U6atac Treatment Differentially Impacts Splicing of Minor Intron Genes

Premature mRNA in eukaryotes contains many non-coding sections of RNA called ‘introns’ that must be removed to form the final mRNA that will undergo translation. The removal or ‘splicing’ of introns is done by specific cellular machinery- the spliceosome which consists of cooperation between small nuclear RNAs (snRNAs) and proteins, forming snRNPs together. The introns most abundant in the human genome are labeled major introns while a small family of introns are called minor introns. Genes with these introns are involved in critical cellular functions of DNA repair, replication, cell cycle, and signalling. Such functions make these genes strongly associated with hallmarks of cancer. All minor introns are spliced by the minor spliceosome, whose catalytic snRNA is coded by the U6atac gene. Additionally, levels of U6atac expression also regulate the expression of minor introns. In this project, U6atac levels were manipulated in two breast cancer cell types and the resulting impact on the splicing and expression of 30 minor intron genes was studied. Splicing analysis of these genes showed specific splicing trends, thereby challenging the literature labeling all minor introns to have poor splicing efficiency. Based on the observed splicing trends, genes were categorized into three classes.