Detecting sequence mobilisation by L1 retrotransposons

Abstract

This dissertation investigates the expression dynamics of active L1 retrotrans- poson subfamilies in melanoma cell lines subjected to stress conditions. Spe- cifically Fetal Bovine Serum (FBS) reduction. The study focuses on three active L1 subfamilies associated with transduction sequences: L1RP (AF148856), AC002980, and LRE3 (AC067958). The primary objective is to establish a ro- bust analytical pipeline for assessing the differential gene expression of these L1 subfamilies in RNA-seq datasets, comparing two distinct conditions: a 10% FBS normal control and a 1% FBS stress-induced condition. The analysis is conducted using the Salmon software, a tool designed for precise transcript quantification from RNA-seq data. Furthermore, the developed pipeline is employed to investigate the feasibility of detecting transcripts originating from the specified L1 subfamilies. The ulti- mate goal is to discern whether there exists a significant difference in the ex- pression of the three L1 retrotransposon subfamilies in melanoma cell lines. This assessment is performed both collectively, considering the three subfami- lies as a group, and individually under the varying conditions. Remarkably, the results indicate no statistically significant differences in the ex- pression levels of the three L1 subfamilies between the normal control and stress-induced conditions. The findings contribute to our understanding of L1 retrotransposon dynamics in melanoma cell lines under different environmental stresses, shedding light on the potential stability of these elements in the face of cellular stressors. The functional annotation of the differentially expressed genes (non-L1 genes) found in the RNA-seq data was performed using the DAVID database. To detect statistically significant enrichments of Gene Ontology terms, func- tional annotations, and pathway associations among the top 100 upregulated and top 100 downregulated genes. The functional annotation clustering of the top 100 upregulated genes reveals that the biological process most significantly impacted under 1% FBS conditions is "Protein biosynthesis". Additionally, it is observed that the downregulated genes under 1% FBS conditions primarily af- fect the biological process of "RNA binding".