Impact of splice site RNA secondary structure stability on splicing

Splicing is a fundamental process for pre-mRNA process maturation in most eukaryotes, playing an essential role in both proteome diversification and gene expression regulation. Despite its relevance, little is known about how splicing events are effectively regulated, this knowledge gap is even more pronounced in plants. Some studies conducted on human data suggest the stability of secondary structures may be one of the regulatory mechanisms for this process, in which more stable structures are frequently associated with alternative splicing events. Given the lack of knowledge in plants, this work aims to investigate RNA secondary structures at the splice site and its relation to alternative and constitutive splicing for plant-based data.

Utilizing publicly available genomic data and splicing events in Humans, Arabidopsis thaliana, and Zea mays (corn), we extracted regions surrounding the splicing sites. These regions were then utilized to predict secondary structures and determine their respective Gibbs free energy values, which directly correlate to the stability of these structures. We subsequently categorized these structures based on their association with either alternative or constitutive splicing events, and plotted them for comparative analysis.

In contrast to the human data, the Arabidopsis data did not demonstrate noteworthy variations in stability between constitutive and alternative splicing. However, for corn, certain types of splicing displayed contrasting signals compared to those observed in humans in which alternative splicing events were associated with structures of lower stability, suggesting a potentially significant discrepancy between these groups of eukaryotes.