Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expression

Area of Science:

• Epigenetics
• Genomics
• RNA Biology

Background:

• Xist is a long noncoding RNA essential for X chromosome inactivation (XCI).
• Xist was traditionally considered a cis-acting RNA, binding only to the inactive X chromosome (Xi).
• Evidence suggested Xist might have functions beyond the Xi under certain conditions.

Purpose of the Study:

• To investigate whether Xist RNA can localize and function beyond the inactive X chromosome.
• To identify the targets and characteristics of Xist binding in trans.
• To determine the role of Xist's Repeat B motif in its in-trans function.

Main Methods:

• Analysis of Xist RNA localization and binding in mouse embryonic stem cells (ES) and fibroblasts (MEFs).
• Gene expression analysis to assess the impact of Xist binding on autosomal genes.
• Studies involving transgenic ES cells with altered Xist expression and deletion of the Repeat B motif.
• Treatment with a small molecule inhibitor (X1) targeting Xist.

Main Results:

• Xist RNA was found to localize beyond the Xi, binding to approximately 100 autosomal genes in ES and MEF cells.
• Target genes are actively transcribed and located in regions with low Polycomb occupancy, differing from human XIST patterns.
• Xist binding leads to down-modulation, but not complete silencing, of autosomal gene expression.
• The Repeat B motif of Xist is critical for its autosomal binding and regulatory function.
• Inhibition of Xist with X1 disrupts autosomal gene suppression.

Conclusions:

• Xist RNA exhibits trans-acting functions in mice, targeting a specific set of ~100 autosomal genes.
• The Repeat B domain is essential for Xist's in-trans binding and regulatory activity.
• Autosomal gene targeting by Xist can be modulated by small molecule inhibitors, offering potential therapeutic avenues.