Defective minor spliceosomes induce SMA-associated phenotypes through sensitive intron-containing neural genes in Drosophila
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ABSTRACT:
PROVIDER: PRJNA575006 | ENA |
REPOSITORIES: ENA
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Project description:The minor spliceosome is evolutionarily conserved in higher eukaryotes, but its biological significance remains poorly understood. Here, by precise CRISPR/Cas9-mediated disruption of the U12 and U6atac snRNAs, we report that a defective minor spliceosome is responsible for spinal muscular atrophy (SMA) associated phenotypes in Drosophila. Using a newly developed bioinformatic approach, we identified a large set of minor spliceosome-sensitive splicing events and demonstrate that three sensitive intron-containing neural genes, Pcyt2, Zmynd10, and Fas3, directly contribute to disease development as evidenced by the ability of their cDNAs to rescue the SMA-associated phenotypes in muscle development, neuromuscular junctions, and locomotion. Interestingly, many splice sites in sensitive introns are recognizable by both minor and major spliceosomes, suggesting a new mechanism of splicing regulation through competition between minor and major spliceosomes. These findings reveal a vital contribution of the minor spliceosome to SMA and to regulated splicing in animals.
2020-04-01 | GSE138183 | GEO
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Project description:Most eukaryotes harbor two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which removes rare, evolutionarily conserved introns. Although hypothesized to serve important regulatory functions, physiologic roles for the minor spliceosome are not well understood. For example, the minor spliceosome component ZRSR2 is subject to recurrent, leukemia-associated mutations, yet functional connections between minor introns, hematopoiesis, and cancers are unclear. Here, we identify that impaired minor intron excision via ZRSR2 loss enhances hematopoietic stem cell self-renewal. CRISPR screens mimicking nonsense-mediated decay of minor intron-containing mRNAs converged on LZTR1, a regulator of Ras-related GTPases. LZTR1 minor intron retention was also discovered in the RASopathy Noonan syndrome, due to intronic mutations disrupting splicing, and diverse solid tumors. These data uncover minor intron recognition as a regulator of hematopoiesis, noncoding mutations within minor introns as cancer drivers, and links between ZRSR2 mutations, LZTR1 regulation, and leukemias.
2021-02-09 | GSE149455 | GEO
Project description:Most metazoans contain two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which recognizes <1% of introns. Despite their rarity, minor introns are exquisitely conserved amongst species, suggesting important regulatory functions. However, physiologic roles for the minor spliceosome and the relevance of recurrent, leukemia-associated mutations affecting minor spliceosome components are not well understood. Here, we identify that mutational loss of the minor spliceosomal factor ZRSR2 enhances hematopoietic stem cell self-renewal via impaired minor intron splicing that converges on LZTR1, a regulator of Ras-related GTPases. LZTR1 minor intron retention is additionally observed in Noonan syndrome and diverse cancers. These data uncover minor intron recognition as a regulator of hematopoiesis and mechanistic links between ZRSR2 mutations, LZTR1, and leukemia.
2020-11-26 | GSE162136 | GEO
Project description:Mutations in the minor spliceosome components such as RNU4atac, a small nuclear RNA (snRNA), are linked to primary microcephaly. We have reported that in the conditional knockout (cKO) mice for Rnu11, a minor spliceosome snRNA, minor intron splicing defect in minor intron-containing genes (MIGs) regulating cell cycle resulted in cell cycle defect with a concomitant increase in yH2aX+ cells and P53-mediated apoptosis. Trp53 ablation in the Rnu11 cKO mice did not prevent microcephaly. Although RNAseq analysis of the double knockout (dKO) pallium reflected transcriptomic shift towards the control from the cKO. We found elevated minor intron retention and alternative splicing across minor introns in the dKO. Disruption of these minor intron-containing genes (MIGs) resulted in cell cycle defect that was detected earlier and was more severe in the dKO, but with delayed detection of yH2aX+ DNA damage. Thus, P53 might also play a role in causing DNA damage in the developing pallium. In all, our findings further refine our understanding of the role of the minor spliceosome in cortical development and identify MIGs underpinning microcephaly in minor spliceosome-related disease.
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Project description:Minor intron-containing genes (MIGs) are crucial cell cycle regulators and are essential for cell survival. Thus, we explored whether MIGs play a role in cancer progression and cancer therapy resistance. Here we show that MIG-expression segregates sensitive and resistant prostate cancer cells from each other and them from benign tissue. Moreover, the rate of minor intron splicing, a crucial regulatory node for MIG-expression, was more efficient in patients with advanced prostate cancer. We show that the increased minor spliceosome (MiS) activity is downstream of the androgen receptor signaling axis in both therapy sensitive and insensitive prostate cancer types. The increased MiS activity was in line with the elevated expression of U6atac snRNA, a crucial MiS component. We propose the expression of U6atac as a potential point of vulnerability in cancer. MIGs are uniquely susceptible to the MiS, so we used siRNA against U6atac, which like protein-coding transcripts, is downregulated. Inhibition of MiS was sufficient to lower the tumor burden significantly in therapy-resistant (prostate) cancer cells and PCa patient-derived organoids. KD cells displayed elevated minor intron retention and alternative splicing across minor introns of MIGs which enriched for MAPK activity, DNA repair and cell cycle regulation. Importantly, these findings were confirmed by MassSpec analysis. Collectively our study nominates the MiS as a driver of highly proliferative, rapidly dividing (prostate) cancer cells that bears strong potential as a therapeutic target for many different cancer types.
2023-06-08 | PXD026949 | Pride
Project description:Spinal muscular atrophy (SMA) is a severe congenital motor neuron degenerative disease caused by loss-of-function mutations in the conserved survival motor neuron gene SMN1. SMN is required for the assembly of small nuclear ribonucleoprotein complexes, the core components of the spliceosome and also affects other molecular processes. It is hypothesized that defective gene expression and pre-mRNA splicing underlie SMA. However the immediate target genes of SMN are unclear. We used the nematode Caenorhabditis elegans as a model to study the function of SMN. We analyzed the transcriptome of a C. elegans smn-1 deletion mutant and identified that multiple biological processes were affected. Specifically the expression of numerous mitochondrial genes and vacuolar H+ -ATPase was significantly reduced while the expression of multiple histone genes was significantly increased. We also found that the U2AF large subunit mutation n4588 could ameliorate the defective expression of genes in the mitochondrial and V-ATPase pathways caused by the smn-1 mutation, which is consistent with our previous finding that uaf-1(n4588) could improve the behavior and lifespan of smn-1 mutants. Our study identified key molecular processes affected by SMN and suggests that mitochondrial and V-ATPase dysfunctions might contribute to SMA.
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Project description: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.
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