Splicing and Junction Mapping

It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years ...

RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to splicing events. Commercial arrays that include probes within exon ...

Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first ...

RNA-seq is a powerful and popular technology for studying posttranscriptional regulation of gene expression, such as alternative splicing. The first step in analyzing RNA-seq data is to map the sequenced reads back to the genome. However, commonly used RNA-seq aligners ...

Fusion gene derived from genomic rearrangement plays a key role in cancer initiation. The discovery of novel gene fusions may be of significant importance in cancer diagnosis and treatment. Meanwhile, next generation sequencing technology provide a sensitive and efficient way ...

Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, ...

Transcripts are frequently modified by structural variations, which leads to either a fused transcript of two genes (known as a fusion gene) or an insertion of intergenic sequence into a transcript. These modifications, called transcriptomic structural variants (TSV), can lead ...

Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity in transcription, but the limitations of the technology have prevented its application to dissect variability in RNA processing events such as splicing. Here, University of Edinburgh researchers present BRIE (Bayesian regression ...

The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The ‘fusion’ or ‘chimeric’ transcripts have improved the diagnosis and prognosis of several tumors, ...

High-throughput sequencing has transformed the study of gene expression levels through RNA-seq, a technique that is now routinely used by various fields, such as genetic research or diagnostics. The advent of third generation sequencing technologies providing significantly longer reads opens ...