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

Area of Science:

• Epigenetics
• Genomics
• Molecular 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.

Purpose of the Study:

• To investigate if Xist RNA targets genes beyond the inactive X chromosome.
• To identify the characteristics and functions of these off-target genes.
• To determine the role of Xist's Repeat B motif and potential small molecule inhibitors in its in-trans activity.

Main Methods:

• Utilized female mouse embryonic stem cells (ES) and mouse embryonic fibroblasts (MEF) as models.
• Analyzed Xist RNA localization and binding patterns using molecular techniques.
• Investigated the impact of Xist overexpression, Repeat B deletion, and Xist inhibitor (X1) treatment on gene expression.

Main Results:

• Xist RNA was found to localize and bind to approximately 100 autosomal genes in both ES and MEF cells.
• Target genes possess active chromatin status and are located in Polycomb-poor regions, distinct from human XIST patterns.
• Xist binding down-modulates autosomal gene expression without causing complete silencing, and this effect is Repeat B-dependent and sensitive to X1 inhibition.

Conclusions:

• Xist RNA exhibits in-trans targeting of specific autosomal genes in mice.
• The Repeat B motif is critical for Xist's autosomal gene targeting and regulatory functions.
• Autosomal gene regulation by Xist can be modulated by small molecule inhibitors, offering potential therapeutic avenues.