RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis

Valosin-containing protein (VCP) is a hexameric ATPase associated with diverse cellular activities. Genetic mutations in VCP are associated with several forms of muscular and neuronal degeneration, including amyotrophic lateral sclerosis (ALS). Moreover, VCP mediates UV-induced proteolysis of RNA polymerase II (RNAPII), but little is known about the effects of VCP mutations on the transcriptional machinery. Here, we used silica particle-assisted chromatin enrichment and mass spectrometry to study proteins co-localized with RNAPII in precursor neurons differentiated from VCP-mutant or control induced pluripotent stem cells. Remarkably, we observed diminished RNAPII binding of proteins involved in transcription elongation and mRNA splicing in mutant cells. One of these is SART3, a recycling factor of the splicing machinery, whose knockdown leads to perturbed intron retention in several ALS-associated genes. Additional reduced proteins are RBM45, EIF5A and RNF220, mutations in which are associated with various neurodegenerative disorders and are linked to TDP-43 aggregation. Conversely, we observed increased RNAPII binding of heat shock proteins such as HSPB1. Together, these findings shed light on how transcription and splicing machinery are impaired by VCP mutations, which might contribute to aberrant alternative splicing and proteinopathy in neurodegeneration. Dysregulation of proteostasis and RNA metabolism are increasingly recognised as critical drivers of neurodegenerative disease. Rafiee et al. focus on RNA polymerase II as the converging point of these two processes, and examine how transcriptional machinery and alternative splicing are affected by ALS-associated VCP mutations.

Automated summary

Valosin-containing protein (VCP) is a hexameric ATPase associated with cellular activities and its mutations are linked to neurodegenerative diseases. The study reveals that VCP mutations impair the binding of transcriptional machinery and mRNA splicing proteins to RNA polymerase II (RNAPII), leading to aberrant alternative splicing and proteinopathy in neurodegeneration.