Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA267075 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1649405.fastq.gz | Fastqsanger.gz | |||
| SRR1649406.fastq.gz | Fastqsanger.gz | |||
| SRR1649407.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:Alternative splicing is prevalent in plants, but little is known about its regulation in the context of developmental and signaling pathways. We describe here a new factor that influences pre-mRNA splicing and is essential for embryonic development in Arabidopsis thaliana. This factor was retrieved in a genetic screen that identified mutants impaired in expression of an alternatively spliced GFP reporter gene. In addition to the known spliceosomal component PRP8, the screen retrieved a previously uncharacterized protein containing a Replication termination factor2 (Rtf2) domain defined by a C2HC2 zinc finger. The Rtf2 protein was discovered in fission yeast, where it stabilizes paused DNA replication forks by an unknown mechanism. When homozygous, a null mutation in Arabidopsis RTF2 (AtRTF2) is embryo-lethal, indicating that it encodes an essential protein. As revealed by quantitative RT-PCR, impaired expression of GFP in atrtf2 and prp8 mutants is attributable to inefficient splicing of the GFP pre-mRNA. A genome-wide analysis using RNA-seq demonstrated that 12% of total introns display a significant degree of retention in atrtf2 mutants. Intron-retaining transcripts are enriched from genes encoding proteins involved in signaling pathways and membrane transport. Affinity purification of AtRTF2 followed by mass spectrometry identified several known and predicted splicing proteins. In a yeast two-hybrid screen, AtRTF2 interacted with Exo70B1, a peripheral subunit of the exocyst, which is involved in vesicle trafficking. Considering these results and previous suggestions that Rtf2 constitutes an ubiquitin-related domain, we discuss possible roles of AtRTF2 in ubiquitin-based regulation of pre-mRNA splicing and membrane signaling to the spliceosome. Rtf2 is SDR1 (= AtRTF2) and was discovered in a genetic suppressor screen using the dms4 mutant. DMS4 was described in Kanno et al (2010) EMBO Rep. 11:65-71. Examination of whole-genome DNA methylation status in transgenic Arabidopsis plants
2014-11-14 | E-GEOD-63238 | biostudies-arrayexpress
Project description:Alternative splicing is prevalent in plants, but little is known about its regulation in the context of developmental and signaling pathways. We describe here a new factor that influences pre-mRNA splicing and is essential for embryonic development in Arabidopsis thaliana. This factor was retrieved in a genetic screen that identified mutants impaired in expression of an alternatively spliced GFP reporter gene. In addition to the known spliceosomal component PRP8, the screen retrieved a previously uncharacterized protein containing a Replication termination factor2 (Rtf2) domain defined by a C2HC2 zinc finger. The Rtf2 protein was discovered in fission yeast, where it stabilizes paused DNA replication forks by an unknown mechanism. When homozygous, a null mutation in Arabidopsis RTF2 (AtRTF2) is embryo-lethal, indicating that it encodes an essential protein. As revealed by quantitative RT-PCR, impaired expression of GFP in atrtf2 and prp8 mutants is attributable to inefficient splicing of the GFP pre-mRNA. A genome-wide analysis using RNA-seq demonstrated that 12% of total introns display a significant degree of retention in atrtf2 mutants. Intron-retaining transcripts are enriched from genes encoding proteins involved in signaling pathways and membrane transport. Affinity purification of AtRTF2 followed by mass spectrometry identified several known and predicted splicing proteins. In a yeast two-hybrid screen, AtRTF2 interacted with Exo70B1, a peripheral subunit of the exocyst, which is involved in vesicle trafficking. Considering these results and previous suggestions that Rtf2 constitutes an ubiquitin-related domain, we discuss possible roles of AtRTF2 in ubiquitin-based regulation of pre-mRNA splicing and membrane signaling to the spliceosome. Rtf2 is SDR1 (= AtRTF2) and was discovered in a genetic suppressor screen using the dms4 mutant. DMS4 was described in Kanno et al (2010) EMBO Rep. 11:65-71.
2014-11-14 | GSE63238 | GEO
Project description:This study investigated the role Rtf2 plays on the replication fork barrier (RFB) activity of RTS1 in S. pombe. We confirm Rtf2 is important for the full barrier activity of the RTS1-Rtf1 RFB. We show that Rtf2 does not enact its enhancing effect on RTS1 RFB activity via binding to Region A of RTS1, but instead we find it to be closely associated with several splicing factors. Analysis of cells deleted for rtf2 by cDNA-Seq reveal splicing defects specifically effecting intron retention, including for the Rtf1 transcript. We show that intron retention within rtf1 is responsible for the reduced barrier activity of RTS1 when rtf2 is deleted. This study reveals Rtf2 to be an important factor for maintaining efficient splicing within the cell.
2021-12-24 | GSE192343 | GEO
Project description:This study investigated the role Rtf2 plays on the replication fork barrier (RFB) activity of RTS1 in S. pombe. We confirm Rtf2 is important for the full barrier activity of the RTS1-Rtf1 RFB. We show that Rtf2 does not enact its enhancing effect on RTS1 RFB activity via binding to Region A of RTS1, but instead we find it to be closely associated with several splicing factors. Analysis of cells deleted for rtf2 by cDNA-Seq reveal splicing defects specifically effecting intron retention, including for the Rtf1 transcript. We show that intron retention within rtf1 is responsible for the reduced barrier activity of RTS1 when rtf2 is deleted. This study reveals Rtf2 to be an important factor for maintaining efficient splicing within the cell.
2021-12-24 | GSE192342 | GEO
Project description:Thousands of genes are activated at later 2-cell embryos, which means that numerous pre-mRNAs are generated during this time. These pre-mRNAs must be accurately spliced to ensure that the mature mRNAs are translated to functional proteins. However, little is known about the roles of pre-mRNA splicing and cellular factors modulating pre-mRNA splicing during early embryonic development. Here, we report that downregulation of SON, a large Ser/Arg (SR)-related protein, reduced embryonic development and caused deficient blastomere cleavage. These embryonic developmental defects resulted from dysregulated nuclear speckle organization and pre-mRNA splicing of a set of cell-cycle-related genes. Furthermore, SON downregulation disturbed the transcriptome (2128 upregulation and 1399 downregulation) in 4-cell embryos. Increased H3K4me3, H3K9me3 and H3K27me3 levels were found in 4-cell embryos after SON downregulation. Taken together, those results demonstrate that accurate pre-mRNA splicing is essential for early embryonic development, and SON plays important roles on nuclear speckle organization, pre-mRNA splicing, the transcriptome establishment and histone methylation reprogramming during early embryonic development.
2025-07-31 | GSE273029 | GEO
Project description:Pre-mRNA splicing is an essential step in gene expression regulation. It is mediated by the spliceosome, a large ribonucleoprotein complex that undergoes dynamic structural and compositional rearrangements during each splicing cycle. Although the mechanisms of splicing and the roles of main spliceosomal components are well defined, the identities and functions of transiently associated spliceosomal proteins remain incompletely understood. Here, we investigated the molecular function of the poorly characterized G-patch domain–containing protein SPAC6F6.19 (herein Sap34, for spliceosome-associated protein of 34 kDa) in Schizosaccharomyces pombe, an ortholog of human GPATCH11. Using affinity purification and a yeast two-hybrid assay, we analyzed its interactome and identified its interaction partners. In addition, long-read sequencing was employed to assess Sap34-dependent changes in splicing efficiency. We found that Sap34 forms a complex with components of the U2 small nuclear ribonucleoprotein (snRNP) and the U4/U6 × U5 tri-snRNP, which are required for early spliceosome assembly and activation. Furthermore, we defined the interaction specificity of Sap34 with other splicing proteins, demonstrating the importance of its C-terminal region for binding to Sap61 and Ini1, and of its G-patch domain for interaction with the ATP-dependent RNA helicase Prp43. Notably, we showed that deletion of sap34 leads to a global reduction in splicing efficiency, predominantly associated with increased intron retention. Together, these findings identify Sap34 as a previously unrecognized and important G-patch domain–containing protein regulating the early steps of pre-mRNA splicing in fission yeast.
2026-04-21 | PXD077306 | Pride
Project description:Cwc23, an essential J-protein critical for pre-mRNA splicing with a dispensable J-domain
| PRJNA120229 | ENA
Project description:J-proteins are structurally diverse, obligatory co-chaperones of Hsp70s, each with a highly conserved J-domain that plays a critical role in stimulation of Hsp70âs ATPase activity. The essential protein, Cwc23, is one of 13 J-proteins found in the cytosol and/or nucleus of Saccharomyces cerevisiae. We report that a partial loss-of-function CWC23 mutant has severe, global defects in pre-mRNA splicing. This mutation leads to accumulation of the excised, lariat form of the intron, as well as unspliced pre-mRNA, suggesting a role for Cwc23 in spliceosome disassembly. Such a role is further supported by the observation that this mutation results in reduced interaction between Cwc23 and Ntr1 (SPP382), a known component of the disassembly pathway. However, Cwc23 is a very atypical J-protein. Its J-domain, although functional, is dispensable for both cell viability and pre-mRNA splicing. Nevertheless, strong genetic interactions were uncovered between point mutations encoding alterations in Cwc23âs J-domain and either Ntr1 or Prp43, a DExD/H-box helicase essential for spliceosome disassembly. These genetic interactions suggest that Hsp70-based chaperone machinery does play a role in the disassembly process. Cwc23 provides a unique example of a J-protein; its partnership with Hsp70 plays an auxiliary, rather than a central, role in its essential cellular function. Splicing-sensitive microarrays were used to probe the defects seen when the C-terminal or N-terminal regions of Cwc23 were disrupted.
2010-06-21 | E-GEOD-18485 | biostudies-arrayexpress
Project description:Influenza A viruses (IAVs) mRNA splicing represents an essential step in the viral life cycle. Here, we show that induction of SRSF5 by IAVs promotes viral replication by enhancing M mRNA splicing. To determine the motif in the M pre-mRNA targeted by SRSF5 RRM2 domain, the RNA eluted from co-precipitation of SRSF5–Flag from IAV-infected srsf5−/− HEK293 cells was subjected to deep sequencing analysis.
2021-12-10 | GSE190492 | GEO
Project description:In this study, we identified many new potential interactors of the Aurora-A kinase using a proteomic approach. A significant portion of Aurora-A interaction network is composed of proteins involved in pre-mRNA splicing, implying that Aurora-A signaling extends beyond its canonical function. Aurora-A directly interacts with many of the RRM domain-containing splicing factors such as SR proteins and hnRNP proteins and phosphorylates them in vitro. Aurora-A shows a subcellar distribution to nuclear speckles, the storehouse of splicing factors, consistent with its potential function in pre-mRNA splicing. Moreover, RNA-seq analysis of pharmacologically inhibited Aurora-A cells identified 261 genes whose RNA splicing is dependent on Aurora-A activity. These splicing affected genes are involved in various biological processes such as transcription, GTPase activity, ciliogenesis, DNA repair, RNA splicing and G2/M transition. Here, for the first time, we uncovered a relationship between Aurora-A activity and mRNA processing through a complex network of factors involved in RNA maturation.
2024-12-11 | PXD021093 | Pride