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Temporal transcriptome and methylome analysis of differentiating mouse embryonic stem cells deficient for Zeb2

ABSTRACT: Temporal transcriptome and methylome analysis of differentiating mouse embryonic stem cells deficient for Zeb2

PROVIDER: PRJNA304744 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2969540.fastq.gz	Fastqsanger.gz
	SRR2969550.fastq.gz	Fastqsanger.gz
	SRR2969560_1.fastq.gz	Fastqsanger.gz
	SRR2969560_2.fastq.gz	Fastqsanger.gz
	SRR2969541.fastq.gz	Fastqsanger.gz

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Temporal DNA methylation analysis (RRBS) for differentiating mouse embryonic stem cells deficient for Zeb2

Project description:In this study we performed temporal profiling of DNA methylation by RRBseq of differentiating mouse embryonic stem cells using an embryoid body protocol. Analysis at d0, d4 and d6 revealed that Zeb2 deficient mESC lose their initially acquired DNA methylation at d6.

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ZEB2 locus regulation in differentiating iPSCs

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ZEB2 locus regulation in differentiating iPSCs

Project description:The multi-domain transcription factor ZEB2 controls embryonic and adult cell fate decisions and maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie Mowat-Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of an approximately 3.5 Mb-long gene-desert, lacking any protein-coding gene sequence. Using temporal high-resolution Targeted Chromatin Capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 gene promoter and this gene desert during neural differentiation of induced pluripotent cells (iPSCs), including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site (TSS). Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis regulatory elements (REs) located in ZEB2’s gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of relevant cell types, and the molecular characterization of identified MOWS patients that lack mutations in ZEB2 protein-coding exons.

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Temporal transcriptome and methylome analysis of differentiating mouse embryonic stem cells deficient for Zeb2

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

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Temporal transcriptome analysis of control and Zeb2 knockout mESC in pluripotency and in neural differentiation

Project description:To capture the Zeb2-dependent transcriptional changes in early cell state/fate decisions we performed RNA-seq on Zeb2 control and Zeb2 knockout cells. We chose three stages, which correspond in control ESCs to the naive pluripotent state (d0; very low amounts of Zeb2 mRNA), multipotent progenitors (d4, low Zeb2 mRNA/protein) and early neural progenitors (d6, high Zeb2 mRNA/protein), respectively.

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