Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels

Background: Introns are ubiquitous in pre-mRNA but are often overlooked. They also play an important role in the regulation of gene expression. Objective and Methods: We mainly use the improved Smith-Waterman local alignment approach to compare the optimal matching regions between introns and mRNA sequences in Caenorhabditis elegans (C. elegans) genes with high and low expression. Results: We found that the relative matching frequency distributions of all genes lie exactly between highly and lowly expressed genes, indicating that introns in highly and lowly expressed genes have different biological functions. Highly expressed genes have higher matching strengths on mRNA sequences than genes expressed at lower levels; the remarkably matched regions appear in UTR regions, particularly in the 3'UTR. The optimal matching frequency distributions have obvious differences in functional regions of the translation initiation and termination sites in highly and lowly expressed genes. The mRNA sequences with CpG islands tend to have stronger relative matching frequency distributions, especially in highly expressed genes. Additionally, the sequence characteristics of the optimal matched segments are consistent with those of the miRNAs, and they are considered a type of functional RNA segment. Conclusion: Introns in highly and lowly expressed genes contribute to the recognition translation initiation sites and translation termination sites. Moreover, our results suggest that the potential matching relationships between introns and mRNA sequences in highly and lowly expressed genes are significantly different and indicate that the matching strength correlates with the ability of introns to enhance gene expression.