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The Changing landscape of the rDNA locus and the regulation of its mobile elements

URL to cite or link to: http://hdl.handle.net/1802/8740

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Thesis (Ph. D.)--University of Rochester. Dept. of Biology, 2009.
R2 retrotransposable elements are "parasites" that reside exclusively in the same location of 28S rRNA gene of the rDNA locus. Upon their insertion, the corresponding rDNA units can no longer form functional ribosomal RNA. Therefore the host must have weapons to keep the propagation of these elements in check. The fact that R2 elements have successfully maintained themselves in the locus for hundreds of millions of years suggests, however, the host does not have the means to rid itself of this parasite. Understanding of the genetic conflict between R2 and its host can provide insights into how mobile elements have helped change the genome over the course of evolution. In this dissertation, many different areas of research including population biology, molecular biology, genetics and computer simulations were used to explain how R2 retrotransposable elements help shape the changing landscape of the rDNA locus as well as how R2 elements are regulated within the rDNA locus. Initially, analyses of 180 Drosophila simulans lines derived from two natural populations showed a continuous pattern of R2 transcript levels in which half the lines had low to undetectable levels of transcripts and the other half had transcript levels varying up to nearly 100-fold. It was then demonstrated that R2 retrotransposition is correlated with R2 transcript level. Seemingly obvious factors such as the rDNA locus size or the number of R2 elements did not correlate with R2 activity. Instead regions of uninserted units as revealed by NotI digestion (cuts R2 elements only) and pulsed-field gel analysis were found to be larger in inactive flies than in active flies. This suggested that it is the distribution of R2 elements in the locus that determines R2 activity. Recombination is the main evolutionary force that influences the rDNA locus. To better understand how recombination affects the variation in rDNA locus size as well as R2 numbers and distribution in flies, we conducted a series of simulations. We compared our population data with a previous random recombination model, and found that model does not fit the empirical data. When recombination was confined to the middle of the locus, the population data could be explained, however, this model is limited because of the arbitrary assignment of the clustering of recombination and lack of regulation of the R2 elements. A domain regulation model in which recombination is clustered around a selectively transcribed region of the locus which in turn is determined by the distribution of R2 elements did comprehensively explain the population data. A preferential transcriptional expression of the Y rDNA locus over the X locus in males of D. melanogaster was observed. This was scored as differential transcription of both full-length and 5' truncated R2 copies between females and males. This dominance was further indicated by the cytological analyses of the premetaphase chromosomes of brain tissues which showed secondary constrictions, indicative of prior transcription of the rDNA locus, only on the Y chromosomes. The Y dominance was found to be independent of genetic background. We suggested that this Y dominance is consistent with previous reports that only one rDNA locus can be expressed. Finally, to further provide support for the transcription domain model, we mapped transcribed R2 copies within the rDNA locus. Using specific oligo probes, two transcribed copies were located to large NotI fragments as predicted by the model. Interestingly rDNA structural changes presumably due to recombination were observed and also involved large NotI fragments as predicted by the simulations.
Contributor(s):
Jun Zhou (1979 - ) - Author

Thomas H. Eickbush - Thesis Advisor

Primary Item Type:
Thesis
Language:
English
Subject Keywords:
Natural population; rDNA locus; Transposable element, Dynamics; Regulation; Retrotransposition activity
Sponsor - Description:
National Science Foundation (NSF) - MCB-0544071
National Institutes of Health (NIH) - GM42790
First presented to the public:
12/9/2010
Originally created:
2009
Date will be made available to public:
2010-12-09   
Original Publication Date:
2009
Citation:
Extents:
Number of Pages - xiii, 219 leaves
License Grantor / Date Granted:
Marcy Strong / 2009-12-09 11:27:30.26 ( View License )
Date Deposited
2009-12-09 11:27:30.26
Date Last Updated
2012-09-26 16:35:14.586719
Submitter:
Marcy Strong

Copyright © This item is protected by copyright, with all rights reserved.

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