Functional characterization of PRP43a, a component for splicing disassembly in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA1159696 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30630862_1.fastq.gz | Fastqsanger.gz | |||
| SRR30630862_2.fastq.gz | Fastqsanger.gz | |||
| SRR30630863_1.fastq.gz | Fastqsanger.gz | |||
| SRR30630863_2.fastq.gz | Fastqsanger.gz | |||
| SRR30630864_1.fastq.gz | Fastqsanger.gz |
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Project description:Pre-mRNA splicing is a crucial regulatory process in eukaryotes, ensuring accurate mRNA maturation and contributing to transcript diversity through alternative splicing (AS). This process is mediated by the spliceosome, a large molecular complex composed of small nuclear RNAs (snRNAs) and proteins. Structural and comparative analysis have showed that splicing factors are highly conserved across eukaryotes, though the extent of their functional conservation remains to be fully elucidated. In Arabidopsis, two homologous genes, PRP43a and PRP43b, encode components involved in spliceosome disassembly. To investigate the roles of these genes, we characterized T-DNA insertion mutants prp43a-1 and prp43b-1. While prp43b-1 homozygous mutants were embryonic lethal, prp43a-1 mutants displayed no significant developmental defects under normal conditions, nor did they exhibit impaired heat tolerance. However, RNA-seq analysis revealed transcriptional changes in prp43a-1 under normal conditions. Gene ontology (GO) analysis indicated and enrichment of stress-related processes among the differentially expressed genes (DEGs), suggesting a role for PRP43a in stress responses. Additionally, differential alternative splicing (DAS) analysis identified numerous PRP43a-dependent intron retention (IR) events, particularly under heat stress, indicating that PRP43a influences AS under environmental conditions. These findings suggest PRP43a as a modulator of splicing and gene expression, with potential roles in stress responses.
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Project description:Functional characterization of splicing regulatory elements
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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:RNA binding protein-RNA interactions mediate a variety of processes including pre-mRNA splicing, translation, decay, polyadenylation and many others. Previous high -throughput studies have characterized general sequence features associated with increased and decreased splicing of certain exons, but these studies are limited by not knowing the mechanisms underlying these associations. Here we utilize ENCODE data from diverse data modalities to identify functional splicing regulatory elements and their associated RNA binding proteins (RBPs). We identify features which make splicing events more sensitive to depletion of RBPs, as well as which RBPs act as splicing regulators sensitive tupon RBP depletion. To analyze the sequence determinants underlying RBP-RNA interactions impacting splicing, we assay tens of thousands of sequence variants in a high-throughput splicing reporter called Vex-seq and confirm a small subset in their endogenous loci using CRISPR base editors. Finally, we leverage other large transcriptomic datasets to confirm the importance of RBPs which we designed experiments around and identify additional RBPs which may act as additional splicing regulators of the exons studied.
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Project description:Conserved role for spliceosomal component PRPF40A in microexon splicing
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Project description:ra07-05_myb82 - functional characterization of vvmyb82 - Functional characterization of the transcription factor VvMYB82 which is a regulator of the different phenolic compound biosynthesis. - To compare wt with a surexpressor of VvMYB82 (Line A311 = 35s::VvMYB) and wt with a loss of function mutant AtMYB82 2 dye-swap - wt vs mutant comparison
2011-07-06 | E-GEOD-30381 | biostudies-arrayexpress
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 Hsp70’s 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 Cwc23’s 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.
2009-10-14 | GSE18485 | GEO
Project description:ra07-05_myb82 - functional characterization of vvmyb82 - Functional characterization of the transcription factor VvMYB82 which is a regulator of the different phenolic compound biosynthesis. - To compare wt with a surexpressor of VvMYB82 (Line A311 = 35s::VvMYB) and wt with a loss of function mutant AtMYB82
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Project description:Microexons (exons ≤30 nts) are important features of neuronal transcriptomes, but pose mechanistic challenges to the splicing machinery. We previously showed that PRP-40, a component of the U1 spliceosome, is globally required for microexon splicing in C. elegans. Here we show that the homologous PRPF40A is also globally required for microexon splicing in mouse neuroblastoma cells. We find that PRPF40A co-regulates microexons along with SRRM4, a neuron-specific regulator of microexon splicing. The relationship between exon size and dependence on PRPF40A/SRRM4 is distinct, with SRRM4-dependence exhibiting a size threshold (~30 nts) and PRPF40A-dependence exhibiting a graded decrease as exon size increases. Finally, we show that PRPF40A knockdown causes an increase in productive splicing of its spliceosomal binding partner Luc7l by skipping of a small “poison exon.” Similar homeostatic cross-regulation is often observed across paralogous RNA binding proteins. Here we find this concept likewise applies across evolutionarily unrelated but functionally and physically coupled spliceosomal components.
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