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Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

ABSTRACT: Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

PROVIDER: PRJNA351754 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4690440.fastq.gz	Fastqsanger.gz
	SRR4690450.fastq.gz	Fastqsanger.gz
	SRR4690441.fastq.gz	Fastqsanger.gz
	SRR4690451.fastq.gz	Fastqsanger.gz
	SRR4690471.fastq.gz	Fastqsanger.gz

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Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling.

Project description:TET-family dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and oxidized methylcytosines in DNA. Here, we show that mouse embryonic stem cells (mESCs), either lacking Tet3 alone or with triple deficiency of Tet1/2/3, displayed impaired adoption of neural cell fate and concomitantly skewed toward cardiac mesodermal fate. Conversely, ectopic expression of Tet3 enhanced neural differentiation and limited cardiac mesoderm specification. Genome-wide analyses showed that Tet3 mediates cell-fate decisions by inhibiting Wnt signaling, partly through promoter demethylation and transcriptional activation of the Wnt inhibitor secreted frizzled-related protein 4 (Sfrp4). Tet1/2/3-deficient embryos (embryonic day 8.0-8.5) showed hyperactivated Wnt signaling, as well as aberrant differentiation of bipotent neuromesodermal progenitors (NMPs) into mesoderm at the expense of neuroectoderm. Our data demonstrate a key role for TET proteins in modulating Wnt signaling and establishing the proper balance between neural and mesodermal cell fate determination in mouse embryos and ESCs.

| S-EPMC5187696 | biostudies-literature

Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-11-21 | GSE89316 | GEO

Antagonistic activities of Sox2 and Brachyury control the fate choice of neuro-mesodermal progenitors

Project description:The spinal cord and mesodermal tissues of the trunk such as the vertebral column and skeletal musculature derive from neuro-mesodermal progenitors (NMPs). Sox2, Brachyury (T) and Tbx6 have been correlated with NMP potency and lineage choice, however, their exact role and interaction in these processes have not been revealed yet. Here we present a global analysis of NMPs and their descending lineages performed on purified cells from E8.5 wild-type and mutant embryos. We show that T, cooperatively with WNT signaling, controls the progenitor state and the switch towards the mesodermal fate. Sox2 acts antagonistically and promotes neural development. Tbx6 reinforces the mesodermal fate choice, represses the progenitor state and confers paraxial fate commitment. Our findings refine previous models and establish new concepts of the molecular principles of mammalian trunk development comprising NMP maintenance, lineage choice and mesoderm formation.

2017-08-17 | GSE93524 | GEO

Tet proteins influence the balance between neuroectoderm and cardiac mesoderm fate choice by inhibiting Wnt signaling

Project description:To determine the global distribution of Tet3 DNA binding sites, we performed ChIP-seq in neural precursor cells (NPCs). We report that Tet3-binding sites clustered close to transcription start sites (TSS), with a low frequency of binding at distal regions relative to the TSS. DNA motif analysis identified a CpG-rich sequence as the highest-ranked motif among Tet3-binding sites. GO analysis of Tet3 target genes showed enrichment for genes related to mesoderm development and neural differentiation. IPA analysis showed that Tet3 target genes were also strongly enriched for components of the Wnt signaling pathway.

2016-11-21 | GSE89315 | GEO

Gene expression analysis of primitive neuroectodermal tumors

2013-05-01 | GSE19404 | GEO

D. simulans vs. Sechellia bodies choice vs. no choice -Affymetrix

Project description:D. simulans vs. Sechellia bodies choice vs. no choice -Affymetrix

| PRJNA110403 | ENA

Gene expression analysis of primitive neuroectodermal tumors

Project description:Central nervous system primitive neuroectodermal tumors (CNS PNET) and medulloblastomas are both embryonal tumors that predominantly occur in children. We used microarrays to analyse a cohort of CNS PNETs and medulloblastomas to identify gene expression related to tumor subgroups. RNA extracted from 23 frozen tumor samples, plus a commercial fetal brain sample, was analysed using Affymetrix U133 plus 2.0 arrays. Tumour subgroups, based on gene expression, were identified using clustering methods.

2013-05-01 | E-GEOD-19404 | biostudies-arrayexpress

D. simulans vs. Sechellia bodies choice vs. no choice -Affymetrix

Project description:Here we show that Drosophila sechelliaM-bM-^@M-^Ta specialist on the fruit of Morinda citrifolia that recently diverged from its generalist sister-species, D. simulansM-bM-^@M-^Thas rapidly accumulated loss-of-function alleles and reduced gene expression at genes affecting olfaction, detoxification, and metabolism. While D. sechellia increases expression of genes involved with oogenesis and fatty acid metabolism when on its host, many more genes show reduced expression in D. sechellia. For several functionally related genes, this decrease in expression is associated with loss-of-function alleles. The rapid accumulation of these alleles potentially affected D. sechelliaM-bM-^@M-^Ys initial adaptation to M. citrifolia, likely contributes to D. sechelliaM-bM-^@M-^Ys poor competitive ability off of its host, and increases ecological isolation between D. sechellia and its sister species. Keywords: comparative hybridization, gene expression 2 species (simulans and sechella) by choice vs no-choice treatment for octanoic & hexanoic acid blend

2008-11-25 | E-GEOD-13723 | biostudies-arrayexpress

CAGE on Drosophila mesodermal embryo samples

Project description:5'Cap-Analysis of Gene Expression (5' CAGE) from mesodermal and whole embryo RNA at three different time intervals during development.

2018-03-07 | E-MTAB-6159 | biostudies-arrayexpress

RNA-seq of WT, Mbd3-/- and rescue hiPSC during neuroectodermal differentiation and of WT and Mbd3-/- in mEpiSC during neuroectodermal differentiation

Project description:Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. In this study, we investigated the structure and function of the nucleosome remodeller and deacetylase (NuRD) complex in human induced pluripotent stem cells (hiPSCs) and in mouse epiblast stem cells (mEpiSCs). We studied gene expression changes at the self-renewal state (0 days) and at 3, 6 and 12 days of neuroectodermal differentiation in WT, Mbd3-/- and rescue hiPSCs and at 2, 4 and 8 days of neuroectodermal differentiation in mEpiSCs. Sequencing libraries were prepared using the NEXTflex Rapid Directional RNA-seq kit (Illumina) or SMARTer® Stranded Total RNA-Seq Kit v2—Pico Input Mammalian (Takara Bio) and sequenced on the Illumina platform at the CRUK Cambridge Institute Genomics Core facility (Cambridge, UK). Illumina sequence files were converted into FASTQ format. The short sequence reads (75 nucleotides) were aligned to the Human reference genome (hg38; http://genome.ucsc.edu/) or to the Mouse reference genome (mm10; http://genome.ucsc.edu/) and assigned to genes using BWA (Li & Durbin, 2009). We used the Subread package (R statistical tool; http://www.r-project.org/) to count aligned reads. Differentially expressed genes were identified using R package edgeR (Chen, Lun, & Smyth, 2016).

2020-03-30 | E-MTAB-8753 | biostudies-arrayexpress

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