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Title: The contribution of retrotransposons to the transcriptomes of murine somatic cells
Author: Gardner, Joseph Michael
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2019
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Retrotransposons comprise approximately 40% of the mouse genome. Once thought to be useless "junk" DNA, there is growing evidence that retrotransposons play crucial roles in genome evolution and gene regulation, and contribute to the transcriptome. Several studies have found functional retrotransposon transcripts in the germline and during early development, but less is known about retrotransposon transcription in adult somatic cells. Retrotransposons are also responsible for generating gene copies in mammalian genomes (retrocopies), and there are several examples of retrocopies evolving into new genes, or being transcribed as non-coding RNA. Using computational approaches, I analyse RNA-seq data to assess the contribution of retrotransposons and retrocopies to the transcriptomes of adult mouse somatic cells, using purified naive B and T lymphocytes. First, I describe the transcriptomes generated using high-quality total RNA-seq data. Second, I quantify and characterise the retrotransposon content of these transcriptomes. Finally, I identify retrocopy transcripts and assess their relationship with the genes from which they originate. I found widespread inclusion of retrotransposons in somatic cell transcriptomes. These transcripts form distinct clusters based on retrotransposon sequence, with endogenous retroviruses being particularly prevalent in retrotransposon-rich transcripts. While these clusters are consistent between cell types, the individual retrotransposons transcribed show cell-type specificity. I also find evidence that retrotransposons may facilitate gene regulation by antisense transcripts. I demonstrate that a subset of retrocopies is transcribed, and the vast majority of these form RNA complementary to their parent mRNA, with high sequence identity. Using differential expression and proteome analysis, I present evidence for post-transcriptional regulation of parent transcripts by retrocopy RNA, possibly through stabilisation of the parent RNA. I also find that while retrocopy expression is not necessarily shared between cell types or mouse strains, certain parent transcripts tend to have an expressed retrocopy in multiple contexts. Overall, this thesis presents evidence of an important role for retrotransposons and retrocopies in the adult somatic transcriptome, and sets the stage for further investigation to experimentally elucidate the functions of these transcripts.
Supervisor: Ferguson-Smith, Anne Sponsor: BBSRC
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
Keywords: bioinformatics ; RNA-seq ; transcriptome ; non-coding RNA ; ncRNA ; long non-coding RNA ; lncRNA ; retrotransposon ; transposon ; transposable element ; retrogene ; retrocopy ; pseudogene ; RNA ; sequencing ; antisense ; endogenous retrovirus ; LINE ; SINE ; LTR ; transcriptomics ; genome ; epigenetics ; lymphocytes ; mouse ; genetics