Identification of open chromatin regions in mouse cardiopharyngeal mesoderm
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA726796 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14385236_1.fastq.gz | Fastqsanger.gz | |||
| SRR14385236_2.fastq.gz | Fastqsanger.gz | |||
| SRR14385237_1.fastq.gz | Fastqsanger.gz | |||
| SRR14385237_2.fastq.gz | Fastqsanger.gz | |||
| SRR14385238_1.fastq.gz | Fastqsanger.gz |
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Project description:In the heart development, mesodermal progenitor cells in pharyngeal apparatus, termed cardiopharyngeal mesoderm, contribute to both atruim and right ventricle. Tbx1 gene, encoding a T-box transctiption factor and gene haploinsufficient in 22q11.2 deletion syndrome, is required for cardiac outflow tranct and branchiomeric muscle development. To understand how TBX1 affect open chromatin status in cardiopharyngeal mesoderm, we performed ATAC-seq in Tbx1-Cre lineage with/without Tbx1 expression.
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Project description:Cardiopharyngeal mesoderm contributes to the formation of the heart and head muscles. However, the mechanisms governing cardiopharyngeal mesoderm specification remain unclear. Indeed, there is a lack of an in vitro model replicating the differentiation of both heart and head muscles to study these mechanisms. Such models are required to allow live-imaging and high throughput genetic and drug screening. Here, we show that the formation of self-organizing or pseudo-embryos from mouse embryonic stem cells (mESCs), also called gastruloids, reproduces cardiopharyngeal mesoderm specification towards cardiac and skeletal muscle lineages. By conducting a comprehensive temporal analysis of cardiopharyngeal mesoderm establishment and differentiation in gastruloids and comparing it to mouse embryos, we present the first evidence for skeletal myogenesis in gastruloids. By inferring lineage trajectories from the gastruloids single-cell transcriptomic data, we further suggest that heart and head muscles formed in gastruloids derive from cardiopharyngeal mesoderm progenitors. We identify different subpopulations of cardiomyocytes and skeletal muscles, which most likely correspond to different states of myogenesis with “head-like” and “trunk-like” skeletal myoblasts. These findings unveil the potential of mESC-derived gastruloids to undergo specification into both cardiac and skeletal muscle lineages, allowing the investigation of the mechanisms of cardiopharyngeal mesoderm differentiation in development and how this could be affected in congenital diseases.
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Project description:We have developed a protocol to generate cardiopharyngeal mesoderm (CPM) in vitro by Mesp1 induction in ES cells. The goal of this study is to compare the transcriptome of CPM-derived cardiac and skeletal myogenic progenitors to identify novel lineage-specific markers. mRNA profiles of CPM-derived D6 (early) and D12 (late), cardiac (BMP) and skeletal myogenic (control) progenitors were generated
2016-01-12 | E-GEOD-74682 | biostudies-arrayexpress
Project description:We used the assay for transposon-accessible chromatin using sequencing (ATAC-seq) on FACS-purified cells to profile chromatin accessibility during early cardiopharyngeal fate choices in Ciona. We obtained ~500 million unique reads from samples comprising cardiopharyngeal mesoderm and mesenchymal cells, as well as whole Ciona embryos and genomic DNA control. We combined ATAC-seq peaks from all the replicates to generate an atlas of 56,090 unique and non-overlapping accessible regions (accessome) covering 9.25% of the C. robusta genome. We used the accessome to analyze differential accessibility and integrated expression data to compare the chromatin and gene expression dynamics underlying cardiopharyngeal fate specification. In summary, we revealed that most changes in accessibility occur upon induction of multipotent cardiopharyngeal progenitors from the founder cells. Comparing differential expression to differential accessibility shows that genes activated in the multipotent progenitors tend to have regions that specifically open nearby them. We found that the elements accessible specifically in multipotent cardiopharyngeal progenitors were enriched in Fox, GATA and nuclear receptor binding motifs. CRISPR-mediated loss of Foxf function followed by FACS, ATAC-seq and RNA-seq showed that Foxf is required to open ~22% of the cardiopharyngeal-specific elements. Notably, elements associated with de novo expressed genes, which turn on either in heart or pharyngeal muscle progenitors, were also opening in multipotent progenitors, whereas only ~10% of differentially expressed genes had differentially accessible elements. Finally, we propose a general model for chromatin dynamics whereby most lineage-specific elements open in multipotent progenitors, and control both early pan-cardiopharyngeal and late cell-type-specific expression.
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Project description:We have developed a protocol to generate cardiopharyngeal mesoderm (CPM) in vitro by Mesp1 induction in ES cells. The goal of this study is to compare the transcriptome of CPM-derived cardiac and skeletal myogenic progenitors to identify novel lineage-specific markers.
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Project description:Profiling open chromatin regions in human myometrial tissues
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Project description:Cardiopharyngeal Mesoderm specification into cardiac and skeletal muscle lineages in gastruloids
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Project description:Endothelial cells (EC) differentiate from multiple sources during embryonic development, including the cardiopharyngeal mesoderm, which gives rise to multiple tissues including the cardiac and branchiomeric muscle. Here, we have used a cardiogenic mesoderm cell differentiation model that also activates an endothelial transcription program. Comparing our chromatin remodeling data with publicly available single-cell RNA-seq data from mouse embryos, we derived a list of over 100 putative regulatory elements activated in EC marker genes. We applied a machine-learning strategy trained with validate enhancers to predict the probability of these sequences to function as enhancers. The computational assay returned over 50% of these sequences to be likely enhancers, some of which previously reported. In addition, using genetic and epigenetic perturbations of some of these elements, we established their requirement for gene expression during endothelial differentiation. Finally, we used the integration of multiple data sources and computational tools to search for transcriptional factor binding motifs related to endothelial cell fate specification. We found motifs of GATA, ETS, and FOS/AP-1 factors as the most significantly enriched in these sequences. Overall, our approach has been efficient in the identification of novel EC regulatory sequences with high likelihood to be enhancers, and validated a subset of them. Motif analyses revealed that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC differentiation in cardiopharyngeal mesoderm.
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Project description:Endothelial cells (EC) differentiate from multiple sources during embryonic development, including the cardiopharyngeal mesoderm, which gives rise to multiple tissues including the cardiac and branchiomeric muscle. Here, we have used a cardiogenic mesoderm cell differentiation model that also activates an endothelial transcription program. Comparing our chromatin remodeling data with publicly available single-cell RNA-seq data from mouse embryos, we derived a list of over 100 putative regulatory elements activated in EC marker genes. We applied a machine-learning strategy trained with validate enhancers to predict the probability of these sequences to function as enhancers. The computational assay returned over 50% of these sequences to be likely enhancers, some of which previously reported. In addition, using genetic and epigenetic perturbations of some of these elements, we established their requirement for gene expression during endothelial differentiation. Finally, we used the integration of multiple data sources and computational tools to search for transcriptional factor binding motifs related to endothelial cell fate specification. We found motifs of GATA, ETS, and FOS/AP-1 factors as the most significantly enriched in these sequences. Overall, our approach has been efficient in the identification of novel EC regulatory sequences with high likelihood to be enhancers, and validated a subset of them. Motif analyses revealed that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC differentiation in cardiopharyngeal mesoderm.
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