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Related Experiment Videos

CASH: a constructing comprehensive splice site method for detecting alternative splicing events.

Wenwu Wu1, Jie Zong2, Ning Wei3

  • 1The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, Hangzhou, China.

Briefings in Bioinformatics
|April 8, 2017
PubMed
Summary

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Comprehensive AS Hunting (CASH) improves alternative splicing (AS) detection by identifying novel AS sites and differentially expressed events. SRSF10 regulation shows evolutionary flexibility but an immutable splicing model across vertebrates.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Alternative splicing (AS) is crucial for cellular function, but current analysis methods are insufficient.
  • RNA-sequencing (RNA-seq) offers vast data for AS event discovery, yet efficient tools are needed.

Purpose of the Study:

  • To introduce Comprehensive AS Hunting (CASH), a novel computational tool for enhanced AS event detection.
  • To analyze the regulation and evolution of splicing factor SRSF10-mediated alternative splicing.

Main Methods:

  • Development and application of the CASH tool for comprehensive splice site and differential AS event identification.
  • Validation of CASH using diverse RNA-seq datasets (species-specific and simulated).
  • Investigation of SRSF10-regulated splicing patterns and their evolutionary trajectory.

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Main Results:

  • CASH demonstrates superior performance over existing AS predictors, identifying novel AS events.
  • SRSF10-regulated splicing events exhibit significant evolutionary conservation and flexibility across species (chickens, mice, humans).
  • A conserved SRSF10-regulated splicing model was identified, dictating exon inclusion or skipping based on binding site.

Conclusions:

  • CASH significantly enhances the detection and study of alternative splicing events and their regulation.
  • SRSF10-regulated splicing presents a unique combination of evolutionary adaptability in events and conserved mechanistic models across vertebrates.