Investigation of the Conservation of Biological Function in Transposable Elements using a Multiple Alignment Strategy
type: CreativeWork
description: The non-coding genome has been relatively understudied since the dawn of modern genetics due to its sheer size and complexity. It was not until the last two decades that recent breakthrough in sequencing technology overcame those difficulties. Among many interesting findings, more than half of the non-coding genome was found to be occupied by transposable elements (TEs), DNA with transposition capability which can either benefit or disrupt gene functions depending on their destination. TEs are considered foreign and viral-like intruders which can affect genome integrity and therefore need to be silenced by several defense mechanisms such as KRAB-zinc finger protein (KZFPs). Despite being repressed and eventually losing their ability to mobilise by neutral drift, many TEs can still persist in the human genome long after they lose their ability to transpose, suggesting the possibility of them being “domesticated”, which means that they can contribute to gene regulation via the co-option of transcription factor binding sites they contain. Coupled with many recent discoveries centered around TEs that found their involvement in gene regulatory pathways and cell development, it has become very interesting to explore the conservation landscape of TEs. Since coding and regulatory regions are more likely to be conserved throughout the evolution process for their functions, we hypothesize that functional regions of TEs are also more likely to be conserved than non-functional regions and leveraged multiple novel approaches and datasets to study this hypothesis. However, when compared to coding regions, the conservation patterns of TEs are harder to detect as they are younger sequences found in fewer species. This makes exploration of conservation on single TE sequences difficult. In this project, we overcome the issue by utilizing the characteristic properties of TEs: a large number of highly similar sequences dispersed in the genome. As TEs in a group are closely related, it …
abstract: The non-coding genome has been relatively understudied since the dawn of modern genetics due to its sheer size and complexity. It was not until the last two decades that recent breakthrough in sequencing technology overcame those difficulties. Among many interesting findings, more than half of the non-coding genome was found to be occupied by transposable elements (TEs), DNA with transposition capability which can either benefit or disrupt gene functions depending on their destination. TEs are considered foreign and viral-like intruders which can affect genome integrity and therefore need to be silenced by several defense mechanisms such as KRAB-zinc finger protein (KZFPs). Despite being repressed and eventually losing their ability to mobilise by neutral drift, many TEs can still persist in the human genome long after they lose their ability to transpose, suggesting the possibility of them being “domesticated”, which means that they can contribute to gene regulation via the co-option of transcription factor binding sites they contain. Coupled with many recent discoveries centered around TEs that found their involvement in gene regulatory pathways and cell development, it has become very interesting to explore the conservation landscape of TEs. Since coding and regulatory regions are more likely to be conserved throughout the evolution process for their functions, we hypothesize that functional regions of TEs are also more likely to be conserved than non-functional regions and leveraged multiple novel approaches and datasets to study this hypothesis. However, when compared to coding regions, the conservation patterns of TEs are harder to detect as they are younger sequences found in fewer species. This makes exploration of conservation on single TE sequences difficult. In this project, we overcome the issue by utilizing the characteristic properties of TEs: a large number of highly similar sequences dispersed in the genome. As TEs in a group are closely related, it …
author: Chansongkrow, Pakkanan
language: eng
keywords: bioinformatic tools, bioinformatics, genome-wide data analysis, transposable elements
license: https://www.repository.cam.ac.uk/bitstreams/c58f7c1b-5407-4675-87a3-c945d7a46535/download
license: https://creativecommons.org/licenses/by/4.0/
date published: 2024-10-31
date modified: 2026-07-22T22:23:59Z
provider: Cambridge University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Cambridge

PropertyValue
property ID: DOI
value: 10.17863/CAM.120987