RBM39 modulates UPR signaling through alternative splicing of IRE1α/ERN1

Area of Science:

• Cellular Biology
• Molecular Biology
• Genetics

Background:

• The unfolded protein response (UPR) maintains endoplasmic reticulum proteostasis via signaling pathways like IRE1α-XBP1.
• Upstream regulators of the IRE1α-XBP1 axis, crucial for adaptive transcription, are not fully understood.

Purpose of the Study:

• To systematically identify regulators of XBP1 splicing using a novel screening platform.
• To elucidate the mechanisms by which RBM39 influences UPR signaling.

Main Methods:

• CRASP-seq, a scalable RNA-coupled CRISPR screening platform, was employed to identify regulators of XBP1 splicing.
• Investigated the impact of RBM39 and U2 snRNP perturbation on ERN1 splicing and IRE1α activity.

Main Results:

• Identified RBM39 as a critical positive regulator of XBP1 splicing.
• Perturbation of RBM39 or U2 snRNP components led to ERN1 alternative splicing (exon-18 skipping), producing a truncated IRE1α isoform that suppresses XBP1 splicing.
• Heat shock reduces RBM39 activity, promoting ERN1 exon-18 skipping and attenuating IRE1α-XBP1 signaling.

Conclusions:

• Discovered a novel regulatory axis connecting canonical splicing machinery to UPR signaling.
• ERN1 alternative splicing acts as a stress-adaptive mechanism to limit UPR output under proteotoxic stress.
• Findings establish ERN1 alternative splicing as a key modulator of cellular stress responses.