The RNA exosome maintains cellular RNA homeostasis by controlling transcript abundance in the brain
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Abstract
Intracellular ribonucleases (RNases) are essential for maintaining accurate RNA levels. Inherited mutations in genes encoding ubiquitous RNases are associated with human diseases, primarily affecting the nervous system. Recessive mutations in genes encoding the evolutionarily conserved RNA exosome, an RNase complex, cause syndromic neurodevelopmental disorders, such as pontocerebellar hypoplasia type 1b (PCH1b), characterized by progressive neurodegeneration. Here, we establish a CRISPR-Cas9-engineered Drosophila model of PCH1b to investigate the cell-type-specific post-transcriptional regulatory functions of the RNA exosome complex in vivo. Pathogenic variants in Rrp40, a subunit of the complex, disrupt RNA exosome activity, leading to widespread transcriptomic dysregulation in brain-enriched cell populations, including defective rRNA processing. These molecular defects coincide with progressive neurodegeneration and behavioral impairments that track with allele severity. Our findings provide a cell-type-resolved view of RNA exosome function in a fully developed animal brain and underscore the critical role of RNA surveillance in safeguarding transcriptome homeostasis and neuronal integrity.
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PCH1B is characterized by marked hypotonia, progressive cerebellar atrophy, and motor neuron dysfunction.
“PCH1B is a subtype characterized by marked hypotonia, progressive cerebellar atrophy, and motor neuron dysfunction and caused by variants in the EXOSC3 gene15,18,21–23,25.”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [15]
The Introduction identifies PCH1b as a pontocerebellar hypoplasia subtype linked to EXOSC3/Rrp40 variants, and the References list an EXOSC3 study whose title mentions spinal motor neuron degeneration. Our copy does not characterize PCH1b by marked hypotonia or progressive cerebellar atrophy; the Discussion’s progressive defects concern mushroom bodies in flies, not the human cerebellum. No page numbers were provided for these passages. (LLM, conf=0.81)
Experimental — accuracy not yet measuredVariants in genes encoding several subunits of the RNA exosome complex have been linked to PCH, including EXOSC3 (PCH1B), EXOSC8 (PCH1C), EXOSC9 (PCH1D), and provisionally EXOSC1 (PCH1F).
“variants in genes encoding several subunits of the RNA exosome complex have been linked to PCH, including EXOSC3 (PCH1B), EXOSC8 (PCH1C), EXOSC9 (PCH1D), and provisionally EXOSC1 (PCH1F)15–25.”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [15]
The Introduction states that mutations in RNA exosome structural-subunit genes cause distinct PCH subtypes, and the Results explicitly link EXOSC3 to PCH1b. The References list disease-associated EXOSC8 and EXOSC9 variants, but our copy does not specify their PCH1C or PCH1D labels, or mention the proposed EXOSC1–PCH1F link (pages unavailable). (LLM, conf=0.87)
Experimental — accuracy not yet measuredPathogenic variants in EXOSC3 cause pontocerebellar hypoplasia type 1B (PCH1B).
“Pathogenic variants in EXOSC3, a noncatalytic subunit of the RNA exosome, cause pontocerebellar hypoplasia type 1B (PCH1B)”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [15]
The RNA exosome plays central roles in ribosomal RNA processing (rRNA) and defects in rRNA processing have been identified in yeast and fly models expressing EXOSC3 variants.
“The RNA exosome also plays central roles in ribosomal RNA processing (rRNA) and defects in rRNA processing have been identified in yeast and fly models expressing EXOSC3 variants15,48.”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [15]
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- Authors
- Higginson, L. A., Wang, X., He, K., Torstrick, M., Kim, M., Wijeratne, H. R. S., Runnebohm, A. M., Benayoun, B. A., MacLean, A., Chanfreau, G. F., & Morton, D. J.
- Affiliations
- University of Southern California (US)
- University of California, Los Angeles (US)
- Indiana University Indianapolis (US)
- Corresponding author
- Morton, Derrick J.
- ORCID
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2026-01
- Volume
- 45
- Issue
- 1
- Pages
- 116729
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC12952294
- OpenAlex
- W4417534870
- Cited by
- 7
- References
- 144
- Citations by year
- 2026: 7
- FWCI
- 2.10
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- SSRN Electronic Journal (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed Central (submittedVersion, cc-by-nd)
- IUScholarWorks (Indiana University) (submittedVersion)
- Funders
- National Institute of Neurological Disorders and Stroke (NS121550, NS131620)
- University of Southern California (P30AG068345)
- Alfred P Sloan Foundation (FG-2023-20698)
- National Institutes of Health
- National Science Foundation
- Simons Foundation (SF811217)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- RNA exosome, RNA homeostasis, ribonuclease, neurodevelopmental disorders, neurodegeneration, rRNA processing, transcriptome dysregulation, post-transcriptional regulation, Drosophila model, brain cell types, behavioral impairment
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