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PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

ABSTRACT: PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

PROVIDER: PRJNA704376 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13771262_1.fastq.gz	Fastqsanger.gz
	SRR13771262_2.fastq.gz	Fastqsanger.gz

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PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

Project description:Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use polyA-tail enriched RNA-seq within the wildtype TX1072 XX cell line after two days of differentiation.

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Project description:In XXTet3-/- mESCs DNA methylation levels are higher than XX wildtype levels. We sought to determine if changes in cytosine modifications observed in XXTet3-/- mESCs impacted gene expression, we performed RNA-seq. 104 genes were up regulated in the mutant XX mESCs relative to wild type controls, and 86 were down regulated To ask whether the XX-specific nuclear enrichment of TET3 is necessary for a developmental transition, we differentiated WT XX and XXTet3-/- mESCs into epiblast-like cells (EpiLCs). Comparison of WT XX and XXTet3-/- EpiLC RNA-seq showed that 404 genes exhibited increased expression and 499 exhibited decreased expression in mutant cells. GO term analysis showed gene expression changes affecting several LIF and BMP signaling pathways. However, despite these changes in signaling pathway driven expression, the expression of mESC markers went down and mEpiLC markers went up comparably upon differentiation WT XX and XXTet3-/- mESCs, suggesting that many key transcriptional changes that characterize this transition can occur without TET3.

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Non-coding CRISPR interference screen to identify regulatory elements of Xist in TX1072 XX SP107 mESCs at the onset of random X inactivation

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Project description:TT-seq and RNA-seq in TX1072 XXΔXic and XO mESCs during differentiation

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