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Zygotic gene activatory network in zebrafish is globally controlled by Pou5f1 SoxB1 enhancers

ABSTRACT: Genetic control of pluripotent mammalian ES cells is determined by a transcriptional network, with a "central core" of transcription factors, Pou5f1, Sox2 and Nanog. Zebrafish homologues of the "core pluripotency factors" Pou5f1, SoxB1 and Nanog-like are also crucially involved in early development. However, the degree of functional similarity of the network between mammals and non-mammals is a matter of debate. To identify the components of Pou5f1-dependent transcriptional networks, we determined the genomic binding sites for Pou5f1 and Sox2 in late blastula stage zebrafish embryos using ChIP-seq. We found that Sox2 and Pou5f1 are co-binding to the regulatory regions of Sox2, Pou5f1, and Nanog-like, as well as to multiple orthologues of mammalian plutipotency network components.

ORGANISM(S): Danio rerio

PROVIDER: GSE39780 | GEO | 2013/08/10

SECONDARY ACCESSION(S): PRJNA171706

REPOSITORIES: GEO

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Zygotic gene activatory network in zebrafish is globally controlled by Pou5f1 SoxB1 enhancers

Project description:Genetic control of pluripotent mammalian ES cells is determined by a transcriptional network, with a "central core" of transcription factors, Pou5f1, Sox2 and Nanog. Zebrafish homologues of the "core pluripotency factors" Pou5f1, SoxB1 and Nanog-like are also crucially involved in early development. However, the degree of functional similarity of the network between mammals and non-mammals is a matter of debate. To identify the components of Pou5f1-dependent transcriptional networks, we determined the genomic binding sites for Pou5f1 and Sox2 in late blastula stage zebrafish embryos using ChIP-seq. We found that Sox2 and Pou5f1 are co-binding to the regulatory regions of Sox2, Pou5f1, and Nanog-like, as well as to multiple orthologues of mammalian plutipotency network components. Deep sequencing was performed using the Illumina GAIIx on DNA samples obtained from Sox2 ChIP, Pou5f1-Flag ChIP and Input Control. Pou5f1 was analysed in technical duplicates to obtain higher sequencing depth.

2013-08-10 | E-GEOD-39780 | biostudies-arrayexpress

Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition

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2013-09-22 | E-GEOD-47558 | biostudies-arrayexpress

Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition

2013-09-22 | GSE47558 | GEO

Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation.

Project description:Purpose: Find out the consequences of Pou5f3/Oct4 and Nanog binding to the nucleosome distribution before and after Zygotic Genome Activation Methods: MNase-seq of the wild-type(WT), Pou5f3 (MZspg) and Nanog (MZnanog) mutant zebrafish embryos at 512-cell stage and dome stage. Results: Nanog, Sox19b and Pou5f3 bind to the High Nucleosome Affinity Regions (HNARs). HNARs are spanning over 600 bp, featuring high in vivo and predicted in vitro nucleosome occupancy and high predicted propeller twist DNA shape value. We suggest a two-step model, where the same intrinsic DNA properties of HNAR promote both high nucleosome occupancy and differential binding of TFs. In the first step, already prior to ZGA, Pou5f3 and Nanog reduce nucleosome occupancy on HNARs genome-wide. In the second step, Nanog and Pou5f3/SoxB1 complex maintain open chromatin state on the subset of HNARs, acting synergistically. Nanog binds to the HNAR center, while the Pou5f3/SoxB1 complex stabilizes the flanks.

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SOXB1 genetic regulation in the developing testes

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Experiment 2: Pou5f1 and Sox2 overexpression experiments with or without protein synthesis inhibition

Project description:Pou5f1 and Sox2 overexpression experiments with and without protein synthesis inhibitor were performed to investigate direct transcriptional targets of Pou5f1 and Sox2

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Experiment 2: Pou5f1 and Sox2 overexpression experiments protein synthesis inhibition

Project description:Pou5f1 and Sox2 overexpression experiments with protein synthesis inhibitor were performed to investigate direct transcriptional targets of Pou5f1 and Sox2 Experiments were performed in biological triplicates. Cy3 and Cy5 channels were split and analyzed separately using Genedata Analyst software, quantile normalised and used for independent comparisons.

2013-07-31 | E-GEOD-41107 | biostudies-arrayexpress

Interrogation of a Context-Specific Transcription Factor Network Identifies Novel Regulators of Pluripotency

Project description:The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs that define pluripotency. These contrasting views were developed from extensive analyses of TFs in pluripotent cells in vitro. An experimentally-validated, genome-wide repertoire of the regulatory interactions that control pluripotency within the in vivo cellular contexts is yet to be developed. To address this limitation, we assembled a TF interactome of adult human male germ cell tumors (GCTs) using the Algorithm for the Accurate Reconstruction of Cellular Pathways (ARACNe) to analyze gene expression profiles of 141 tumors comprising pluripotent and differentiated subsets. The network (GCTNet) comprised 1305 TFs, and its Ingenuity Pathway analysis identified pluripotency and embryonal development as the top functional pathways. We experimentally validated GCTNet by functional (silencing) and biochemical (ChIP-seq) analysis of the core pluripotency regulatory TFs POU5F1, NANOG, and SOX2 in relation to their targets predicted by ARACNe. To define the extent of the in vivo pluripotency network in this system, we ranked all TFs in the GCTNet according to sharing of ARACNe-predicted targets with those of POU5F1 and NANOG using an Odds-Ratio analysis method. To validate this network, we silenced the top 10 TFs in the network in H9 ES cells. Silencing of each led to downregulation of pluripotency and induction of lineage; 7 of the 10 TFs were identified as pluripotency regulators for the first time. ChIP for three TFs OCT4, SOX2 and NANOG in two pluripotent cell line

2014-11-05 | E-GEOD-62983 | biostudies-arrayexpress

Danio rerio

Project description:Zygotic gene activatory network in zebrafish is globally controlled by Pou5f1 SoxB1 enhancers

| PRJNA171706 | ENA