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An ancestral Wnt-Brachyury feedback loop and vertebrate-specific recruitment of mesoderm-determining target genes revealed by comparative Brachyury target screens

ABSTRACT: An ancestral Wnt-Brachyury feedback loop and vertebrate-specific recruitment of mesoderm-determining target genes revealed by comparative Brachyury target screens

PROVIDER: PRJNA756953 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15565709.fastq.gz	Fastqsanger.gz
	SRR15565710.fastq.gz	Fastqsanger.gz
	SRR15565711.fastq.gz	Fastqsanger.gz
	SRR15565712.fastq.gz	Fastqsanger.gz
	SRR15565713.fastq.gz	Fastqsanger.gz

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An ancestral Wnt-Brachyury feedback loop and vertebrate-specific recruitment of mesoderm-determining target genes revealed by comparative Brachyury target screens

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An ancestral Wnt-Brachyury feedback loop and vertebrate-specific recruitment of mesoderm-determining target genes revealed by comparative Brachyury target screens

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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.

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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.

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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.

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BRACHYURY directs histone acetylation to target loci during mesoderm development.

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Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state

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