Document Type


First Faculty Advisor

Steven Weicksel

Second Faculty Advisor

Kristin Scaplen


chromatin; circular chromatin chromosome conformation capture (4C); HOX genes; gene regulation; gene expression


Bryant University

Rights Management



The rapid growth and division of cells as they proliferate and penetrate to surrounding tissues defines the collection of disease states known as cancer. Abnormal gene expression drives this uncontrollable replication of cells. In recent studies, aberrant HOX gene expression has been noted in a multitude of cancer types such as myeloid leukemia, prostate cancer, and breast cancer [1]. Within cancerous cells with aberrant HOX expression, late expressing HOX genes are suppressed while early expressing HOX genes are reactivated. HOX genes are significant in controlling early phases of organismal development such as cell cycle, cell movement, and gene expression. Likewise, HOX genes are in later embryonic stages are important for regulation of limb development, body spatial plan formation, and apoptosis processes. As stated above, HOX genes that are expressed early in development tend to regulate cell cycle, differentiation, and migratory processes, mechanisms commonly manipulated by cancer. There are various essential factors that determine the regulation of these genes and their expression levels. One aspect that is considered a master regulator is organization of the chromatin containing genes. Specifically, gene expression is dependent on how tightly or loosely they are packaged in chromatin (DNA plus certain proteins). Genes that are expressed tend to be more open (loosely) allowing for regulatory proteins to bind to chromatin sequence driving generation of their encoded product. Moreover, the tightly packed chromatin results in subsequent gene product to not be produced. Many studies have demonstrated that alterations in the spatial architecture of chromatin results in improper regulation in cancer cells. Likewise, aberrant HOX genes have been readily present in sample of cancerous cells. Therefore, the hypothesis for the following thesis is that organization of chromatin is a critical regulator for HOX genes and mutations in the structure of the chromatin leads to abnormal HOX gene expression. Using zebrafish embryos and cell lines we generated a map of contact points made between chromatin loops within topological associated domains of hox genes with the circular chromosome conformation capture (4C) technique (AIM1). These contact points were further analyzed with a comparative genomic profile to other fish species to identify the binding sites for key regulatory proteins (AIM2), which was tested functionally in future experimentation. Future studies can use the significant information collected through sequencing and analysis techniques in this thesis to expose the connection between HOX expression and disease state formation.

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