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RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

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MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data.

Christopher J Green¹, Matthew R Gazzara^1,2, Yoseph Barash^1,3

¹Department of Genetics, Perelman School of Medicine, Philadelphia, PA, USA.

Bioinformatics (Oxford, England)

|October 3, 2017

Summary

MAJIQ-SPEL is a new web tool that helps researchers visualize and quantify complex alternative splicing (AS) events from RNA sequencing data. It also suggests primers for experimental validation, aiding in the study of gene isoforms.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative splicing (AS) is a major source of gene and protein diversity.
Complex AS events generate numerous isoforms, posing challenges for visualization and validation.
RNA sequencing (RNA-Seq) data reveals widespread AS across genes.

Purpose of the Study:

To develop a user-friendly web tool for analyzing complex alternative splicing events.
To facilitate the visualization, quantification, and experimental validation of gene isoforms.
To address the limitations in interpreting and validating intricate splicing patterns.

Main Methods:

Development of the MAJIQ-SPEL web tool.
Input of local splicing variations (LSVs) quantified from RNA-Seq data.
Integration of a primer design algorithm for experimental validation.
Visualization of LSVs and affected protein domains on the UCSC Genome Browser.

Main Results:

MAJIQ-SPEL effectively visualizes and quantifies gene isoforms from RNA-Seq data.
The tool handles both binary and complex, non-binary splicing variations.
Primer design suggestions and visualization on the UCSC Genome Browser are provided for experimental validation.

Conclusions:

MAJIQ-SPEL simplifies the analysis of complex alternative splicing events.
The tool aids in the interpretation and experimental validation of gene isoforms.
MAJIQ-SPEL enhances downstream analysis of splicing variations and their functional impact.