Date of Award

Fall 9-5-2025

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Bioinformatics & Computational Biology

First Advisor

Rodney Dale

Abstract

Type II collagens (Col2) are essential proteins providing flexibility and structure to vertebrate animals. During development type II collagens play a vital role in the formation of many structures, such as the cartilage of the skeleton, the notochord, the retina and many other tissues. Conserved throughout vertebrates, cartilage is composed of two main cell types: chondrocytes, which make up the bulk of the structure, and perichondral cells, which form the epithelial layer that surrounds chondrocytes and is essential for bone growth and joint protection. While much is known about the expression and regulation of type II collagens in chondrocytes, specifically the regulation and secretion of type II collagen Alpha-1 (Col2a1), little is known about the genetic regulation and expression of Col2a1 in the perichondrium. This study used the experimental benefits of the vertebrate Danio rerio, the common zebrafish, to explore the genetic regulation and expression of the zebrafish Col2a1 ohnolog in the perichondrium. Specifically, we focus on the zebrafish gene col2a1b, one of two zebrafish paralogs of human COL2A1gene, which we have previously found to be only expressed in the perichondrium and is not expressed in the chondrocytes of cartilage structures in fish. To study this gene, I first had to complete genome sequencing around this locus. In this study, bioinformatic and comparative genomic analyses have been used to finish genomic sequence gaps that are absent in the published zebrafish genome near the telomeric end of chromosome 11, where col2a1b resides. We have identified evolutionarily conserved, putative transcription factor regulatory elements near the col2a1b first exon using tools DCODE.org from NCBI and the JASPAR transcription factor binding site database. The generation and imaging of transgenic fish constructed using reporter plasmids including putative regulatory elements has shown expression patterns that support the hypothesis that these are conserved regulatory elements, and that col2a1a and col2a1b have functions shared with their COL2A1 orthologous gene from other species. Overall, these findings provide evidence that the zebrafish paralogs col2a1a and col2a1b share similar genetic regulation and that understanding these mechanisms may provide insight into the development of therapeutic strategies for diseases and disorders involving human COL2A1.

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