Escape from X inactivation is directly modulated by Xist noncoding RNA

Area of Science:

• Genetics
• Epigenetics
• Developmental Biology

Background:

• X-chromosome inactivation (XCI) silences one X chromosome in XX females via Xist noncoding RNA.
• Some X-linked genes escape XCI, maintaining expression on the inactive X chromosome.

Purpose of the Study:

• To investigate if Xist RNA can silence XCI escapee genes beyond early embryogenesis.
• To explore the role of Xist RNA in regulating the three-dimensional topology of the inactive X chromosome.

Main Methods:

• Increasing endogenous Xist RNA levels in vitro and in vivo.
• Analyzing differentiated cells and mouse pre- and post-implantation embryos.
• Investigating the role of SPEN in Xist-mediated silencing and topological domain elimination.

Main Results:

• Xist RNA can silence escapee genes in differentiated cells and in mouse embryos, extending beyond early development.
• Xist RNA, dependent on SPEN, eliminates topologically associating domain-like structures in clusters of escapees.
• Xist-mediated silencing and topological domain elimination are initially reversible but become irreversible with sustained Xist upregulation, leading to DNA methylation.

Conclusions:

• Xist RNA controls gene activity and the 3D topology of the inactive X chromosome beyond early developmental stages.
• The findings reveal a broader regulatory role for Xist RNA in maintaining X chromosome silencing and structure.