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Alternative RNA Splicing02:18

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Quantification of gene expression while taking into account RNA alternative splicing.

Meiping Zhang1, Yun-Hua Liu1, Chih-Sheng Chang1

  • 1Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, United States.

Genomics
|October 27, 2018
PubMed
Summary

Quantifying gene expression with RNA alternative splicing is challenging. Shot-gun RNA sequencing (RNA-seq) is the most accurate method for measuring transcript and gene expression, offering high reproducibility.

Keywords:
Gene expression quantificationMicroarrayQuantitative real-time PCRRNA alternative splicingRNA sequencing

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Gene expression analysis is crucial for functional genomics.
  • Inconsistent quantification across different methods challenges research conclusions.
  • RNA alternative splicing complicates accurate gene expression measurement.

Purpose of the Study:

  • To address inconsistencies in gene expression quantification.
  • To evaluate methods considering RNA alternative splicing.
  • To identify the optimal method for accurate transcript and gene expression measurement.

Main Methods:

  • Comparison of quantitative real-time PCR (qPCR), Northern hybridization, microarray, and serial analysis of gene expression.
  • Evaluation of shot-gun RNA sequencing (RNA-seq) for gene expression quantification.
  • Assessment of RNA-seq reproducibility across individuals.

Main Results:

  • Traditional methods (qPCR, Northern, microarray, SAGE) struggle with quantifying spliced transcripts.
  • Shot-gun RNA-seq accurately quantifies expression of individual transcripts and overall gene expression.
  • Shot-gun RNA-seq demonstrates high reproducibility (r = 0.90-0.98) between individuals.

Conclusions:

  • RNA alternative splicing necessitates advanced quantification techniques.
  • Shot-gun or full-length RNA-seq is the preferred method for precise gene expression analysis.
  • RNA-seq provides reliable and reproducible gene expression data, even with alternative splicing.