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TranscriptomicsIdentification of RNAs associated with the Caenorhabditis elegans spliced-leader trans-splicing proteins SNA-2, SNA-3, SNR-2 and SUT-1 proteins by RIP-Seq.
This study aimed to identify RNAs bound to the C. elegans SNA-2, SNA-3, SUT-1 and SNR-2 proteins involved in spliced leader 1 trans-splicing through use of RNA immunoprecipitation sequencing (RIP-Seq). Four IP sample replicates and four control sample replicates were sequenced for each protein.
ORGANISM(S): Caenorhabditis elegans 
2024-04-24 | E-MTAB-13193 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of C. elegans operons
Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons1. In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the...
ORGANISM(S): Caenorhabditis elegans 
2005-07-13 | E-SMDB-1388 | biostudies-arrayexpress
TranscriptomicsGlobal analysis of Caenorhabditis elegans operons
Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons. In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the ...
ORGANISM(S): Caenorhabditis elegans 
2005-07-22 | E-GEOD-2975 | biostudies-arrayexpress
TranscriptomicsHigh-resolution genome-wide transcriptomics analysis of O. dioica during recovery from growth arrest
Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in th...
ORGANISM(S): Oikopleura dioica 
2015-01-26 | E-GEOD-50848 | biostudies-arrayexpress
TranscriptomicsGenome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica
Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in th...
ORGANISM(S): Oikopleura dioica 
2015-01-26 | E-GEOD-50849 | biostudies-arrayexpress
ProteomicsPre-mRNA splicing function of the ubiquitin-like protein Hub1/UBL-5 in Caenorhabditis elegans
The conserved ubiquitin-like protein Hub1/UBL-5 associates with proteins non-covalently. In yeast and human cells, Hub1 promotes splicing of precursor mRNAs with weak introns and alternative splicing, however, its splicing function has remained elusive in multicellular organisms. We demonstrate the ...
ORGANISM(S): Caenorhabditis elegans 
2024-05-21 | PXD033914 | Pride
Trans-splicing and c. elegans Outron-containing transcripts Spliceosome Pre-mrna splicing 
ProteomicsMolecular characterisation of the SL1 snRNP and other factors involved in spliced leader trans-splicing in the nematode Caenorhabditis elegans using immunoprecipitation and LC-MS/MS.
Spliced leader trans-splicing is an essential RNA processing step that is required for the formation of mRNA in many eukaryotes, including C. elegans. However, the factors involved in this reaction are not well known. Here we perform a molecular analysis of key components in this reaction by immuno...
ORGANISM(S): Caenorhabditis elegans 
2022-06-24 | PXD024763 | Pride
Nematode Small nuclear ribonucleoproteins Rna processing 
TranscriptomicsUsing GRO-seq experiments to determine the mechanism of C. elegans dosage compensation's control of transcription
Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends...
ORGANISM(S): Caenorhabditis elegans 
2013-06-18 | E-GEOD-43084 | biostudies-arrayexpress
ProteomicsFunctional characterisation of nematode spliced leader 1 trans-splicing factors SUT-1, SNA-2, SNA-3 and SNR-2 by immunoprecipitation and LC-MS/MS.
Spliced leader trans-splicing is an essential RNA processing step that is required for the formation of mRNA in many eukaryotes, including C. elegans. However, the role of factors involved in this reaction is not well known. Here we further characterise the function of SNA-2, SNA-3, SUT-1 and SNR-2 ...
ORGANISM(S): Caenorhabditis elegans 
2024-04-23 | PXD040352 | Pride
Small nuclear ribonucleoproteins Rna processing Caenorhabditis elegans 
TranscriptomicsmRNA-seq of L1 larvae recovering from arrest
We used RNA-seq to sequence the transcriptome of worms arrested in the first larval stage after hatching without food and starved for 12 hours, then a timecourse of animals recovering from arrest after feeding. We collected samples after 12 hours of starvation and 1, 3 and 6 hours after feeding. Fou...
ORGANISM(S): Caenorhabditis elegans 
2012-04-25 | E-GEOD-33023 | biostudies-arrayexpress
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