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EXOSC3 S1-domain variants implicated in PCH1b alter RNA exosome cap subunit abundance and thermal stability disrupting rRNA processing and targeting of AU-rich mRNA

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Runnebohm, Avery M., Wijeratne, H.R. Sagara, Barron, Monica P., Smith-Kinnaman, Whitney R., Rooney, James D., Peck Justice, Sarah A., Cureton, Lauryn A., Holland, Annalise +5 more·2025·bioRxiv (Cold Spring Harbor Laboratory)
DOI 10.1101/2025.05.31.657176PMC PMC12154690
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Abstract

Missense variants in EXOSC3, an RNA exosome subunit, have been identified in patients with PCH1b. We investigated three missense variants in the S1 domain of EXOSC3, including one variant of uncertain significance (VUS) and two pathogenic variants (hence S1 variants). EXOSC3 S1 variant cell lines were generated using CRISPR-Cas9 resulting in widespread proteome changes including decreases in some RNA exosome subunits paired with increases in the catalytic subunit DIS3. Thermal stability, analyzed by PISA, revealed extensive destabilization of RNA exosome cap subunits and the cap-associated exonuclease EXOSC10. Functionally, S1 variants altered rRNA processing with corresponding protein compensation observed in rRNA processing proteins outside the RNA exosome. Exogenous overexpression of EXOSC3 rescues many molecular defects caused by S1 variants suggesting that protein destabilization and turnover strongly contribute to molecular defects. Overall, our findings define the mechanisms through which cells respond to EXOSC3 S1 variant disruption of RNA processing homeostasis.

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  • The RNA exosome has specialized functions in RNA splicing and regulation of AU-rich element (ARE)-containing transcripts.

    “In addition to RNA turnover, the RNA exosome has specialized functions in RNA splicing and the regulation of AU-rich element (ARE)-containing transcripts44–47.”

    From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [47]

    The Introduction (page unavailable) describes AU-rich binding proteins targeting RNAs to the exosome, and the Results section on AU-rich mRNA targeting reports altered targeting of ARE-containing transcripts in EXOSC3 variant cells. The copy describes snRNA processing but does not establish a specialized function for the exosome in RNA splicing; a search for splicing found no supporting passage. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • Total RNA-Seq analysis of homozygous EXOSC3 D132A/D132A HEK293T cells relative to controls revealed more modest changes to the transcriptome than observed for EXOSC3 G191 cell lines.

    “We have also performed total RNA-Seq analysis of homozygous EXOSC3 D132A/D132A HEK293T cells relative to controls, which revealed more modest changes to the transcriptome than observed for the EXOSC3 G191 cell lines47.”

    From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [47]

    The Results section, “Differential transcript abundance indicates RNA exosome function is altered by S1 variants” (page unavailable), reports total RNA sequencing of D132A/D132A cells relative to controls and substantial transcript changes. It does not compare those changes with EXOSC3 G191 cell lines, so the claim that they were more modest is not supported by this source. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • In our recent studies, we observed rRNA processing defects in human cell lines expressing EXOSC3 variants although in an allele-specific manner.

    “In our recent studies, we have also observed rRNA processing defects in human cells lines expressing EXOSC3 variants although in an allele-specific manner47.”

    From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [47]

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Authors
Runnebohm, A. M., Wijeratne, H. R. S., Barron, M. P., Smith-Kinnaman, W. R., Rooney, J. D., Peck Justice, S. A., Cureton, L. A., Holland, A., Ghalei, H., Pelletier, S., Doud, E. H., Vilseck, J. Z., & Mosley, A. L.
Affiliations
  • Indiana University Health (US)
  • Indiana University Indianapolis (US)
  • Indiana University School of Medicine (US)
  • Department of Biology, Marian University, Indianapolis, IN
  • Emory University (US)
Corresponding author
Mosley, Amber L.
ORCID
Venue
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Published
2025-06-01
DOI
10.1101/2025.05.31.657176
PMC
PMC12154690
OpenAlex
W4410940018
Cited by
4
References
8
Citations by year
2026: 3 · 2025: 1
Type
posted content
Language
en
Open access
Licence
Locations
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
  • IUScholarWorks (Indiana University) (submittedVersion, cc-by-nc-nd)
Funders
National Institute of Neurological Disorders and Stroke (R01NS121550)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
EXOSC3, RNA exosome, missense mutations, DIS3, rRNA processing, protein thermal stability, protein destabilization, variants of uncertain significance

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