Date of Award

7-7-2023

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Genetics & Genomics)

Degree Name

Doctor of Philosophy (PhD)

Degree Type

Dissertation

Abstract

Transposable elements (TEs) are mobile genetic elements that make up a large proportion of mammalian genomes. Although TEs are highly prevalent genomic sequences, they have been understudied as they were once labeled as “junk DNA.” Despite their initial status as simple genomic parasites, recent studies have implicated TEs as cis-regulatory elements, supplying promoters, enhancers, and boundary elements. Functional testing of regulatory activity, however, remains a significant bottleneck. Nonetheless, due to their repetitive nature, TEs provide a unique model to examine the evolution of cis-regulatory elements, which has traditionally been difficult to study due to lack of homology at the sequence level. In this thesis, I develop experimental and computational approaches that take advantage of TE repetitiveness to explore how they provide and evolve as cis-regulatory elements. The first part of my thesis tests whether TEs have the regulatory capacity to be gene regulatory modules as hypothesized in the gene-battery model. Using LTR18A as a representative TE subfamily, I employ massively parallel reporter assay (MPRA) to systematically test TEs for regulatory activity. I show that sequence variation that arose through natural evolution can be used to identify transcription factor binding motifs that drive cell-type specific enhancer activity. By functionally testing computationally reconstructed ancestral sequences, I demonstrate that enhancer activity generally decreases over the course of evolution, much of which can be directly attributed to the gain or loss of transcription factor motifs. Using present day primate genomes, I show that both motifs are conserved at rates higher than expected based on neutral evolution and that some elements are potential enhancers in human based on epigenomic marks. These results provide a model for the origin, evolution, and co-option of TE-derived regulatory elements and present a framework to study regulatory activity in any TE subfamily. In the second part of my thesis, I investigate whether models in the field, which have focused on a single TE subfamily or a single cell/tissue type, generalize to TEs across the genome. Using ENCODE candidate cis-regulatory element (cCRE) annotations in human and mouse, I confirm that about a quarter of regulatory elements are associated with TEs, with a clear bias against proximity to known genes and preference for cell-type specific activity. I find that TEs contribute up to 2% of conserved cCREs and 8-36% of novel, lineage-specific cCREs in human and mouse. Based on principles from my LTR18A work, I develop an approach to examine the phylogenetic origins of transcription factor motifs that are associated with TEs providing cCREs. I explore the effects of TE insertion site on cCRE annotation and transcription factor binding. Altogether, this work sets the foundation for a holistic understanding of gene regulation that incorporates TEs and advances our knowledge for how simple genomic parasites took part in shaping the genomes of mammals, including us.

Language

English (en)

Chair and Committee

Ting Wang

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Genetics Commons

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