Thesis
Genomic and fitness consequences of heat stress-induced transposon mobilization in Drosophila
University of Iowa
Master of Science (MS), University of Iowa
Summer 2023
DOI: 10.25820/etd.007073
Abstract
Transposable elements (TEs) are mobile genetic elements that can change their position or duplicate within the genome. They are also major components of most eukaryotic genomes. Importantly, the extent of their impact on genome function and evolution remains a matter of intense interrogation. To gain insight into this matter, the genomic and fitness consequences of heat shock-induced de novo transposon insertions were investigated in Drosophila melanogaster. Generationally repeated heat shock exposure resulted in copy number expansions of genomic retrotransposons as well as select rDNA elements. Interestingly, some of these copy number expansions were followed by plateaus and/or rapid reductions. These copy number changes were initially quantified via qPCR and Illumina next-generation sequencing methods. To overcome the limitations of these methods, Oxford Nanopore long-read sequencing was also employed to comprehensively annotate genomic insertion sites of transposons in the heat shock mutation accumulation lines (HSMALs). These results largely confirmed previous findings that retrotransposons were activated during heat shock events, although specific DNA transposons also showed significant increases in copy number. Furthermore, Hi-C analysis found that heat stress-induced de novo transposon insertions can alter the 3D chromatin architecture, as nearby TAD structures were altered at insertion sites. RNA-seq studies also demonstrate that gene expression was altered in HSMALs, likely due to de novo transposon insertions and/or changes in 3D chromatin architecture. Decreased fecundity in HSMALs indicates a mutational load was generated relative to control lines, likely as a result of transposon proliferation. This finding implicates heat shock-induced de novo transposon insertions as the causative agent for pervasive deleterious effects, whether through insertional mutagenesis or increased epigenetic repression of proximal genomic regions. Recovery of fecundity levels in inter-replicate crosses of HSMALs reveals that recessive mutations are associated with a large fraction of the detected deleterious effects.
Details
- Title: Subtitle
- Genomic and fitness consequences of heat stress-induced transposon mobilization in Drosophila
- Creators
- John Atagozli
- Contributors
- Josep Comeron (Advisor)Ana Llopart (Committee Member)Chi-Lien Cheng (Committee Member)
- Resource Type
- Thesis
- Degree Awarded
- Master of Science (MS), University of Iowa
- Degree in
- Integrated Biology
- Date degree season
- Summer 2023
- DOI
- 10.25820/etd.007073
- Publisher
- University of Iowa
- Number of pages
- ix, 51 pages
- Copyright
- Copyright 2023 John Atagozli
- Language
- English
- Date submitted
- 07/24/2023
- Description illustrations
- Illustrations, graphs, charts
- Description bibliographic
- Includes bibliographical references (pages 42-51).
- Public Abstract (ETD)
Transposable elements (TEs) are DNA sequences that can change their position or duplicate within the genome. Because of this ability to relocate within the genome, TEs are often referred to as “jumping genes.” Furthermore, when TEs insert at new locations within the genome, they can compromise existing genes present at or around the insertion sites. This selfish characteristic of TE mobilization has garnered these elements the notorious label of “genomic parasites.” The present study was conducted to investigate the effects of heat shock-induced TE mobilization on the genome and fitness of the common fruit fly, Drosophila melanogaster. Exposure to heat shock was repeated for multiple generations to accumulate new TE insertions. This resulted in the proliferation of genomic TEs, although these expansions were followed by rapid reductions in some cases. Methods used to quantify the genomic copy number of TEs include qPCR, Illumina next-generation sequencing, and Oxford Nanopore long-read sequencing. Additionally, it was found that relocation of TEs due to heat stress has consequences for chromatin structure, which refers to the 3-dimensional physical organization of the genomic DNA in the nucleus. Evidence was found for chromatin structure alteration around new TE insertion sites. Significant gene expression changes were also observed in flies that experienced TE copy number increases due to generational heat stress exposure. Lastly, treated flies demonstrated decreased fertility levels. This was evidenced by decreases in the average number of offspring produced by treated flies in comparison to untreated flies. This finding suggests that heat shock-induced TE insertions are responsible for detrimental changes in the treated fruit flies.
- Academic Unit
- Biology
- Record Identifier
- 9984454642902771
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