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Novel RNA-Binding Proteins Isolation by the RaPID Methodology

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Small molecule inhibition of CPSF3 impacts R-loop distribution and abundance.

Cristina R Hofman¹, Victor Tse¹, Jiaxin Hu¹

¹UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, 6001 Forest Park Road, Dallas, TX 75390-9041.

Biorxiv : the Preprint Server for Biology

|July 14, 2025

Summary

New research shows that inhibiting Cleavage and Polyadenylation Specific Factor 3 (CPSF3) with compounds like YT-II-100 increases overall R-loop formation. However, this effect doesn't apply to specific genes, suggesting complex R-loop regulation.

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Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

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Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

R-loops are nucleic acid structures involved in cellular processes but can cause genomic instability when accumulated.
R-loop formation is linked to transcription and the Cleavage and Polyadenylation Specific Factor 3 (CPSF3) enzyme.
CPSF3 inhibition has been associated with transcriptional changes and R-loop alterations.

Purpose of the Study:

To investigate the impact of the novel CPSF3 inhibitor YT-II-100 on global and gene-specific R-loop formation.
To compare the effects of YT-II-100 with the known compound JTE-607.

Main Methods:

Treatment of cells with YT-II-100 and JTE-607.
Assessing global R-loop abundance using molecular assays.
Evaluating R-loop formation at specific gene loci known to be sensitive to R-loop regulation.

Main Results:

YT-II-100 treatment led to a global increase in R-loop formation.
R-loop formation at specific control genes was not significantly altered by YT-II-100.
Similar results were observed with the compound JTE-607, indicating a need for careful interpretation.

Conclusions:

Inhibiting CPSF3 with YT-II-100 globally increases R-loop formation, but not necessarily at all gene loci.
The regulation of R-loop formation may differ between global levels and specific genomic regions.
Caution is advised when interpreting R-loop modulation studies using JTE-607 and YT-II-100, as mechanisms may vary.