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Gene reactivation upon erosion of X-chromosome inactivation in female hiPSCs is predictable yet variable and persists through differentiation

ABSTRACT: Gene reactivation upon erosion of X-chromosome inactivation in female hiPSCs is predictable yet variable and persists through differentiation

PROVIDER: PRJNA1090865 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28421117_1.fastq.gz	Fastqsanger.gz
	SRR28421117_2.fastq.gz	Fastqsanger.gz
	SRR28421118_1.fastq.gz	Fastqsanger.gz
	SRR28421118_2.fastq.gz	Fastqsanger.gz
	SRR28421119_1.fastq.gz	Fastqsanger.gz

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Gene reactivation upon erosion of X-chromosome inactivation in female hiPSCs is predictable yet variable and persists through differentiation

Project description:Female human induced pluripotent stem cells frequently undergo X-chromosome inactivation (XCI) erosion, marked by XIST RNA loss and partial reactivation of the inactive X (Xi). This overlooked phenomenon limits our understanding of its impact on stem cell applications. Here, we show that XCI erosion is frequent and heterogeneous, leading to the reactivation of several X-linked genes. These are primarily located on the short arm of the X chromosome, particularly near escape genes and within H3K27me3-enriched domains, with reactivation linked to reduced promoter DNA methylation. Interestingly, escape genes further increase their expression from Xi upon XCI erosion, highlighting the critical role of XIST in their dosage regulation. Importantly, global (hydroxy)methylation levels and imprinted regions remain unaffected, and analysis of trilineage commitment and cardiomyocyte formation reveals that XCI erosion persists across differentiation. These findings underscore the need for greater awareness of the implications of XCI erosion for stem cell research and clinical applications.

2025-05-13 | GSE262239 | GEO

Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (Bisulfite-seq)

Project description:During culture, female human pluripotent stem cells (hPSCs), including human induced PSCs (hiPSCs) exhibit a propensity for erosion of X-chromosome inactivation (XCI). This phenomenon is characterized by loss of XIST RNA expression and reactivation of a subset of X-linked genes from the inactive X chromosome (Xi). XCI erosion, despite its common occurrence, is often overlooked by the stem cell community, hindering a complete understanding of its impact on both fundamental and translational applications of hiPSCs. Investigating erosion dynamics in female hiPSCs, our study reveals that XCI erosion is a frequent yet heterogeneous phenomenon, resulting in reactivation of several X-linked genes. The likelihood of a gene to erode increases for those located on the short arm of the X chromosome and within H3K27me3-enriched domains. Paradoxically, genes that typically escape XCI are hypersensitive to loss of XIST RNA and XCI erosion. This implies that XIST RNA normally restrain expression levels of these genes on the Xi. Importantly, increased X-linked gene expression upon erosion does not globally impact (hydroxy)methylation levels in hiPSCs or at imprinted regions. By exploring diverse differentiation paradigms, such as trilineage commitment and cardiac differentiation, our study reveals the persistence of abnormal XCI patterns throughout differentiation. This finding has significant implications for fundamental research, translational applications, and clinical use of stem cells. We underscore the importance of raising awareness within the stem cell community regarding XCI erosion and advocate for its inclusion in comprehensive hiPSC quality control.

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Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (RNA-Seq)

Project description:During culture, female human pluripotent stem cells (hPSCs), including human induced pluripotent stem cells (hiPSCs), exhibit a propensity for erosion of X-chromosome inactivation (XCI). This phenomenon is characterized by the loss of XIST RNA expression and reactivation of a subset of X-linked genes from the inactive X chromosome (Xi). Despite its common occurrence, XCI erosion is often overlooked by the stem cell community, hindering a complete understanding of its impact on both fundamental and translational applications of hiPSCs. Our study investigates erosion dynamics in female hiPSCs and reveals that XCI erosion is a frequent yet heterogeneous phenomenon, resulting in the reactivation of several X-linked genes. The likelihood of a gene to erode increases for those located on the short arm of the X chromosome and within H3K27me3-enriched domains. Paradoxically, genes that typically escape XCI are hypersensitive to the loss of XIST RNA and XCI erosion. This implies that XIST RNA normally restrains expression levels of these genes on the Xi. Importantly, increased X-linked gene expression upon erosion does not globally impact (hydroxy)methylation levels in hiPSCs or at imprinted regions. By exploring diverse differentiation paradigms, such as trilineage commitment and cardiac differentiation, our study reveals the persistence of abnormal XCI patterns throughout differentiation. This finding has significant implications for fundamental research, translational applications, and clinical use of stem cells. We underscore the importance of raising awareness within the stem cell community regarding XCI erosion and advocate for its inclusion in comprehensive hiPSC quality control.

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Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (RNA-AMP-Seq)

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Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (Bisulfite-seq)

Project description:Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (Bisulfite-seq)

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Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (RNA-Seq)

Project description:Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (RNA-Seq)

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Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (RNA-AMP-Seq)

Project description:Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation (RNA-AMP-Seq)

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Xi-reactivation in female human induced pluripotent stem cells (hiPSCs)

Project description:Female human induced pluripotent stem cell (hiPSC) lines exhibit considerable variability in X-inactivation status. Some lines maintain one transcriptionally active X chromosome (Xa) and one inactive X (Xi) from donor cells. However, hiPSC lines that have two Xas are infrequently produced. We show here Xinactivation status in female hiPSC lines depends on derivation conditions. hiPSC lines generated using the Kyoto method, which employs leukemia inhibitory factor (LIF)-expressing SNL feeders, frequently had two Xas. Lines derived on other feeders maintained an Xi. In addition, there appears to be a window in which SNL feeders promote Xi-reactivation. Upon differentiation, Xa/Xa hiPSCs silenced one X. The efficient production of Xa/Xa hiPSC lines provides unprecedented opportunities to understand human X-reactivation and inactivation. Gene expression patterns were compared between several human embryonic stem cell (hESC) and hiPSC lines. Gene expression ratios between genes on X and those on autosomes were calculated from each cell lines.

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Xi-reactivation in female human induced pluripotent stem cells (hiPSCs)

2013-02-06 | GSE44044 | GEO