Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors

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

ORGANISM(S): Mus musculus

PROVIDER: GSE165107 | GEO | 2022/05/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ChIP-seq]

Project description:The mammalian heart arises from various populations of Mesp1-expressing cardiovascular progenitors (CPs) that are specified during the early stages of gastrulation. Mesp1 acts as a master regulator of CP specification and differentiation. However, how Mesp1 regulates the chromatin landscape of nascent mesodermal cells to define the temporal and spatial patterning of the distinct populations of CP remains unknown. Here, by combining ChIP-seq, RNA-seq and ATAC-seq during mouse pluripotent stem cell differentiation, we defined the temporal remodelling of the chromatin landscape mediated by Mesp1. We identified different enhancers that are temporally regulated to erase the pluripotent state and specify the pools of CPs that mediate heart development. We found that Mesp1 acts as a pioneer transcription factor (TF) and identified Zic TFs as essential cofactors that regulate Mesp1 pioneer activity at key mesodermal enhancers, thereby regulating the chromatin remodelling and gene expression associated with the specification of the different populations of CPs in vivo. Our study identifies the dynamics of the chromatin landscape and enhancer remodelling associated with temporal patterning of early mesodermal cells into the distinct populations of CPs that mediate heart development.

2022-05-18 | GSE165102 | GEO

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ATAC-seq]

2022-05-18 | GSE165101 | GEO

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [RNA-seq]

2022-05-18 | GSE165103 | GEO

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors

Project description:Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors

| PRJNA693264 | ENA

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ChIP-seq]

Project description:Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ChIP-seq]

| PRJNA693270 | ENA

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [RNA-seq]

Project description:Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [RNA-seq]

| PRJNA693271 | ENA

Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ATAC-seq]

Project description:Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ATAC-seq]

| PRJNA693269 | ENA

Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors.

Project description:The mammalian heart arises from various populations of Mesp1-expressing cardiovascular progenitors (CPs) that are specified during the early stages of gastrulation. Mesp1 is a transcription factor that acts as a master regulator of CP specification and differentiation. However, how Mesp1 regulates the chromatin landscape of nascent mesodermal cells to define the temporal and spatial patterning of the distinct populations of CPs remains unknown. Here, by combining ChIP-seq, RNA-seq and ATAC-seq during mouse pluripotent stem cell differentiation, we defined the dynamic remodelling of the chromatin landscape mediated by Mesp1. We identified different enhancers that are temporally regulated to erase the pluripotent state and specify the pools of CPs that mediate heart development. We identified Zic2 and Zic3 as essential cofactors that act with Mesp1 to regulate its transcription-factor activity at key mesodermal enhancers, thereby regulating the chromatin remodelling and gene expression associated with the specification of the different populations of CPs in vivo. Our study identifies the dynamics of the chromatin landscape and enhancer remodelling associated with temporal patterning of early mesodermal cells into the distinct populations of CPs that mediate heart development.

| S-EPMC7613098 | biostudies-literature

Early patterning and specification of cardiac progenitors in gastrulating mesoderm.

Project description:Mammalian heart development requires precise allocation of cardiac progenitors. The existence of a multipotent progenitor for all anatomic and cellular components of the heart has been predicted but its identity and contribution to the two cardiac progenitor 'fields' has remained undefined. Here we show, using clonal genetic fate mapping, that Mesp1+ cells in gastrulating mesoderm are rapidly specified into committed cardiac precursors fated for distinct anatomic regions of the heart. We identify Smarcd3 as a marker of early specified cardiac precursors and identify within these precursors a compartment boundary at the future junction of the left and right ventricles that arises prior to morphogenesis. Our studies define the timing and hierarchy of cardiac progenitor specification and demonstrate that the cellular and anatomical fate of mesoderm-derived cardiac cells is specified very early. These findings will be important to understand the basis of congenital heart defects and to derive cardiac regeneration strategies.

| S-EPMC4356145 | biostudies-other

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic.

Project description:Transcription factors regulate their target genes by binding to regulatory regions in the genome. Although the binding preferences of TP53 are known, it remains unclear what distinguishes functional enhancers from nonfunctional binding. In addition, the genome is scattered with recognition sequences that remain unoccupied. Using two complementary techniques of multiplex enhancer-reporter assays, we discovered that functional enhancers could be discriminated from nonfunctional binding events by the occurrence of a single TP53 canonical motif. By combining machine learning with a meta-analysis of TP53 ChIP-seq data sets, we identified a core set of more than 1000 responsive enhancers in the human genome. This TP53 cistrome is invariably used between cell types and experimental conditions, whereas differences among experiments can be attributed to indirect nonfunctional binding events. Our data suggest that TP53 enhancers represent a class of unsophisticated cell-autonomous enhancers containing a single TP53 binding site, distinct from complex developmental enhancers that integrate signals from multiple transcription factors.

| S-EPMC4937571 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data