Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers
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PROVIDER: PRJNA445646 | ENA |
REPOSITORIES: ENA
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Project description:Fibroblasts can be directly reprogrammed toward a cardiac fate by introducing cardiogenic transcription factors (TFs), although the underlying mechanisms of the cardiac reprogramming process remain unclear. Three cardiac TFs, GATA4, MEF2C, and Tbx5 (referred to as GMT) can activate cardiac genes in fibroblasts and their cardiogenic activity is enhanced by the Hand2 TF and the Akt1 kinase. To understand the mechanistic basis of cardiac reprogramming, we performed a genome-wide analysis of cardiogenic TF binding sites and active enhancers, which were annotated by H3K27ac histone modification, during the reprogramming process. We found that cardiogenic TFs rapidly co-occupy core regulatory elements of cardiac genes and activate myriad cardiac enhancers that are enriched predominantly in Mef2 binding sites. Addition of Hand2 and Akt1 to the GMT reprogramming cocktail expands the spectrum of co-occupied active cardiac enhancers. As reprogramming proceeds over time, reprogramming TFs continue to activate additional cardiac enhancers, which are also enriched for Mef2 motifs, while fibroblast enhancers are silenced. This transition of the enhancer landscape strongly correlated with changes in the fibroblast and cardiac transcriptome. To test the relevance of cardiac reprogramming enhancers to the regulation of cardiogenesis in vivo, we assayed a collection of reprogramming enhancers in transgenic mouse embryos and found that they directed highly specific expression patterns in the developing heart. Our findings demonstrate that Hand2 and Akt1 enhance reprogramming by facilitating cardiac enhancer occupancy and identify Mef2 as a central effector of cardiac reprogramming, which coordinates the actions of accessory factors across a broad landscape of cardiac enhancers.
2019-04-15 | GSE112315 | GEO
Project description:Fibroblasts can be directly reprogrammed toward a cardiac fate by introducing cardiogenic transcription factors (TFs), although the underlying mechanisms of the cardiac reprogramming process remain unclear. Three cardiac TFs, GATA4, MEF2C, and Tbx5 (referred to as GMT) can activate cardiac genes in fibroblasts and their cardiogenic activity is enhanced by the Hand2 TF and the Akt1 kinase. To understand the mechanistic basis of cardiac reprogramming, we performed a genome-wide analysis of cardiogenic TF binding sites and active enhancers, which were annotated by H3K27ac histone modification, during the reprogramming process. We found that cardiogenic TFs rapidly co-occupy core regulatory elements of cardiac genes and activate myriad cardiac enhancers that are enriched predominantly in Mef2 binding sites. Addition of Hand2 and Akt1 to the GMT reprogramming cocktail expands the spectrum of co-occupied active cardiac enhancers. As reprogramming proceeds over time, reprogramming TFs continue to activate additional cardiac enhancers, which are also enriched for Mef2 motifs, while fibroblast enhancers are silenced. This transition of the enhancer landscape strongly correlated with changes in the fibroblast and cardiac transcriptome. To test the relevance of cardiac reprogramming enhancers to the regulation of cardiogenesis in vivo, we assayed a collection of reprogramming enhancers in transgenic mouse embryos and found that they directed highly specific expression patterns in the developing heart. Our findings demonstrate that Hand2 and Akt1 enhance reprogramming by facilitating cardiac enhancer occupancy and identify Mef2 as a central effector of cardiac reprogramming, which coordinates the actions of accessory factors across a broad landscape of cardiac enhancers.
2019-04-15 | GSE112316 | GEO
Project description:Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers (ChIP-seq data set)
| PRJNA445650 | ENA
Project description:Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers (RNA-seq data set)
| PRJNA445652 | ENA
Project description: Not available
| S-EPMC6754266 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-04-15 | GSE112317 | GEO
Project description:We show that mismatch-repair (MMR) signature mutations can activate colorectal cancer (CRC)-specific enhancers, through analysis of enhancer DNA associated with the active enhancer histone mark H3K27ac. We demonstrate that MMR mutations activate enhancers using a xenograft metastasis model, where mutations are induced naturally via CRISPR/Cas9 inactivation of MLH1 prior to tumor cell injection.
2019-02-07 | GSE126188 | GEO
Project description:Homeobox B cluster (HoxB) genes play important roles in RA-induced early ESCs differentiation. In this study, we identified two enhancers synergistically regulate HoxB genes expressions through 3D chromatin structure and thus regulate RA-induced early ESCs differentiation. 4C data showed interactions between HoxB genes and the two enhancers. CRISPR/Cas9-mediated individual or compound deletion of the two enhancers significantly inhibits HoxB genes expressions while transcriptome analysis revealed that RA induced early ESCs differentiation was blocked in the enhancer KO cells. Our study suggests new mechanism by which two enhancers regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure.
2021-03-01 | GSE165725 | GEO
Project description:Cardiac fibroblasts are critical to proper heart function through multiple interactions with the myocardial compartment. Loosely defined based on their mesenchymal origin, capacity to adhere to plastic and to secrete extracellular matrix, cardiac fibroblasts have been largely neglected due to heterogeneity and lack of proper markers. Objective: To identify genes uniquely expressed in the cardiac fibroblast pool, we performed an unbiased comparative analysis between cardiac and tail fibroblasts, and tracked cardiac fibroblasts after injury to determine their contribution to myocardial regeneration. Methods and Results: High-throughput cell surface and intracellular profiling identified homogeneously expressed MSC markers in cardiac fibroblasts, as well as a surprising number of cardiogenic markers, some expressed at higher levels than in cardiomyocytes. Genetically marked fibroblasts contributed to interstitial but not cardiomyocyte compartments in infarcted hearts. Conclusions: The core transcriptional identity of cardiac fibroblasts reflects their embryological origin, provoking novel interpretations for studies on more specialized cardiac progenitors, and offering a novel perspective for reinterpreting cardiac regenerative therapies 3 biological replicates plated over 5 days after isolation pooled out of 2 animals were used for both tail and heart fibroblasts (6 total samples analysed)
2014-05-20 | E-GEOD-50531 | biostudies-arrayexpress
Project description:Rationale: Cardiac development is a complex process that results in the first integrated, multi-lineage embryonic tissue. Imperfect developmental progression leads to congenital heart disease, the most common birth defect with developmental corruption affecting more than 1% of all live births. Interrogation of individual genes has provided the backbone for cardiac developmental biology, yet a comprehensive transcriptome derived from natural cardiogenesis is required to establish an unbiased roadmap to gauge innate developmental milestones necessary for stem cell-based differentiation and in vitro disease modeling. Objective: Establish a contextual expression database of spatial-temporal cardiac structures, and validate a predictive tool to diagnose and predict cardiogenic outcomes from individual pluripotent stem cell lines. Methods and Results: Stage-specific cardiac structures were dissected from eight distinctive embryonic time points to produce a genome-wide expressome analysis across the spectrum of early to late cardiogenesis. Hierarchical clustering of the time course dataset demonstrated discrete gene expression profiles during natural embryonic development. In reference to the native cardiogenic expression roadmap, disruptive iPSC-derived cardiac expression profiles were revealed from pro-cardiogenic 3-factor (SOX2, OCT4, KLF4) compared to non-cardiogenic 4-factor (addition of c-MYC) reprogramming regimens upon stage-specific differentiation. Expression of cardiac-related genes from 3F-iPSC differentiated in vitro at day 0, 5, and 11 recapitulated expression of natural embryos at days 0, E7.5-E8.5, and E14.5-E18.5, respectively. In contrast, 4F-iPSC demonstrated variable gastrulation gene expression profiles beginning at day 5 of differentiation. Differential gene expression within the pluripotent ground state between the archetypical high cardiogenic potential of embryonic stem cells recapitulated in 3F-iPSC vs. the low cardiogenic potential of 4F-iPSC revealed 23 distinguishing candidate genes. Upon subsequent differentiation, cell line-specific gene expression differences were magnified to 399 genes at day 5 and 726 genes at day 11. A confirmed panel of 20 genes, differentially expressed between high and low cardiogenic cell lines, was transformed into a predictive score that was sufficient to correctly rank independent iPSC lines according to cardiogenic potential. Conclusions: Transcriptome analysis attuned to the embryonic developing heart provides a robust platform to probe coordinated cardiac specification and maturation from stem cell-based cardiogenesis model systems. Based on this genome-wide expressome roadmap, a panel of pre-cardiac genes was extracted that allowed differential prognosis of cardiogenic competency from individual reprogrammed cell lines at the pluripotent state. The overall experimental design includes 3 time points (Day0, Day5, Day11) and 3 different stem cell lines: R1 embryonic stem cells (ESCs), H9 induced pluripotent stem cells (H9-iPSCs) generated/reprogrammed by 3 transcription factors (called 3F-iPSCs), and 19BL induced pluripotent stem cells (19BL-iPSCs) generated/reprogrammed by 4 transcription factors (called 4F-iPSC). At each time point, each cell line has 3 biological replicates. In total, there are 27 samples. R1-embryonic stem cells (R1-ESCs): Day0 undifferentiated ESCs - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates. 3F-iPSC (H9 iPSCs): Day 0 undifferentiated - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates. 4F-iPSC (19BL-iPSCs): Day0 undifferentiated - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates.
2013-09-23 | E-GEOD-43197 | biostudies-arrayexpress