dc.contributor.advisor |
Ganley, Austen |
|
dc.contributor.author |
Sharma, Diksha |
|
dc.date.accessioned |
2021-04-29T22:45:28Z |
|
dc.date.available |
2021-04-29T22:45:28Z |
|
dc.date.issued |
2021 |
en |
dc.identifier.uri |
https://hdl.handle.net/2292/54996 |
|
dc.description.abstract |
In most eukaryotes the ribosomal RNA genes (rDNA) exist as a tandem array(s) of repeats with high variability in copy number within and between species. The rDNA is central to many critical cellular activities for which its multi-copy nature is believed to be important. However, while the mechanism of rDNA copy number variation is understood, little is known about rDNA dynamics at the population level, partly because of difficulties in measuring copy number. The predominant bioinformatics method for estimating rDNA copy number does so using mean coverage. To overcome limitations arising from biases in read coverage that can reduce the accuracy of the mean coverage method, I developed a novel bioinformatics approach to measure rDNA copy number from whole genome sequence data using the modal (most frequent) coverage. I validated this approach using Saccharomyces cerevisiae isolates with different, known rDNA copy numbers and show that my approach produces robust and reliable results down to whole genome sequence coverages of ~3X.
Different species are thought to maintain different “homeostatic” rDNA copy numbers to which copy number returns when perturbed. To test whether this holds true for different populations within the same species, I applied my pipeline to investigate intra-species variation in rDNA copy number between different S. cerevisiae and human populations. Using 788 1002 Yeast Genome Project S. cerevisiae isolates from around the world, I show that different populations have different homeostatic rDNA copy numbers. Consistent with this, I find there is no recovery towards a common copy number following growth for ~60 generations. In contrast, I found little correlation between phylogeny and rDNA copy number, unlike what is seen above the species level in fungi. I ruled out ploidy differences and high variation in S. cerevisiae copy number driving this lack of correlation. Instead, I suggest that environmental differences drive the rDNA copy number population differences I observe, although my analyses only provide equivocal support for this explanation.
I then applied my pipeline to test whether different human populations have different rDNA copy numbers. Using two different datasets totaling 430 individuals from populations across the world, I failed to find evidence for rDNA copy number differences between populations, except for the Papuan population in one dataset. However, this Papuan copy number difference was not replicated in the other dataset.
Together, my work establishes a robust and simple platform for determining rDNA copy number from whole genome sequence data. I provide evidence for population-level differences in rDNA copy number in S. cerevisiae, whereas for humans the results are equivocal and further studies are required to establish whether inter-population homeostatic differences exist. Application of my pipeline has enabled a better understanding of rDNA copy number, and provides robust methodology for determining the significance of rDNA copy number changes in many contexts, including cancer. |
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dc.publisher |
ResearchSpace@Auckland |
en |
dc.relation.ispartof |
PhD Thesis - University of Auckland |
en |
dc.relation.isreferencedby |
UoA |
en |
dc.rights |
Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. |
en |
dc.rights |
Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. |
|
dc.rights.uri |
https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm |
en |
dc.rights.uri |
http://creativecommons.org/licenses/by-nc-sa/3.0/nz/ |
|
dc.title |
A new method for investigating ribosomal RNA gene copy number dynamics |
|
dc.type |
Thesis |
en |
thesis.degree.discipline |
Biological Sciences |
|
thesis.degree.grantor |
The University of Auckland |
en |
thesis.degree.level |
Doctoral |
en |
thesis.degree.name |
PhD |
en |
dc.date.updated |
2021-04-27T22:05:32Z |
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dc.rights.holder |
Copyright: The author |
en |
dc.rights.accessrights |
http://purl.org/eprint/accessRights/OpenAccess |
en |
dc.identifier.wikidata |
Q112956681 |
|