Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response

Area of Science:

• Molecular Biology
• Virology
• Cellular Stress Response

Background:

• Viral infections activate cellular double-stranded RNA (dsRNA) sensors.
• Ribonuclease L (RNase L) is an endonuclease activated by dsRNA, cleaving single-stranded RNA.
• The impact of RNase L-induced RNA fragmentation on gene expression remains unclear.

Purpose of the Study:

• To investigate how RNase L-mediated RNA fragmentation influences cellular gene expression and antiviral responses.
• To elucidate the molecular pathways involved in the cellular response to RNase L activity.
• To compare the effects of RNase L with a generic endonuclease, RNase A.

Main Methods:

• Induction of RNase L activity in cells.
• Analysis of RNA fragmentation and gene expression.
• Investigation of cellular signaling pathways (ZAKα, p38, JNK).
• Assessment of translational regulation of stress-responsive genes.
• Comparison with RNase A treatment.

Main Results:

• RNase L-induced RNA fragmentation activates the ribotoxic stress response via ZAKα, potentially involving stalled or collided ribosomes.
• Activated p38 and JNK pathways promote antiviral outcomes like programmed cell death.
• RNase L activity was found to limit the translation of stress-responsive genes.
• The generic endonuclease RNase A mimicked many molecular phenotypes of RNase L, indicating RNA cleavage can trigger antiviral programs.

Conclusions:

• Widespread RNA cleavage by RNase L initiates a complex antiviral program involving the ribotoxic stress response and programmed cell death.
• RNase L plays a dual role by inducing antiviral responses while simultaneously suppressing the translation of certain stress genes.
• RNA cleavage, rather than specific dsRNA sensing, can be a sufficient trigger for cellular antiviral defense mechanisms.