Document Type

Dissertation - Open Access

Award Date

2020

Degree Name

Doctor of Philosophy (PhD)

Department / School

Pharmaceutical Sciences

First Advisor

Wenfeng An

Keywords

Activity, Evaluate, L1, Profile, Promoter, Retrotransposition

Abstract

Transposable elements, also called jumping genes, comprise almost 45% of the human genome. In contrast, only 1% of the human genome is protein-coding sequences. The function and advantages of maintaining such massive copies of transposable elements in the human genome are still unclear. Long interspersed element 1 (L1), the most substantial group and the only active autonomous transposable element in the human genome, has revealed its unique roles in many diseases. The insertional mutagenesis induced by L1 retrotransposition events could threaten human genomic stability and generate unexpected mutations. L1 overexpression has been documented in both somatic and germline cells and, most prominently, across different cancer samples. A recent study in colorectal cancer samples by whole genome sequencing showed that L1 insertions could initiate tumorigenesis. Because of the many challenges to studying the L1 pathological impact on the human genome, an animal model is urgently needed. The high similarity between human and mouse L1s motivates us to have a comprehensive understanding of endogenous mouse L1 elements. A previous study estimated that over 3000 L1 elements are currently active in the mouse genome. Both open reading frames and functional internal promoters are required for successful retrotransposition events. To capture and understand L1 activity in the mouse genome, we utilized bioinformatics expertise to create a potential active L1 pool by filtering out any element not possessing intact ORFs or less than a 2- monomer length promoter. After cloning representative L1s directly from the mouse genome, we evaluated those L1s with both promoter and retrotransposition activity by our dual-luciferase reporter assay. In our study, we have demonstrated L1 elements transcriptional profiles across different young subfamilies. With our high throughput assay, we compared promoters’ expression across three different cell lines. Our study revealed that cellular environmental factors could significantly influence L1 expression levels. Our research also demonstrated that loci location, mutations, and incomplete monomer length are critical for transcription. Moreover, our data suggest that high promoter activity is essential, but not a determining factor for L1 retrotransposition activity. Our study extended current knowledge in L1 biology and provided many potential future directions for the study of L1.

Library of Congress Subject Headings

Transposons.
Genomes.
Human genome.
Transcription factors.
Mice -- Genetics.

Format

application/pdf

Number of Pages

156

Publisher

South Dakota State University

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Rights Statement

In Copyright