Date of Award


Document Type

Thesis and Dissertation

Degree Name

Master of Science (MS)


School of Biological Sciences

First Advisor

Thomas M. Hammond


Integration of foreign DNA into a host genome is often detrimental to the host organism, as the DNA is often of viral or transposon origin. Many organisms have established DNA surveillance and genome integrity mechanisms to defend against these harmful DNA insertions. Neurospora crassa, a filamentous fungus belonging to the Ascomycota group, has several DNA defense mechanisms to combat foreign DNA integration to its genome. One such mechanism is Meiotic Silencing of Unpaired DNA (MSUD). During meiosis, this remarkable system can detect unpaired genes on homologous chromosomes during sexual reproduction and silence their expression throughout meiosis. In order for the detection of this unpaired DNA (unDNA), the MSUD machinery must be able to, somehow, search through N. crassa’s 40 million base-pair genome for homology and be able to pick out individual genes that lack a pairing partner on its respective homologous chromosome.

In the following studies, we present research to describe what parameters are sufficient and required for unDNA to be characterized as unpaired to the MSUD machinery. First, to shed light upon how unDNA is detected, we designed experiments to determine what physical properties of DNA affect MSUD. To do this, we introduced large unpaired regions of DNA surrounding an unpaired genetic marker into the N. crassa genome. These large unpaired regions may form complex unpaired DNA structures that may affect how MSUD detects unDNA. We have found that as the length of unDNA increases, detection of unDNA by MSUD becomes less efficient, suggesting that these large, unpaired regions may be interfering with MSUD’s ability to detect unpaired genes.

Secondly, we designed experiments to observe how sequence homology plays a role in detection of unDNA. To achieve this, we designed several fragments of DNA that have patterns of interspersed homology to a common genetic marker. These fragments all share similar levels of homology to the genetic marker, while the pattern of dispersed homology differs. We have found that certain patterns of dispersed homology are more efficient at being detected as unpaired than others, suggesting that sequence-level homology patterns may play a role in homology searching.


Imported from ProQuest Rhoades_ilstu_0092N_11064.pdf

Page Count


Available for download on Thursday, February 27, 2020