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Integrated detection and quantification of aberrant transcripts with novel splicing events

ABSTRACT: Integrated detection and quantification of aberrant transcripts with novel splicing events

PROVIDER: PRJNA1217796 | ENA |

REPOSITORIES: ENA

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Integrated detection and quantification of aberrant transcripts with novel splicing events

Project description:Splicing misregulation, such as the inclusion of previously unknown cryptic exons, is implicated in numerous diseases. Recent methods have increased accurate and efficient detection of such splicing alterations occurring in disease phenotypes. However, the quantification and differential analyses of non-canonical splicing alterations remains focused at a splice event level, thus preventing a complete view of the effects on the downstream transcriptomic landscape. Here, we present a novel and integrated pipeline, SpliCeAT, that (1) detects and quantifies differential non-canonical splicing events from short-read bulk RNA-seq data, (2) augments the canonical transcriptome with novel transcripts containing these non-canonical splicing events, and (3) performs transcript-level differential analysis to identify and quantify aberrant cryptic exon-containing transcripts based on this augmented transcriptome. Using TDP-43, an ALS/FTD-associated RNA-binding protein as an example, we identified and catalogued aberrant splicing events in embryonic mouse brains. The accuracy of our integrated pipeline was further confirmed and validated with long-read isoform sequencing. Furthermore, by comparing neuronal TDP-43 knockouts in mice with a publicly available human dataset with TDP-43 pathology, we identified and validated 4 common genes, namely, Kalrn/KALRN, Poldip3/POLDIP3, Rnf144a/RNF144A, and Unc13a/UNC13A, with cryptic exons. In summary, our integrated pipeline, novel splice events are identified, incorporated and quantified at the transcript level, thereby enabling more complete transcriptome profiling of well-annotated genomes in in the case of pathological splicing misregulation.

2025-02-02 | GSE288457 | GEO

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New Approach for Detection of Normal Alternative Splicing Events and Aberrant Spliceogenic Transcripts with Long-Range PCR and Deep RNA Sequencing.

Project description:RNA sequencing is a promising technique for detecting normal and aberrant RNA isoforms. Here, we present a new single-gene, straightforward 1-day hands-on protocol for detection of splicing alterations with deep RNA sequencing from blood. We have validated our method's accuracy by detecting previously published normal splicing isoforms of STK11 gene. Additionally, the same technique was used to provide the first comprehensive catalogue of naturally occurring alternative splicing events of the NBN gene in blood. Furthermore, we demonstrate that our approach can be used for detection of splicing impairment caused by genetic variants. Therefore, we were able to reclassify three variants of uncertain significance: NBN:c.584G>A, STK11:c.863-5_863-3delCTC and STK11:c.615G>A. Due to the simplicity of our approach, it can be incorporated into any molecular diagnostics laboratory for determination of variant's impact on splicing.

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Ribosome profiling and mRNA seq demonstrate that insertion of common resistance cassettes in yeast drives aberrant transcription

Project description:Our study found that insertion of commonly used selection cassettes in yeast can drive aberrant transcription events and disrupt expression of neighboring genes. We performed ribosome profiling and mRNA-seq on yeast strains where ORFs had been replaced with common selection cassettes and observed aberrant transcripts. Aberrant transcripts positioned near adjacent genomic loci repressed protein synthesis of those genes by transcription interference (ablating normal length transcript production) coincident with translation of competitive uORFs on the long transcript which prevented translation of the main ORF seen by ribosome profiling.

2022-11-29 | GSE207189 | GEO

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