Targeting Xist with compounds that disrupt RNA structure and X inactivation

Area of Science:

• Genomics
• Molecular Biology
• Drug Discovery

Background:

• Most of the human genome is non-coding RNA (ncRNA), but drugs primarily target proteins.
• Targeting ncRNA is challenging due to its conformational flexibility and structural complexity.
• An increasing number of diseases are linked to ncRNA, highlighting the need for ncRNA-targeting drugs.

Purpose of the Study:

• To devise a screening strategy for identifying small molecules that bind ncRNA.
• To identify and characterize small molecules targeting the Xist ncRNA.
• To investigate the functional consequences of Xist ncRNA targeting.

Main Methods:

• Developed a screening strategy to identify small molecules binding ncRNA.
• Used in vitro and in vivo assays to test compound binding to Xist ncRNA.
• Employed small-angle X-ray scattering to analyze RNA conformation.
• Assessed the impact of compound binding on protein interactions, epigenetic modifications, and cellular processes.

Main Results:

• Identified a drug-like small molecule (X1) that specifically binds the RepA motif of Xist ncRNA.
• X1 binding reduces the conformational flexibility of RepA.
• X1 displaces PRC2 and SPEN proteins, suppresses H3K27 trimethylation, and inhibits X-chromosome inactivation.
• X1 exhibits female-specific inhibition of cell differentiation and growth.

Conclusions:

• ncRNA can be systematically targeted by drug-like compounds.
• Small molecules can disrupt RNA structure and epigenetic function.
• This approach expands the chemical space for drug development targeting ncRNA-related diseases.