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Updated: Jul 17, 2026

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
CTCF, a candidate trans-acting factor for X-inactivation choice
Wendy Chao1, Khanh D Huynh, Rebecca J Spencer
1Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
The study identifies CTCF as a key factor in X-chromosome selection during X-inactivation in mammals. CTCF binding sites within the Tsix gene form an epigenetic switch, regulating which X chromosome is silenced.
Area of Science:
- Epigenetics
- Genomics
- Mammalian genetics
Background:
- X-inactivation is a crucial process in female mammals, silencing one of the two X chromosomes.
- This process is regulated by the noncoding Xist (inactive X-specific transcript) gene and antagonized by the Tsix gene.
- The choice/imprinting center within Tsix plays a role in X-chromosome selection.
Purpose of the Study:
- To identify trans-acting factors involved in X-chromosome selection during X-inactivation.
- To investigate the role of CTCF in the choice/imprinting center of the Tsix gene.
Main Methods:
- Utilized enhancer-blocking assays to test the function of CTCF binding sites.
- Investigated the effect of CpG and non-CpG methylation on CTCF binding in vitro.
- Analyzed the impact of deleting the choice/imprinting center in Tsix on X-chromosome selection.
Main Results:
- Identified CTCF, an insulator and transcription factor, as a candidate for X-chromosome selection.
- Demonstrated that the choice/imprinting center contains tandem CTCF binding sites functional in enhancer-blocking assays.
- Showed that CTCF binding is sensitive to CpG methylation and abolished by non-CpG methylation.
Conclusions:
- CTCF and Tsix cooperate to establish a regulated epigenetic switch for X-inactivation.
- Methylation patterns at CTCF binding sites likely control X-chromosome choice.
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