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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE272545 | GEO | 2024/11/08

REPOSITORIES: GEO

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

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

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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).

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EOMES interacts with RUNX3 and BRG1 to promote innate memory cell formation through epigenetic reprogramming

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Gene expression of sorted Eomes+ and Eomes‒ γδ T cells from spleen of Eomes-IRES-GFP mice.

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