Date of Award
Master of Science (MS)
Department of Mathematics
Sexual reproduction and genetic exchange via meiosis are important and highly conserved processes in many living organisms. Occasionally, complications occur during meiosis that can result in chromosome abnormalities. In humans, improper chromosome development can cause life altering disorders such as Down Syndrome, Edwards Syndrome, and Patau Syndrome. Unfortunately, despite its importance, gaps remain in our knowledge of how this process works. For instance, little is known about how homolog identification occurs and what proteins identify matching chromosomes during pairing. This fundamental process occurs early during meiosis and ensures proper development of gametes.
Understanding the proteins involved during homolog pairing may be possible by studying a process called meiotic silencing by unpaired DNA (MSUD) in the eukaryotic fungus, Neurospora crassa. During MSUD, unpaired regions (or regions that do not match during homolog identification) are thought to produce special RNA molecules. Discovery of these molecules should help elucidate how unpaired DNA is identified.
This is because it is possible that the proteins involved in identifying unpaired regions in MSUD are the same proteins that identify homologs in meiosis. Furthermore, these proteins could contribute to homology searches required for DNA repair, which could contribute in the development of cancer research.
To gain a complete understanding of unpaired DNA detection, the Neurospora crassa transcriptome must be identified. The transcriptome represents all the RNA molecules found within an organism at a certain point in time or stage of development. Knowledge of the transcriptome can be used in efforts towards identifying the theoretical RNA molecules of MSUD. The meiotic transcriptome can be determined by performing an RNA-seq analysis on all the RNA transcripts produced during meiosis. These RNA are then aligned to the N. crassa genome. Then, a special algorithm is used to identify key regions of the genome that may prove particularly useful in MSUD research (i.e. transcriptionally quiescent regions). Given the sheer size of the data sets required for identifying these regions, the algorithm must be time and memory efficient due to computational constraints.
Groskreutz, Katie Marie, "Identification of Transcriptionally Quiescent Regions in the Neurospora Crassa Genome" (2014). Theses and Dissertations. 111.