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EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling

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

ORGANISM(S): Mus musculus

PROVIDER: GSE272849 | GEO | 2024/11/08

REPOSITORIES: GEO

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EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling

Project description:In this study we analysed the dynamic changes in the epigenetic landscape during the first embryonic lineage decision following pluripotency exit. At gastrulation, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. This is driven by the binding of two T-box transcription factors (TFs) EOMES and TBXT. We aimed to characterise interaction partners of EOMES and TBXT while bound on chromatin during gastrulation via ChIP-MS approach. We detected the ATP-dependent chromatin remodelling complex SWI/SNF as interaction partner of the TFs to modulate CREs accessibility. For ChIP-MS, mouse embryonic stem cells deficient for both T-box TFs Eomes and Tbxt (dKO), which express GFP-tagged EOMES or TBXT from a dox-inducible locus (dKOEoGFP or dKOTbxtGFP), were differentiated for 4 days as embryoid bodies (EBs) under Activin A treatment. EBs were singularised and cross-linked with formaldehyde for 8 min. The chromatin fraction was isolated and fragmented using sonication. Proteins precipitated with anti-GFP anti-body (ab290, abcam) were digested using trypsin, and desalted in HyperSep spin columns. Uninduced dKOEoGFP or dKOTbxtGFP EBs (nodox) were used as controls. Pulldowns were done for three biological replicates. Desalted peptides were analysed by LC-MS/MS with a Q-Exactive Plus mass spectrometer (Thermo Scientific, San Jose, CA) coupled to an EASY-nLCTM 1000 UHPLC system (Thermo Scientific).

2022-11-25 | MSV000090784 | MassIVE

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ChIP-Seq]

Project description:In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. We show that the default state of NE differentiation is actively overcome by the activity of the Tbx transcription factor (TF) EOMES binding to closed ME CREs. We found the ATP-dependent chromatin remodelling complex SWI/SNF is recruited by EOMES to target ME enhancers. The recruitment of the complex by EOMES leads to the remodelling of the enhancer landscape at ME genes. The ME enhancer landscape is remodelled by the activity of EOMES independent on gene expression genome wide.

2024-11-08 | GSE272549 | GEO

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [RNA-Seq]

2024-11-08 | GSE272547 | GEO

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ATAC-Seq]

2024-11-08 | GSE272545 | GEO

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling

Project description:EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling

| PRJNA1139118 | ENA

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ATAC-Seq]

Project description:EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ATAC-Seq]

| PRJNA1137325 | ENA

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ChIP-Seq]

Project description:EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ChIP-Seq]

| PRJNA1137327 | ENA

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [RNA-Seq]

Project description:EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [RNA-Seq]

| PRJNA1137328 | ENA

SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility.

Project description:Notch signaling plays a key role in many cell fate decisions during development by directing different gene expression programs via the transcription factor CSL, known as Su(H) in Drosophila Which target genes are responsive to Notch signaling is influenced by the chromatin state of enhancers, yet how this is regulated is not fully known. Detecting a specific increase in the histone variant H3.3 in response to Notch signaling, we tested which chromatin remodelers or histone chaperones are required for the changes in enhancer accessibility to Su(H) binding. We show a crucial role for the Brahma SWI/SNF chromatin remodeling complex, including the actin-related BAP55 subunit, in conferring enhancer accessibility and enabling the transcriptional response to Notch activity. The Notch-responsive regions have high levels of nucleosome turnover which depend on the Brahma complex, increase in magnitude with Notch signaling, and primarily involve histone H3.3. Together these results highlight the importance of SWI/SNF-mediated nucleosome turnover in rendering enhancers responsive to Notch.

| S-EPMC6500979 | biostudies-literature

Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters.

Project description:Precise nucleosome-positioning patterns at promoters are thought to be crucial for faithful transcriptional regulation. However, the mechanisms by which these patterns are established, are dynamically maintained, and subsequently contribute to transcriptional control are poorly understood. The switch/sucrose non-fermentable chromatin remodeling complex, also known as the Brg1 associated factors complex, is a master developmental regulator and tumor suppressor capable of mobilizing nucleosomes in biochemical assays. However, its role in establishing the nucleosome landscape in vivo is unclear. Here we have inactivated Snf5 and Brg1, core subunits of the mammalian Swi/Snf complex, to evaluate their effects on chromatin structure and transcription levels genomewide. We find that inactivation of either subunit leads to disruptions of specific nucleosome patterning combined with a loss of overall nucleosome occupancy at a large number of promoters, regardless of their association with CpG islands. These rearrangements are accompanied by gene expression changes that promote cell proliferation. Collectively, these findings define a direct relationship between chromatin-remodeling complexes, chromatin structure, and transcriptional regulation.

| S-EPMC3690861 | biostudies-literature

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