Small nuclear RNAs (snRNAs) play a vital role in various cellular functions for all animals, including rRNA processing and pre-mRNA splicing. RNA polymerase II transcribes the majority of the spliceosomal snRNA genes, with the exception of U6 and U6atac which are synthesized by RNA polymerase III. Significant differences have been identified between the promoters of each class of snRNA genes, despite the same protein complex binding to the 5' flanking region prior to transcription. In the insect Drosophila melanogaster, the snRNA genes transcribed by RNA polymerase II have two distinct promoter proximal sequence elements, called PSEA and PSEB. Genes transcribed by RNA polymerase III likewise have a PSEA but a TATA box rather than a PSEB. Through utilization of web-based tools and development of novel python scripts, I have taken a bioinformatics approach to further investigate instances of conservation and divergence of snRNA gene promoters across seven insect species. Similar to observations from a previous but more limited research project, I found that the insect snRNA genes analyzed here had PSEAs that were more conserved in the 5' half and more divergent in the 3' half. Furthermore, I identified nucleotide positions within the PSEAs of most of the species where nucleotides were conserved in the Pol III genes that were different from those conserved in the Pol II genes. Most likely, these positions that are "conserved-to-be-different" play a critical role in determining the RNA polymerase specificity of insect snRNA genes as has been previously determined experimentally for the fruit fly D. melanogaster.
