Date of Award
Genetics and Biochemistry
Transposable elements (TEs) are sequences of DNA that can move, or transpose, within a genome. Retrotransposons are TEs that propagate via a “copy and paste” mechanism where the elements are transposed to a new genomic location via an RNA intermediate. Short interspersed element (SINE)-VNTR-Alu elements (SVAs) are non-autonomous retrotransposons that use long interspersed element 1 proteins to mobilize. SVAs are currently active in the human genome and often are characterized by the mobilization of sequences adjacent to the 3’ and 5’ ends of insertions, known as transduction events (TDs). TDs were a focus of this study due to their contribution to genome expansion, exon shuffling, and gene duplication. We analyzed 547 SVA elements across 35 genetically diverse individuals from the Human Genome Structural Variation Consortium. We identified 187 full-length elements, 12 of which carried 3’ TDs, 13 harbored 5’ TDs, and five held both 3’ and 5’ TDs. Four TDs contained exons of genes, including HGSNAT, UQCRC1, and RP11-137H2.4. Utilizing TDs, we screened the dataset for source elements, i.e., active TEs capable of producing offspring, by querying the human reference genome (GRCh38) using BLAT to identify the origin of the TDs and SVA source elements. We found that Chromosomes 3, 10, and 11 showed enrichment for active SVA elements. Novel TDs were identified and can be used to study genome expansion due to their ability to take additional sequences from each genomic location. Source elements can cause insertions that drive disease and genome expansion, exemplifying their significance.
Golba, Emily C., "Identification of SVA-Mediated 3’ and 5’ Transductions in Human Genome Sequences" (2023). Honors College Theses. 12.