Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

Abstract

RNA splicing is the central process of intron removal in eukaryotes known to regulate various cellular functions such as growth, development, and response to external signals. The canonical sequences indicating the splicing sites needed for intronic boundary recognition are well known. However, the roles and evolution of the local folding of intronic and exonic sequence features adjacent to splice sites has yet to be thoroughly studied. Here, focusing on four fungi (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Candida albicans), we performed for the first time a comprehensive high-resolution study aimed at characterizing the encoding of intronic splicing efficiency in pre-mRNA transcripts and its effect on intron evolution. Our analysis supports the conjecture that pre-mRNA local folding strength at intronic boundaries is under selective pressure, as it significantly affects splicing efficiency. Specifically, we show that in the immediate region of 12-30 nucleotides (nt) surrounding the intronic donor site there is a preference for weak pre-mRNA folding; similarly, in the region of 15-33 nt surrounding the acceptor and branch sites there is a preference for weak pre-mRNA folding. We also show that in most cases there is a preference for strong pre-mRNA folding further away from intronic splice sites. In addition, we demonstrate that these signals are not associated with gene-specific functions, and they correlate with splicing efficiency measurements (r = 0.77, P = 2.98 × 10 −21) and with expression levels of the corresponding genes (P = 1.24 × 10 −19 ). We suggest that pre-mRNA folding strength in the above-mentioned regions has a direct effect on splicing efficiency by improving the recognition of intronic boundaries. These new discoveries are contributory steps toward a broader understanding of splicing regulation and intronic/transcript evolution.

Codon bias confers stability to humanmRNAs

“…A study of transcriptome miRNA-binding sites has shown that effective miRNA-binding sites tend to dwell in G-poor and U-rich environments [76]. In addition, while our analyses are CDS-based, it has been shown that GC-content of both introns and exons is important in splicing via RNA structures [77][78][79]. Taken together, we propose that codon bias is able to exert its effects at multiple levels, consequently effecting gene and protein expression.…”

Synonymous codons influencing gene expression in organisms

“…Thus, it may be assumed that any synonymous change that promotes mRNA secondary structure around these regions would impact splicing and adversely affect the protein production. 36 Several review articles have described the influence of synonymous codons on gene expression. 34,[37][38][39][40] In this review, we give an account of the recent evidences from ribosome profiling, in vivo translation, and heterologous expression experiments on the influence of synonymous codons on gene expression.…”

On the Ribosomal Density that Maximizes Protein Translation Rate

“…Furthermore, it is important to mention that there are various additional constraints shaping the coding regions of endogenous genes. These include various regulatory signals related to various gene expression steps, co-translational folding, and the functionality of the protein [52], [58], [63], [29], [8], [47]. Thus, under these additional constraints we do not necessarily expect to see ribosome densities that maximize the translation rate.…”