Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB20389 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The analysis of roles of DROL1 and SUDL1 in defining intron-exon junctions
| PRJDB20390 | ENA
Project description:Alternative splicing (AS) is a key regulatory process in eukaryotes. Despite its importance, the impact of AS on proteome diversity in plants remains largely unexplored. Traditional tryptic digestion has limitations in detecting junction peptides because evolutionarily conserved nucleotide usage at exon boundaries increases the frequency of lysine- and arginine-coding triplets at exon ends, making detection of exon–exon and exon–intron junctions challenging. To address this gap, we performed a comprehensive analysis of the Arabidopsis proteome using the protease AspN combined with extensive offline fractionation. AspN is an endoprotease that cleaves at the N-terminal side of aspartic acid residues. To further enhance detection of alternatively spliced proteins, we analyzed both wild-type plants and the AS mutant acinus pinin. This approach enabled identification of isoform-specific peptides—both annotated and previously unannotated—using in-house algorithms and rigorous filtering steps. Our findings demonstrate that alternative splicing contributes substantially to proteome diversity in plants.
2026-06-08 | PXD068586 | Pride
Project description:Arabidopsis thaliana T-DNA genome junctions
| PRJNA393613 | ENA
Project description:We employ multi-step affinity purification followed by high-throughput sequencing to determine the location of EJC complexes assembled on a cellular transcriptome in Drosophila S2 cells, finding 6% of the intron-containing genes were not associated with EJCs, and within genes with multiple introns, only specific exon-exon junctions assembled an EJC. RIP-Seq, 3 samples
2014-11-04 | E-GEOD-33475 | biostudies-arrayexpress
Project description:We employ multi-step affinity purification followed by high-throughput sequencing to determine the location of EJC complexes assembled on a cellular transcriptome in Drosophila S2 cells, finding 6% of the intron-containing genes were not associated with EJCs, and within genes with multiple introns, only specific exon-exon junctions assembled an EJC.
2014-11-04 | GSE33475 | GEO
Project description:We performed lariat sequencing to profile the diversity of spliced RNA lariats in S. pombe identify annotated and alternate introns. Three different growth conditions were used to grow S. pombe wt and S. pombe Δdbr1. Lariat sequencing of the Δdbr1 strains and RNAseq of the wt and Δdbr1 strains were done to profile intron lariats and exon-exon junctions in RNA transcripts.
2015-09-03 | E-GEOD-68345 | biostudies-arrayexpress
Project description:Defining context-dependent m6A RNA methylomes in Arabidopsis
| PRJNA1028096 | ENA
Project description:The exon junction complex (EJC) is a highly conserved ribonucleoprotein complex which binds RNAs during splicing and remains associated with them following export to the cytoplasm. While the role of this complex in mRNA localization, translation and degradation has been well characterized, its mechanism of action in splicing a subset of Drosophila and human transcripts remains to be elucidated. Here, we describe a novel function for the EJC and its splicing subunit RnpS1 in preventing transposon accumulation in both Drosophila germline and surrounding somatic follicle cells. This function is mediated specifically through the control of piwi transcript splicing, where in the absence of RnpS1 the fourth intron of piwi is retained. Within this intron the polypyrimidine tract is disrupted by a transposon-adjacent A/T-rich sequence that confers dependence on RnpS1. Finally, we demonstrate that RnpS1-dependent removal of this intron requires splicing of the flanking introns, suggesting a model in which the EJC facilitates the splicing of weak introns following its initial deposition at adjacent exon junctions. These data demonstrate a novel role for the EJC in regulating piwi intron excision and provide a mechanism for its function during splicing.
2014-08-14 | GSE59327 | GEO