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Map Brachyury-bound enhancers by ChIP-seq

ABSTRACT: To gain new mechanistic insights into highly-regulated lineage specification and morphogenetic processes during early embryogenesis, we applied ChIP-seq to identify transcriptional programs mediated by a key developmental regulator - Brachyury.

ORGANISM(S): Mus musculus

PROVIDER: GSE54978 | GEO | 2014/03/10

SECONDARY ACCESSION(S): PRJNA238192

REPOSITORIES: GEO

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Map Brachyury-bound enhancers by ChIP-seq

Project description:To gain new mechanistic insights into highly-regulated lineage specification and morphogenetic processes during early embryogenesis, we applied ChIP-seq to identify transcriptional programs mediated by a key developmental regulator - Brachyury. Embryonic stem cells were differentiated into Brachyury-positive mesoendoderm cells. And, ChIP-seq experiments were carried out by two independent Brachyury antibodies.

2014-03-10 | E-GEOD-54978 | biostudies-arrayexpress

High-resolution Brachyury DNA-binding Sites Mapping by ChIP-exo

Project description:Mapping ultra high resolution of Brachyury:DNA interaction would provide us with valuable new mechanistic insights into complex molecular transactions at Brachyury-bound enhancers. Embryonic stem cells were differentiated into Brachyury-positive mesoendoderm cells. And, ChIP-exo experiment was then performed to identify detailed Brachyury-DNA binding profiles.

2014-03-10 | E-GEOD-54963 | biostudies-arrayexpress

High-resolution Brachyury DNA-binding Sites Mapping by ChIP-exo

2014-03-10 | GSE54963 | GEO

The molecular basis of specific functions of Brachyury and Eomes for mesoderm and endoderm lineage specification

Project description:The Tbx factors Eomesodermin (Eomes) and Brachyury instruct endoderm and mesoderm specification. Both Tbx factors have common large overlap in chromatin binding sites, however their embryonic phenotypes of mutants largely differ. In this study, we delineate the distinct binding patterns and gene target sets of Eomes and Brachyury providing a molecular model of distinct fate specification programs.

2023-07-26 | GSE194192 | GEO

Probing Brachyury Function during ES cell differentiaiton

Project description:To probe how Brachyury regulates its target genes, we performed mRNA-seq to analyze gene expression changes after Brachyury depletion by the lentivirus-mediated shRNA

2014-03-10 | GSE54984 | GEO

Genome wide maps of H3K4me3, H3K27me3 and H3K27ac in Brachyury mutants and RNA-seq data of Brachyury mutants

Project description:The transcription factor BRACHYURY is the founding member of the T-box family of proteins. A conserved residue (Y88 in BRACHYURY) was previously suggested to be important for interaction with KDM proteins that demethylate H3K27me3. We generated Brachyury mutant mouse embryonic stem cell (ESC) lines. For a wild type control (Thet) we derived an embryonic stem cell line from blastocysts, containing a single wild type copy of the Brachyury locus (T +/2J; 2J is a large genomic deletion of the entire Brachyury locus). We mutated the remaining wild type copy of Brachyury to code for Alanin instead of the conserved tyrosine (Y88) residue (T_Y88A). We derived embryos from these ESCs, compare expression profiles (RNAseq) from Thet and TY88A caudal end mesoderm of early embryos (stages: TS12 and TS13), and complement the expression data with histone methylation ChIPseq data for H3K4me3, HeK27me3 and H3K27ac. Of note: due to the different requirements of cellular material for RNAseq and ChIPseq we differentiated the same ESC used for the embryo generation (in vivo, RNA-seq) to generate early caudal end mesoderm in vitro (ChIPseq). In addition, this dataset contains a ChIPseq track for BRACHURY in wild type ESCs, differentiated into early mesoderm in vitro with the same protocol as for the histone ChiIPseq.

2017-10-01 | GSE94142 | GEO

BRACHYURY orchestrates distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells

Project description:The transcription factor BRACHYURY (T, BRA) is one of the first markers of gastrulation and lineage specification in mammals. Despite its wide use and importance in stem cell and developmental biology, its genomic targets are largely unknown. Here, we used differentiated human embryonic stem cells to study the role of BRA in Bmp4-induced mesoderm and Activin-induced endoderm progenitors by ChIP-seq. We show that BRA has distinct genome-wide binding landscapes in these two populations. Our data illuminate the function of BRA in the context of human embryonic development and show that the regulatory role of BRA is context-dependent. ChIP-seq of BRACHYURY (T, BRA) in two cell types: endoderm and mesoderm progenitors derived from human embryonic stem cells after 36 hours of growth in chemically-defined media (described in Bernardo et al., Cell Stem Cell, 2011, 9:144-155). Input DNA samples are included as a control.

2015-05-18 | E-GEOD-60606 | biostudies-arrayexpress

Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity [ChIPmentation]

Project description:Chordomas are rare spinal tumors addicted to expression of the developmental transcription factor brachyury. In chordomas, brachyury is super-enhancer associated and preferentially downregulated by pharmacologic transcriptional CDK inhibition, leading to cell death. To understand the underlying basis of this sensitivity, we dissect the brachyury transcription regulatory network and compare the consequences of brachyury degradation with transcriptional CDK inhibition. Brachyury defines the chordoma super-enhancer landscape and autoregulates through binding its super-enhancer, and its locus forms a transcriptional condensate. Transcriptional CDK inhibition and brachyury degradation disrupt brachyury autoregulation, leading to loss of its transcriptional condensate and transcriptional program. Compared with transcriptional CDK inhibition, which globally downregulates transcription, leading to cell death, brachyury degradation is much more selective, inducing senescence and sensitizing cells to anti-apoptotic inhibition. These data suggest that brachyury downregulation is a core tenet of transcriptional CDK inhibition and motivates developing strategies to target brachyury and its autoregulatory feedback loop.

2021-02-08 | GSE153971 | GEO

Probing Brachyury Function during ES cell differentiaiton

Project description:To probe how Brachyury regulates its target genes, we performed mRNA-seq to analyze gene expression changes after Brachyury depletion by the lentivirus-mediated shRNA WT and Brachytury Knockdown embryoid bodies were collected at EB day 4. Subsequently, mRNA-seq expriments were performed with whole embryoid bodies

2014-03-10 | E-GEOD-54984 | biostudies-arrayexpress

gene profiling changes induced by regulation of Brachyury expression

Project description:Chordoma is a rare malignant bone tumor on axial skeleton, locally invasive and has a high rate of recurrence. Despite extensive studies, the mechanisms of tumor recurrence after surgical intervention, as well as resistance to radiation and chemotherapy, remain elusive. In this study, cell lines PCH1 and PCH2 were established and characterized by chordoma specific markers. We found that the embryonic transcription factor brachyury inhibits taxol induced apoptosis in different cells, including PCH1 and U2OS cells. Brachyury regulated genes were identified in PCH1 and U2OS using microarray. Brachyury is an embryonic transcription factor involved in embryo development. We emplored the downstream genes related to apoptosis of Brachyury by microarray in different cell lines: U2OS, PCH1 and H460.

2017-09-12 | GSE103716 | GEO

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