Gene reactivation upon erosion of X chromosome inactivation in female hiPSCs is predictable yet variable and persists through differentiation
Female human induced pluripotent stem cells frequently undergo X-chromosome inactivation (XCI) erosion, marked by X-inactive specific transcript (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.
Authors
- Ana Rita Grosso (ORCID: https://orcid.org/0000-0001-6974-4209)
- Maria Arez (ORCID: https://orcid.org/0000-0001-5564-3490)
- Mélanie Eckersley-Maslin (ORCID: https://orcid.org/0000-0002-0168-0373)
- Joana Jeremias (ORCID: https://orcid.org/0009-0007-4326-1277)
- Francisca Cazaux Mateus (ORCID: https://orcid.org/0000-0001-8536-6412)
- Annalisa Mupo (ORCID: https://orcid.org/0000-0002-2771-0462)
- Miguel Casanova (ORCID: https://orcid.org/0000-0001-8622-6550)
- Rui Sousa‐Luís (ORCID: https://orcid.org/0000-0002-2589-144X)
- Pedro Barbosa (ORCID: https://orcid.org/0000-0002-3892-7640)
- Paulo Caldas (ORCID: https://orcid.org/0000-0001-6730-4461)
- Simão Teixeira da Rocha (ORCID: https://orcid.org/0000-0002-9683-7942)
- Ana Cláudia Raposo (ORCID: https://orcid.org/0000-0003-2737-7265)
- Frederico Água (ORCID: https://orcid.org/0009-0002-0784-3847)
- David Oxley
Institutions
- Babraham Institute (GB)
- University of Lisbon (PT)
- Peter MacCallum Cancer Centre (AU)
- Institute for Biotechnology and Bioengineering (PT)
- Universidade Nova de Lisboa (PT)
Publication Details
- Journal
- Stem Cell Reports
- Published
- 2025-04-05
- DOI
- https://doi.org/10.1016/j.stemcr.2025.102472
- Citations
- 8
- Primary Topic
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Type
- article
- Field-Weighted Citation Impact
- 14.54
Funders
- Fundação para a Ciência e a Tecnologia
- HORIZON EUROPE Marie Sklodowska-Curie Actions