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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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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Differential splicing analysis based on isoforms expression with NBSplice.

Gabriela Alejandra Merino1, Elmer Andrés Fernández2

  • 1Instituto de Investigación y Desarrollo en Bioingeniería y Bioinformática (IBB), Universidad Nacional de Entre Ríos, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta 11 Km 10.5, E3100XAD Oro Verde, Argentina; Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE), Universidad Católica de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Armada Argentina 3555, X5016DHK Córdoba, Argentina.

Journal of Biomedical Informatics
|January 24, 2020
PubMed
Summary
This summary is machine-generated.

NBSplice, a new R package, analyzes gene isoform expression to detect differential splicing (DS) in diseases. It accurately identifies isoform-specific changes, outperforming existing methods and aiding biomarker discovery in cancer.

Keywords:
Alternative splicingCancerGene isoformsRNA-seqTranscriptomics

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Translational Medicine

Background:

  • Alternative splicing alterations are linked to human diseases, making their study vital for translational medicine.
  • Current differential splicing (DS) analysis primarily uses exon-based RNA-seq approaches, overlooking specific gene isoforms.
  • Existing DS tools have not fully leveraged recent advancements in RNA-seq isoform quantification.

Purpose of the Study:

  • To introduce NBSplice, an R package designed for differential splicing analysis using gene isoform expression data.
  • To enable the inference of alternative splicing pattern changes by estimating differences in relative transcript expressions between conditions.
  • To improve the accuracy and sensitivity of DS detection compared to current methodologies.

Main Methods:

  • Developed the NBSplice R package for differential splicing analysis based on isoform expression data.
  • Evaluated NBSplice using a synthetic RNA-seq dataset with controlled differential splicing events.
  • Applied NBSplice to a real cancer dataset to identify novel differentially spliced genes.

Main Results:

  • NBSplice accurately predicted differential splicing occurrence in synthetic data.
  • The package demonstrated superior performance over existing methods in accuracy, sensitivity, F-score, and false discovery rate control.
  • Analysis of a colorectal cancer dataset revealed new differentially spliced genes with potential biomarker applications.

Conclusions:

  • NBSplice offers a robust approach for differential splicing analysis by focusing on isoform expression.
  • The tool enhances the understanding of pathological processes driven by alternative splicing changes.
  • NBSplice facilitates the discovery of novel disease biomarkers, particularly in cancer research.