Date of Award


Degree Name

Master of Science


Molecular Biology Microbiology and Biochemistry

First Advisor

Rader, Bethany


Advancement in the study of host-microbe interactions has shown that microbes can induce and maintain long lasting changes in gene expression in host cells to facilitate beneficial symbiosis through changes in methylation of the host’s genomic DNA. The beneficial symbiosis between Hawaiian Bobtail squid, Euprymna scolopes and Gram negative bioluminescent bacteria Vibrio fischeri provides an excellent system for studying beneficial microbes’ effect on host DNA methylation. The symbiosis is highly specific, in that only V. fischeri colonizes the squid’s symbiotic organ from a background of 106 diverse bacteria per mL of sea water. DNA methylation (DNAm) refers to the covalent addition of methyl (CH3) groups to the nucleotides of organism’s genomic DNA. The most well researched DNA methylation type is 5- methyl cytosine methylation (5mC). Previous publications show DNAm provides an extra tier of regulation for organisms to control their gene expression, without altering their DNA sequences. Two types of DNAm have been discovered in invertebrate systems: gene promoter methylation and gene body methylation. The amount of methylated cytosine on gene bodies is positively correlated with the specific gene’s expression state. We hypothesize that V. fischeri plays an important role in regulating host DNA methylation during both colonization of the animals (juvenile) and maintenance of the symbiosis I (adult). To start to address this hypothesis, our specific aims are (1) validate DNA methylation in E. scolopes; (2) identify DNA methylation machinery genes in squid at the transcript level and quantify the level of their expression based on state of symbiosis; (3) analyze squid DNA methylation at the whole genome level as well as gene specific level.

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