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Using the E1A Minigene Tool to Study mRNA Splicing Changes
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Codon Usage and Splicing Jointly Influence mRNA Localization.

Christine Mordstein1, Rosina Savisaar2, Robert S Young3

  • 1MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.

Cell Systems
|April 11, 2020
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Summary
This summary is machine-generated.

Gene expression is influenced by both codon usage and splicing. High GC content boosts expression in unspliced genes, while splicing enhances expression of AT-rich variants by aiding mRNA export.

Keywords:
codon usageevolutionmRNA exportsaturation mutagenesissplicingsynthetic biology

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Area of Science:

  • Molecular Biology
  • Genomics
  • Gene Expression Regulation

Background:

  • Most human genes undergo splicing, a process impacting codon usage patterns.
  • Codon usage effects on gene expression are often studied using unspliced genes, potentially missing crucial regulatory mechanisms.
  • Guanine-cytosine (GC) content is notably higher in single-exon and first exons of multi-exon genes.

Purpose of the Study:

  • To investigate the interplay between codon usage (nucleotide composition) and splicing on gene expression.
  • To determine how splicing affects the expression of genes with varying GC content.
  • To elucidate the mechanisms by which splicing influences mRNA localization and protein yield.

Main Methods:

  • Creation of synonymous reporter genes with diverse nucleotide compositions (GC-rich vs. AT-rich).
  • Measurement of protein yield, mRNA yield, and mRNA localization in both spliced and unspliced reporter gene variants.
  • Comparative analysis of gene expression levels based on nucleotide content and splicing status.

Main Results:

  • High GC content enhanced protein yield, mRNA levels, translation, and cytoplasmic mRNA localization in unspliced reporters.
  • Splicing did not significantly alter the expression of GC-rich reporter gene variants.
  • Splicing promoted expression of AT-rich variants by increasing steady-state mRNA and protein levels, partly via enhanced cytoplasmic mRNA localization.

Conclusions:

  • Splicing plays a differential role in gene expression depending on nucleotide composition, favoring AT-rich variants.
  • Splicing may facilitate the nuclear export of AU-rich mRNAs, thereby increasing their cytoplasmic presence and translation.
  • Codon usage and splicing-dependent regulatory effects on gene expression are likely under evolutionary selection in the human genome.