Drosophila U6atac snRNA mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE24148 | GEO | 2010/10/11
SECONDARY ACCESSION(S): PRJNA130027
REPOSITORIES: GEO
Similar Datasets
Project description:A Drosophila line (l(2)k01105) with a P-element insertion in U6atac snRNA, an essential component of the U12-type spliceosome, was used to investigate the impact of disrupted U12-dependent splicing during larval development. A custom-designed exon array was used to study the expression of genes containing U12-type introns and genes involved in downstream pathways affected by deficient U12-dependent splicing. Flies homozygous for the U6atac mutation (U6atac/U6atac) were compared to heterozygotes (U6atac/CyO-GFP) which have a normal phenotype. Samples from homozygous and heterozygous U6atac mutant larvae at 1st, 2nd and 3rd larval instar were labelled with three colours and hybridized three samples per array. Three independently harvested biological replicates were made, with dye swap, except only two replicates for 3rd stage heterozygous control. This study presents exon-level data. Supplementary files: Raw data (.gpr) files. Series variables and repeats information.
2010-10-11 | E-GEOD-24148 | biostudies-arrayexpress
Project description:We identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of the U11/U12-65K protein, a known unique component of the minor spliceosome that functions during the early steps of minor intron recognition as a component of the U11/U12 di-snRNP. We show that both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with the U11/U12-65K protein, which uses the N-terminal region to interact with U11 snRNP during the intron recognition step. Finally, we show that while RBM41 knockout cells are viable, they show alterations in the splicing of U12-type introns, particularly differential U12-type 3' splice site usage. Together, our results highlight the role 3’-terminal stem-loop of U12 snRNA as a dynamic binding platform for the paralogous U11/U12-65K and RBM41 proteins, which function at distinct stages of minor spliceosome assembly/disassembly cycle.
2024-02-04 | GSE246283 | GEO
Project description:Exogenous signals from drug-stressed cancer cells accelerate the proliferation of neighboring tumor cells and promote them to acquire a more aggressive phenotype. We have recently found an exciting phenomenon: drug-stressed cancer cells secrete various components of the spliceosome: proteins and a number of snRNAs. We have observed this phenomenon both in vitro (culture media from cancer cell lines [Pavluykov M. et al.//Cancer Cell, 2018]) and in vivo (ovarian cancer ascites after chemotherapy [Shender V. et al//Mol. Сell. Proteomics, 2014]). The aim of this study was to elucidate the role of secreted spliceosomal snRNAs in intercellular communication. We constructed synthetic U12 and U6atac snRNAs close to the natural structure, including some non-canonical nucleotides imitating post-transcriptional RNA modification. Proteomic analysis of SKOV3 cells transfected with U6atac or U12 snRNA analogs has shown that both exogenous snRNAs lead to an increase of abundance of proteins related to cell cycle regulation and M phase. It has been recently shown that a number of spliceosomal proteins affect regulation of the cell cycle, in particular the M phase (Maslon et al., 2014). Here we demonstrated that not only spliceosomal proteins but also spliceosomal snRNAs (U12 and U6atac) affect activation of mitotic cell cycle genes. This study reveals previously unknown signaling molecules in the microenvironment of ovarian cancer that have potential clinical significance.
2024-05-29 | PXD027950 | Pride
Project description:Somatic mutations in the spliceosome gene ZRSR2 (located on the X chromosome) are associated with myelodysplastic syndrome (MDS). ZRSR2 is involved in the recognition of 3' splice site during the early stages of spliceosome assembly; however, its precise role in RNA splicing has remained unclear. Here, we characterize ZRSR2 as an essential component of the minor spliceosome (U12-dependent) assembly. shRNA mediated knockdown of ZRSR2 leads to impaired splicing of the U12-type introns, and RNA-Sequencing of MDS bone marrow reveals that loss of ZRSR2 activity causes increased mis-splicing. These splicing defects involve retention of the U12-type introns while splicing of the U2-type introns remain mostly unaffected. ZRSR2 deficient cells also exhibit reduced proliferation potential and distinct alterations in myeloid and erythroid differentiation in vitro. These data identify a specific role for ZRSR2 in RNA splicing and highlight dysregulated splicing of U12-type introns as a characteristic feature of ZRSR2 mutations in MDS. RNA sequencing was performed on 16 bone marrow samples (MDS and normal) and six samples of control or ZRSR2 shRNA transduced TF-1 cells and data was analysed for aberrant splicing caused by ZRSR2 mutations/deficiency.
2015-01-15 | E-GEOD-63816 | biostudies-arrayexpress
Project description:Mpn1 proteins are evolutionarily conserved exonucleases that modify spliceosomal U6 small nuclear RNAs (snRNAs) post-transcriptionally. Mutations in the human MPN1 gene are associated to the genodermatosis Clericuzio-type poikiloderma with neutropenia (PN). Mpn1 deficiency leads to aberrant U6 3M-bM-^@M-^Y end processing and accelerated U6 decay through unknown molecular mechanisms. Here we show that in mpn1M-NM-^T fission yeast cells U6 is barely bound by the protective Lsm2-8 complex, undergoes extensive oligoadenylation and is degraded by the nuclear RNA exonuclease Rrp6 independently of the poly(A) polymerase Cid14/Trf4. Mpn1 processes U6 in a spliceosome-dependent manner, as mutant U6 molecules that fail to join the spliceosome are not substrates for Mpn1. Moreover, human U6atac, the U6-like snRNA of the minor spliceosome, is a novel substrate for hMpn1. We unveil mechanistic details of a new U6 degradation pathway and further corroborate the notion that inefficient canonical and minor pre-mRNA splicing promotes PN. the 3' termini of human U6, U6atac and vtRNA1-1 transcripts from PN patient derived cells and from PN patient cells, compensated with hMPN1 were sequenced.
2014-08-08 | E-GEOD-60196 | biostudies-arrayexpress
Project description:Exogenous signals from drug-stressed cancer cells accelerate the proliferation of neighboring tumor cells and promote to acquire a more aggressive phenotype. We have recently found an exciting phenomenon: drug-stressed cancer cells secrete various components of the spliceosome: proteins and a number of snRNAs. We have observed this phenomenon both in vitro (culture media from cancer cell lines [Pavluykov M. et al., 2018]) and in vivo (ovarian cancer ascites after chemotherapy [Shender V. et al., 2014]). The aim of this study was to elucidate the role of secreted spliceosomal snRNAs in intercellular communication. We constructed synthetic U12 and U6atac snRNAs close to the natural structure, including some non-canonical nucleotides imitating post-transcriptional RNA modifications. RNAseq analysis of SKOV3 cells transfected with U6atac or U12 snRNA analogs has shown that both exogenous snRNAs lead to an increase of abundance of proteins related to cell cycle regulation and M phase. It has been recently shown that a number of spliceosomal proteins affect regulation of the cell cycle, in particular the M phase [Maslon et al., 2014]. Here we demonstrated that not only spliceosomal proteins but also spliceosomal snRNAs (U12 and U6atac) affect cell cycle gene expression. This study revealed previously unknown signaling molecules in the microenvironment of ovarian cancer that have potential clinical significance.
2024-04-24 | GSE241912 | GEO
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
Project description:Somatic mutations in the spliceosome gene ZRSR2— located on the X chromosome — are associated with myelodysplastic syndrome (MDS). ZRSR2 is involved in the recognition of 3΄ splice site during the early stages of spliceosome assembly; however, its precise role in RNA splicing has remained unclear. Here, we characterize ZRSR2 as an essential component of the minor spliceosome (U12-dependent) assembly. shRNA mediated knockdown of ZRSR2 leads to impaired splicing of the U12-type introns, and RNA-Sequencing of MDS bone marrow reveals that loss of ZRSR2 activity causes increased mis-splicing. These splicing defects involve retention of the U12-type introns while splicing of the U2-type introns remain mostly unaffected. ZRSR2 deficient cells also exhibit reduced proliferation potential and distinct alterations in myeloid and erythroid differentiation in vitro. These data identify a specific role for ZRSR2 in RNA splicing and highlight dysregulated splicing of U12-type introns as a characteristic feature of ZRSR2 mutations in MDS.
2015-01-15 | GSE63816 | GEO
Project description:Mpn1 proteins are evolutionarily conserved exonucleases that modify spliceosomal U6 small nuclear RNAs (snRNAs) post-transcriptionally. Mutations in the human MPN1 gene are associated to the genodermatosis Clericuzio-type poikiloderma with neutropenia (PN). Mpn1 deficiency leads to aberrant U6 3M-bM-^@M-^Y end processing and accelerated U6 decay through unknown molecular mechanisms. Here we show that in mpn1M-NM-^T fission yeast cells U6 is barely bound by the protective Lsm2-8 complex, undergoes extensive oligoadenylation and is degraded by the nuclear RNA exonuclease Rrp6 independently of the poly(A) polymerase Cid14/Trf4. Mpn1 processes U6 in a spliceosome-dependent manner, as mutant U6 molecules that fail to join the spliceosome are not substrates for Mpn1. Moreover, human U6atac, the U6-like snRNA of the minor spliceosome, is a novel substrate for hMpn1. We unveil mechanistic details of a new U6 degradation pathway and further corroborate the notion that inefficient canonical and minor pre-mRNA splicing promotes PN. the 3' termini of U6 or tagged-U6 species from the indicated mutant cells were compared to wt yeast strain
2014-08-08 | E-GEOD-60195 | biostudies-arrayexpress
Project description:Mpn1 proteins are evolutionarily conserved exonucleases that modify spliceosomal U6 small nuclear RNAs (snRNAs) post-transcriptionally. Mutations in the human MPN1 gene are associated to the genodermatosis Clericuzio-type poikiloderma with neutropenia (PN). Mpn1 deficiency leads to aberrant U6 3M-bM-^@M-^Y end processing and accelerated U6 decay through unknown molecular mechanisms. Here we show that in mpn1M-NM-^T fission yeast cells U6 is barely bound by the protective Lsm2-8 complex, undergoes extensive oligoadenylation and is degraded by the nuclear RNA exonuclease Rrp6 independently of the poly(A) polymerase Cid14/Trf4. Mpn1 processes U6 in a spliceosome-dependent manner, as mutant U6 molecules that fail to join the spliceosome are not substrates for Mpn1. Moreover, human U6atac, the U6-like snRNA of the minor spliceosome, is a novel substrate for hMpn1. We unveil mechanistic details of a new U6 degradation pathway and further corroborate the notion that inefficient canonical and minor pre-mRNA splicing promotes PN. The 3' termini of total RNA containing 2'3' cyclic phosphate from Mpn1-proficient and deficient human and yeast cells was sequenced
2014-08-08 | E-GEOD-60197 | biostudies-arrayexpress