Nkx2-5 mutations in patients.
2016-12-01 | GSE85902 | GEO
Project description:While the heart is the first organ to form during development, the earliest molecular mechanisms surrounding specification and differentiation are not clear. In vertebrates, the first marker of cardiac specification is the expression of the homeobox transcription factor Nkx2-5 and its paralogs. While some downstream targets of Nkx2-5 have been discovered, they alone are not sufficient to completely rescue Nkx2-5 knock-downs, suggesting that other targets of Nkx2-5 regulation remain unknown. In order to identify early targets of Nkx2-5, Xenopus laevis embryos were injected with synthetic Nkx2-5 mRNA and changes in gene expression measured using Affymetrix GeneChips. To interpret the data, X. laevis genomic annotation was augmented using cross-species information from the CrossGene database followed by gene ontology enrichment, network analysis, spatial expression, and Nkx2-5 binding site predictions. This allowed us to compile a list of 99 UniGene clusters representing likely early targets of Nkx2-5. Nkx2-5+GFP or GFP mRNA was injected into 8 cell Xenopus embryos. Total RNA was collected at St. 11.5. comparison of gene expression profiles for treated vs, control
2011-12-01 | E-GEOD-29791 | biostudies-arrayexpress
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
Project description:Nkx2-5-GFP+ cells were collected by FACS from whole embryos (E8.0-8.5, 5-12 ps) and dissected heart tubes (E9.0-9.5, 15-21 ps). Because limited numbers of cells were obtained from individual embryos (~300 cells at E8, ~1500 cells at E9.5) mRNA was amplified twice with T7 RNA polymerase and fluorescent cDNA targets were synthesized by the indirect method with either Cy5 or Cy3. Targets from individual Nkx2-5 heterozygous and homozygous null cells were co-hybridized with cDNA probes printed on glass slide microarrays. Two microarray clone sets were used for each hybridization: the NIA/NIH 15,000 clone set derived from mouse non-cardiac embryonic tissue, and a ~6000 cardiac clone set derived in house.
2006-11-27 | E-MEXP-533 | biostudies-arrayexpress