Ciliates are important model organisms that have been used to study many aspects of cellular biology, including telomeres, histone modifications, and ribozymes. These unicellular eukaryotes house both a germline genome and a somatic genome in distinct nuclear structures within a single cell. One of their most unique features is their ability to undergo complex programmed genome rearrangements, during which their germline genome is fragmented and rearranged to form a new somatic genome. This rearrangement process results in a highly specialized somatic genome with many polyploid short chromosomes that are rich with genes. While all ciliates can undergo this developmental process, Oxytricha trifallax experiences particularly complex rearrangements that result in a more radically unconventional structure in its somatic genome.
Much of the previous work studying Oxytricha has been focused on the complex rearrangements that it undergoes during sexual development and the mechanisms that allow it to perform these genome rearrangements events at the level of accuracy required for proper somatic function afterwards. Due to this particular focus on Oxytricha sexual development, the rest of Oxytricha’s unique biology has not been studied to the same degree. For my thesis I examined two aspects of Oxytricha biology that have not been well understood.
In Chapter 1 I report the results of a proteomic survey of both types of nuclei found within the vegetative cell, the somatic macronucleus and the germline micronucleus. We performed mass spectrometry on enriched samples of both nuclear types and analyzed the enrichment of proteins between the two. Despite some mitochondrial contamination, we found that many categories of functional proteins were enriched in one of the two nuclei. We validated the appropriate nuclear localization of specific proteins from each subcategory through imaging Our results confirmed many previously predicted aspects of the two nuclei and provide a valuable resource for further studies on nuclear proteins in Oxytricha.
In Chapter 2 I describe various features of a comparative analysis between the somatic genomes of multiple strains of Oxytricha trifallax. Previous work from the lab has focused primarily on the reference strains JRB310 and JRB510, which are most commonly used due to their ability to mate. We generated four new draft assemblies of the somatic genomes of strains JRB27, JRB39, SLC89, and SLC92. Many metrics demonstrate that these new assemblies are largely complete. Our analyses of these new strains revealed that there are numerous strain-specific chromosomes in Oxytricha that can encode genes. While they do not seem to encode core genes that would be missing otherwise, they are prime candidates for further examination to identify mating type-related genes.
| Identifer | oai:union.ndltd.org:columbia.edu/oai:academiccommons.columbia.edu:10.7916/ptw2-w396 |
| Date | January 2023 |
| Creators | Lu, Michael |
| Source Sets | Columbia University |
| Language | English |
| Detected Language | English |
| Type | Theses |
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