Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE235651 | GEO | 2024/01/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation.

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

Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [ATAC-seq]

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

Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [RNA-seq]

2024-01-26 | GSE235649 | GEO

Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation

Project description:Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation

| PRJNA986836 | ENA

Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [ATAC-seq]

Project description:Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [ATAC-seq]

| PRJNA986840 | ENA

Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [RNA-seq]

Project description:Identification of endothelial gene regulatory elements during cardiopharyngeal lineage differentiation [RNA-seq]

| PRJNA986839 | ENA

Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements.

Project description:BackgroundMutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated.ResultsHere we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes.ConclusionsOur findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architecture.

| S-EPMC6790052 | biostudies-literature

Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-07-01 | E-GEOD-67838 | biostudies-arrayexpress

PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-17 | E-GEOD-53508 | biostudies-arrayexpress

Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-07-01 | GSE67838 | GEO