Related Experiment Video

Updated: May 17, 2025

Combined DNA-RNA Fluorescent In situ Hybridization FISH to Study X Chromosome Inactivation in Differentiated Female Mouse Embryonic Stem Cells
15:54

Combined DNA-RNA Fluorescent In situ Hybridization FISH to Study X Chromosome Inactivation in Differentiated Female Mouse Embryonic Stem Cells

Published on: June 14, 2014

27.7K

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

Ana Cláudia Raposo1, Paulo Caldas2, Joana Jeremias3

  • 1iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.

Stem Cell Reports
|April 4, 2025
PubMed

Insights

Female stem cells often lose X-chromosome inactivation (XCI), leading to gene reactivation. This erosion impacts stem cell applications and requires further investigation for reliable use in research and medicine.

Area of Science:

  • Stem cell biology
  • Epigenetics
  • Genetics

Background:

  • Female human induced pluripotent stem cells (hiPSCs) frequently exhibit X-chromosome inactivation (XCI) erosion.
  • This erosion involves loss of X-inactive specific transcript (XIST) RNA and reactivation of genes on the inactive X chromosome (Xi).
  • The implications of XCI erosion for stem cell function and applications remain largely unexplored.

Purpose of the Study:

  • To investigate the frequency, characteristics, and consequences of XCI erosion in female hiPSCs.
  • To determine the genomic locations and regulatory mechanisms associated with XCI erosion.
  • To assess the impact of XCI erosion on stem cell differentiation and gene dosage regulation.

Main Methods:

  • Analysis of XIST RNA expression and Xi gene reactivation in hiPSCs.
  • Genomic mapping of reactivated genes and correlation with epigenetic marks (DNA methylation, H3K27me3).
  • Assessment of trilineage differentiation potential and cardiomyocyte formation in cells with XCI erosion.

Main Results:

  • XCI erosion is a frequent and heterogeneous event in female hiPSCs, causing reactivation of multiple X-linked genes.
  • Reactivated genes are predominantly located on the X chromosome's short arm, near known escape genes and H3K27me3 domains.
  • Reduced promoter DNA methylation correlates with gene reactivation, and escape genes show increased expression from Xi upon erosion.
  • XCI erosion persists through trilineage differentiation and cardiomyocyte formation, without affecting global methylation or imprinted regions.

Conclusions:

  • XCI erosion is a significant epigenetic alteration in female hiPSCs with functional consequences.
  • The phenomenon impacts X-linked gene dosage regulation and is linked to specific genomic and epigenetic features.
  • Awareness of XCI erosion is crucial for the accurate interpretation of results and the clinical application of female-derived stem cells.
Keywords:
DNA methylationX-chromosome inactivation, XCIepigeneticsinduced pluripotent stem cells, hiPSCs

More Related Videos

Pooled shRNA Screen for Reactivation of MeCP2 on the Inactive X Chromosome11:15

Pooled shRNA Screen for Reactivation of MeCP2 on the Inactive X Chromosome

Published on: March 2, 2018

7.2K
Generation of Human Primordial Germ Cell-like Cells at the Surface of Embryoid Bodies from Primed-pluripotency Induced Pluripotent Stem Cells12:06

Generation of Human Primordial Germ Cell-like Cells at the Surface of Embryoid Bodies from Primed-pluripotency Induced Pluripotent Stem Cells

Published on: January 11, 2019

12.3K

Related Concept Videos

Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
1.6K
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
6.2K
Somatic to iPS Cell Reprogramming01:29

Somatic to iPS Cell Reprogramming

Reprogramming alters the gene expression in somatic cells, transforming them into induced pluripotent stem (iPS) cells over several generations. Scientists can reprogram cells by introducing genes for four transcription factors—Oct4, Sox2, Klf4, and c-Myc (OSKM) by viral or non-viral methods. These factors are also known as Yamanaka factors after Shinya Yamanaka, who first generated iPS cells using mouse skin cells. Yamanaka was awarded the Nobel Prize in Physiology or Medicine in 2012...
2.2K
X-Inactivation01:58

X-Inactivation

The human X chromosome contains over ten times the number of genes as in the Y chromosome. Since males have only one X chromosome, and females have two, one might expect females to produce twice as many of the proteins, with undesirable results.
37.9K
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
9.1K
Epigenetic Regulation01:37

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
3.0K