Author ORCID Identifier

Year of Publication


Degree Name

Master of Science (MS)

Document Type

Master's Thesis


Arts and Sciences



First Advisor

Dr. Elizabeth Duncan


The outer epithelial layer covering an organism, commonly known as the epidermis, is crucial for maintaining homeostasis and for the wound healing processes after injury. The planarian epidermis allows flatworms to heal their wounds and virtually restore any missing tissues. Immediately after amputation, planarians contract their muscle and stretch their epidermis to heal the wound area. However, how the planarian epidermis coordinates with other tissues and mechanisms after the initial wound healing processes begins is not understood in detail. I hypothesized that epidermal cell stretching upon wound healing induces transcriptional changes that are required for effective regeneration. To test this hypothesis, I first developed a new technique for isolating the planarian epidermis from both intact and regenerating worms. Next, I optimized a custom method to deplete ribosomal RNA from total planarian RNA for preparation of RNA-seq libraries. I show that this method depletes ~99% of rRNA from planarian RNA samples. I then conducted RNA-seq experiments on isolated planarian epidermis to identify genes that change expression after tissue injury. Using these two new methods in combination, I was able to detect more epidermal enriched genes compared to similar published datasets.

Excitingly, I uncovered functional roles of several genes that were identified using our methods. For example, I showed that SHOC2 is required for eye spot maintenance and for normal blastema growth and regeneration in planarians. I also identified several wound-induced genes that are expressed in the planarian epidermis. Furthermore, at least one newly identified wound-induced gene, a novel gene WI-12 is required for planarian tail regeneration when the head fragments are amputated at a certain position. In sum, our work established tools for isolating the planarian epidermis and depleting almost all rRNA from planarian RNA samples, paving the way to detect and dissect the roles of epidermal genes in maintaining homeostasis and initiating regeneration in planarians.

Digital Object Identifier (DOI)

Funding Information

This study was supported by Centers of Biomedical Research Excellence Pilot Project Award (no,: P20 GM121327) in 2020.

This study was also supported by the National Institutes of Health 1R35 Grant (no.: 1R35GM142679-01) in 2021.

Available for download on Saturday, May 20, 2023