The RNA Exosome and Genetic Disease

Abstract

The RNA exosome is an evolutionarily conserved, riboexonuclease complex that processes/degrades numerous classes of non-coding RNA. The 10-subunit core exosome forms an ring-like structure composed of an upper ring of three S1/KH cap subunits (yeast Rrp4/40/Csl4-human EXOSC2/3/1), a lower ring of six PH-like subunits (yeast Rrp41/42/43/45/46/Mtr3-human EXOSC4/7/8/9/5/6), and a 3′-5’ riboexonuclease subunit, Rrp44/DIS3, at the base. The nuclear exosome contains an eleventh, cap-associated riboexonuclease subunit, Rrp6/EXOSC10. RNAs are targeted directly to Rrp6 or threaded through the central channel of the exosome to Rrp44 for processing/degradation. Recently, mutations in four exosome subunit genes, EXOSC1/CSL4, EXOSC2/RRP4, EXOSC3/RRP40, EXOSC8/RRP43, and EXOSC9/RRP45 have been linked human diseases. Mutations in EXOSC2 cause a novel syndrome characterized by retinitis pigmentosa, hearing loss, and mild intellectual disability. In contrast, mutations in EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b and 1c, respectively - autosomal recessive diseases characterized by cerebellar hypoplasia and neuronal degeneration with early mortality - and mutations in EXOSC9 cause cerebellar atrophy. We also recently collaborated to identify novel mutations in the EXOSC5 gene. To gain insight into the functional consequences of the mutations in these genes encoding structural subunits of the RNA exosome that have been identified in patients, we generated the corresponding mutations in the S. cerevisiae genes and examined their function in budding yeast. We find that rrp variants cause differential effects on cell growth and RNA exosome function, which could shed light on why impairments in different exosome subunits cause distinct and tissue specific phenotypes. We have complemented these functional studies with RNA-Seq analysis to identify specific RNA targets that are differentially affected by the changes in RNA exosome subunits that model human disease as well as a high copy suppressor screen. To extend our functional studies of EXOSC2 and EXOSC3 mutations to mammalian cells, we have performed a proteomic analysis of variant and wildtype EXOSC2 and EXOSC3 proteins expressed in neuronal cells. These data support a model where differential interactions with RNA exosome cofactors could underlie disease-specific phenotypes.