A comprehensive map of intron branchpoints and lariat RNAs in plants
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ABSTRACT:
PROVIDER: PRJNA482052 | ENA |
REPOSITORIES: ENA
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Project description:Lariat is formed by excised intron, in which the 5' splice site joints with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by DBR1 (RNA debranching enzyme 1), recent findings in animals showed that many lariat RNAs were widely detected under physiological conditions. In contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing datasets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13872, 5199, 29582, and 13478 BPs in Arabidopsis, tomato, rice, and maize, respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ~20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10580 lariat RNAs accumulate in wild type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns, and the expression of these lariat RNAs significantly correlated with the incidence of back-splicing of parent exons. Collectively, our results provide the first comprehensive map of intron BPs and lariat RNAs in plants, and uncover a novel link between lariat turnover and splicing.
2019-04-17 | GSE117416 | 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:The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of the first viable DBR1 knockout cell line, we find the predominantly nuclear Dbr1 enzyme to encode the sole debranching activity in human cells. Dbr1 preferentially debranches substrates that contain canonical U2 binding motifs, suggesting that branchsites discovered through sequencing do not necessarily represent those favored by the spliceosome. We find that Dbr1 also exhibits specificity for particular 5' splice site sequences. We identify Dbr1 interactors through co-immunoprecipitation mass spectroscopy. We present a mechanistic model for Dbr1 recruitment to the branchpoint through the intron-binding protein AQR. In addition to a 20-fold increase in lariats, Dbr1 depletion increases exon skipping. Using ADAR fusions to timestamp lariats, we demonstrate a defect in spliceosome recycling. In the absence of Dbr1, spliceosomal components remain associated with the lariat for a longer period of time. As splicing is co-transcriptional, slower recycling increases the likelihood that downstream exons will be available for exon skipping.
2023-06-26 | MSV000092263 | MassIVE
Project description:We constructed a DBR1 knockout cell line (C22) using CRISPR in HEK293T cells. Through mapping of lariat reads, lariat levels in the DBR1 - samples are shown to increase dramatically (~20x) relative to wild type cells. Over 60% of this increase in lariat levels is abrogated upon rescue of DBR1 - cells with a DBR1 expression vector
2022-01-29 | GSE195469 | GEO
Project description:Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.
2022-11-26 | GSE204834 | GEO
Project description:Using wild type HEK293T cells and our DBR1 CRISPR knockout cell line (C22), we investigated the effect of AQR knockdown on cellular lariat levels. Samples were taken after transfection with either one of two AQR-targeting siRNAs or a non-targeting control siRNA. After sequencing the samples, lariat mapping of the reads revealed that AQR knockdown increased the lariat recovery rate by ~50% relative to the level observed in the negative control samples.
2022-01-31 | GSE195668 | GEO
Project description:The turnover of introns spliced from pre-mRNA occurs first by debranching the lariat intron followed by destruction of the linear intron by other nucleases. We have identified a novel component of intron turnover, DRN1 (YGR093W). In order to identify RNAs affected by Drn1 turnover, we used a microarray containing probes specific to ~400 yeast non-coding RNAs to analyze a strain deleted for Drn1. These data implicated Drn1 in the turnover of a number of introns spliced from ribosomal-protein genes. Two-color experiment with biological replicate and dye swap.
2010-05-16 | E-GEOD-15418 | biostudies-arrayexpress
Project description:The turnover of introns spliced from pre-mRNA occurs first by debranching the lariat intron followed by destruction of the linear intron by other nucleases. We have identified a novel component of intron turnover, DRN1 (YGR093W). In order to identify RNAs affected by Drn1 turnover, we used a microarray containing probes specific to ~400 yeast non-coding RNAs to analyze a strain deleted for Drn1. These data implicated Drn1 in the turnover of a number of introns spliced from ribosomal-protein genes.
2009-12-31 | GSE15418 | GEO
Project description:We performed lariat sequencing to profile the diversity of spliced RNA lariats in S. pombe identify annotated and alternate introns.
2015-09-03 | GSE68345 | GEO
Project description:Comprehensive single-cell map of mouse gonadal development at stages E10.5, E11.5 and E12.5
2022-05-03 | E-MTAB-11480 | biostudies-arrayexpress