Chromosomal instability by mutations in the novel minor spliceosome component CENATAC

Abstract

Aneuploidy is the leading cause of miscarriage and congenital birth defects, and a hallmark of cancer. Despite this strong association with human disease, the genetic causes of aneuploidy remain largely unknown. Through exome sequencing of patients with constitutional mosaic aneuploidy, we identified biallelic truncating mutations in CENATAC (CCDC84). We show that CENATAC is a novel component of the minor (U12-dependent) spliceosome that promotes splicing of a specific, rare minor intron subtype. This subtype is characterized by AT-AN splice sites and relatively high basal levels of intron retention. CENATAC depletion or expression of disease mutants resulted in excessive retention of AT-AN minor introns in~100 genes enriched for nucleocytoplasmic transport and cell cycle regulators, and caused chromosome segregation errors. Our findings reveal selectivity in minor intron splicing and suggest a link between minor spliceosome defects and constitutional aneuploidy in humans.

At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression

“…In such cases, the outcome is typically increased minor intron retention combined with the activation of nearby cryptic U2-type splice sites. In more rare cases, splicing of the U12-type intron in question appears to be unperturbed and the splicing defect is observed only due to activation of U2-type cryptic splice sites such as those described for the SNRNPE , RCD8/EDC4 and SLC9A8 genes ( Figure 4 ; Turunen et al, 2008 ; de Wolf et al, 2021 ; Norppa and Frilander, 2021 ).…”

“…A typical outcome in these diseases is intron retention resulting from splicing defects. However, several studies have also demonstrated that the splicing defects are not limited to U12-type introns but can also spread to the flanking U2-type introns ( Argente et al, 2014 ; Madan et al, 2015 ; Cologne et al, 2019 ; de Wolf et al, 2021 ; Olthof et al, 2021 ) in a subset of mRNAs. The most plausible explanation for these observations is that splicing of the affected U2-type introns is dependent on stabilizing exon-definition interactions with the neighboring U12-type introns ( Figure 1B ).…”

“…One such case has been described in the transcriptomic analysis of patients suffering from Microcephalic Osteodysplastic Primordial Dwarfism type I/Taybi-Linder Syndrome (MOPD 1/TALS) by Cologne et al (2019) . The study described an alternative splicing switch in patient cells from U12- to U2-type 5′ss usage within intron 5 of the CCDC84 gene (later renamed CENATAC ; de Wolf et al, 2021 ), while the 3′ss was shared between the two intron types ( Figure 3 ). Splicing by the major spliceosome is expected to increase levels of the CENATAC protein since use of the minor pathway leads to incorporation of a PTC, and possibly a decay of the target mRNA by the NMD pathway.…”

“…Splicing by the major spliceosome is expected to increase levels of the CENATAC protein since use of the minor pathway leads to incorporation of a PTC, and possibly a decay of the target mRNA by the NMD pathway. Interestingly, the CENATAC protein has recently been identified as a novel component of the minor spliceosome and particularly necessary for splicing of the AT-AN subtype of U12-type introns ( de Wolf et al, 2021 ). Both the U12-type and U2-type 5′ss sequences are phylogenetically highly conserved, suggesting that the competing 5′ss elements are part of an autoregulatory feedback mechanism regulating the cellular levels of the CENATAC protein.…”

“…The consequences of competitive intron recognition by either minor and major spliceosome on cryptic splicing have thus far been studied in cases where the splicing of U12-type introns has been compromised ( Turunen et al, 2008 ; Cologne et al, 2019 ; de Wolf et al, 2021 ; Norppa and Frilander, 2021 ; Olthof et al, 2021 ). In such cases, the outcome is typically increased minor intron retention combined with the activation of nearby cryptic U2-type splice sites.…”