Abstract
SummaryIn the human genome, most genes undergo splicing, and patterns of codon usage are splicing dependent: guanine and cytosine (GC) content is the highest within single-exon genes and within first exons of multi-exon genes. However, the effects of codon usage on gene expression are typically characterized in unspliced model genes. Here, we measured the effects of splicing on expression in a panel of synonymous reporter genes that varied in nucleotide composition. We found that high GC content increased protein yield, mRNA yield, cytoplasmic mRNA localization, and translation of unspliced reporters. Splicing did not affect the expression of GC-rich variants. However, splicing promoted the expression of AT-rich variants by increasing their steady-state protein and mRNA levels, in part through promoting cytoplasmic localization of mRNA. We propose that splicing promotes the nuclear export of AU-rich mRNAs and that codon- and splicing-dependent effects on expression are under evolutionary pressure in the human genome.
Highlights
Mammalian genomes are characterized by a large regional variation in base composition (Bernardi, 1993)
We first parent retrocopy analyzed a set of 49 parent-retrogene pairs n= 49 for which both the parent and the retrocopy open reading frames (ORFs) have been retained in human and mouse
We found that the retrocopies had a significantly higher GC4 content than their parents (Figure 1D)
Summary
Mammalian genomes are characterized by a large regional variation in base composition (Bernardi, 1993). This can potentially influence gene expression in multiple ways: nucleotide composition affects the physical properties of DNA, the thermodynamic stability of RNA folding, the propensity of RNA to interact with other RNAs and proteins, the codon adaptation of mRNA to tRNA pools, and the propensity for RNA modifications, such as m6A (Dominissini et al, 2012) and ac4C (Arango et al, 2018). Heterologous expression experiments typically report large positive effects of increased GC content on protein production in a wide variety of transgenes, including fluorescent reporter genes, human cDNAs, and virus genes (Bauer et al, 2010; Kosovac et al, 2011; Kotsopoulou et al, 2000; Kudla et al, 2006; Zolotukhin et al, 1996). Genomewide analyses of endogenous genes typically show little or no correlation of GC content with expression (Duan et al, 2013; Lercher et al, 2003; Rudolph et al, 2016; Semon et al, 2005)
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