Abstract
Retrotransposons (RTs) comprise approximately half of the human genome and contribute to chromatin structure, regulatory motifs, and protein-coding sequences. Since RT insertions can disrupt functional genetic elements as well as introduce new sequence motifs to a region, they have the potential to effect the function of genes that harbour insertions as well as those nearby. A detailed characterization of RT density in genes could help inform predictions of the functional consequence of de novo as well as polymorphic insertions. The research presented here examines the selective pressures that modify the distribution of RTs within genes. It further examines these pressures by determining the association of RTs with evidence of differential gene expression. The findings of this study indicate that RTs are under purifying selection within genes. These results further indicate that factors that are associated with the RTs (e.g.: orientation with respect to the the gene, presence of a polyadenylation motif), and factors associated with the gene (e.g: tissue-specificity, coding sequence density) are modifiers of this selection. Moreover these results show that the presence of a RT is associated with differential gene expression, indicating that altered gene expression may be a potential mediator for the phenotypic change that results in the selection of RTs within genes. Future studies can use the results presented here to create a model for predicting the degree of impact of new RT insertions.