Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [ATAC-seq]
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ABSTRACT:
PROVIDER: PRJNA986840 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25007553.fastq.gz | Fastqsanger.gz | |||
| SRR25007553_1.fastq.gz | Fastqsanger.gz | |||
| SRR25007553_2.fastq.gz | Fastqsanger.gz | |||
| SRR25007554.fastq.gz | Fastqsanger.gz | |||
| SRR25007554_1.fastq.gz | Fastqsanger.gz |
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Project description:Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation
| PRJNA986836 | ENA
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.
2024-01-26 | GSE235650 | GEO
Project description:Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [RNA-seq]
| PRJNA986839 | ENA
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.
2024-01-26 | GSE235649 | GEO
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.
2019-11-25 | GSE126691 | GEO
Project description:Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and branchiomeric muscles. The enhancers activated during endothelial differentiation within the cardiopharyngeal mesoderm are not completely known. Here, we use a cardiogenic mesoderm differentiation model that activates an endothelial transcription program to identify endothelial regulatory elements activated in early cardiogenic mesoderm. Integrating chromatin remodeling and gene expression data with available single-cell RNA-seq data from mouse embryos, we identify 101 putative regulatory elements of EC genes. We then apply a machine-learning strategy, trained on validated enhancers, to predict enhancers. Using this computational assay, we determine that 50% of these sequences are likely enhancers, some of which are already reported. We also identify a smaller set of regulatory elements of well-known EC genes and validate them using genetic and epigenetic perturbation. Finally, we integrate multiple data sources and computational tools to search for transcriptional factor binding motifs. In conclusion, we show EC regulatory sequences with a high likelihood to be enhancers, and we validate a subset of them using computational and cell culture models. Motif analyses show that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC regulation in cardiopharyngeal mesoderm.
| S-EPMC10957928 | biostudies-literature
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.
2021-10-10 | GSE173700 | GEO
Project description:Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (ATAC-Seq)
| PRJNA912664 | ENA
Project description:To assay Rnf149 function during early cardiopharyngeal specification, bulk RNAseq was performed to profile the FACS-purified cardiopharyngeal lineage cells isolated from20 hpf Ciona larvae with CRISPR/Cas9-mediated Rnf149 mutagenesis.
2022-03-07 | GSE171152 | GEO
Project description:In vertebrates, pluripotent pharyngeal mesoderm progenitors produce the cardiac precursors of the second heart field as well as the branchiomeric head muscles and associated stem cells. However, the cellular and molecular mechanisms underlying the transition from multipotent progenitors to distinct heart and muscle precursors remain obscured by the complexity of vertebrate embryos. Here, using the ascidian Ciona intestinalis as a simple chordate model for cardiopharyngeal development, we show that bipotent progenitors are transcriptionally primed to activate both heart and pharyngeal muscle regulatory programs, which become restricted to the corresponding precursors following a conserved pattern of asymmetric divisions. Localized expression of COE (Collier/OLF1/EBF) then orchestrates the transition to a pharyngeal muscle fate both by promoting an MRF (Myogenic Regulatory Factor)-associated core myogenic program in myoblasts and by maintaining an undifferentiated state in their sister precursors through Notch-mediated lateral inhibition. Using single cell lineage tracing, we show that the latter are stem-like muscle precursors, which form most of the juvenile body wall muscles following proliferation, self-renewal, re-activation of MRF, and migration. We discuss the implications of our findings for the development and evolution of the cardiopharyngeal mesoderm in chordates. We combined fluorescence-activated cell sorting (FACS) and whole genome transcription profiling following perturbations of COE function to characterize the transcriptional dynamics underlying the specification of heart and ASM precursors in the ascidian cardiopharyngeal lineage. We used whole genome transcription profiling of FACS-purified cell populations isolated from 21 hpf larvae expressing FoxF>COE, FoxF>COE::WRPW or the FoxF>NLS::lacZ control. To gain insights into the transcriptional dynamics underlying fate specification in the cardiopharyngeal lineage, we also purified B7.5-lineage cells from control embryos and larvae collected every two hours from 8 to 28 hpf. This time window encompasses all developmental transitions from early TVC specification till ASM ring formation and initial differentiation.
2014-07-17 | E-GEOD-54746 | biostudies-arrayexpress