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An important type of nuclear organization known as somatic homolog pairing occurs in Diptera, in which homologous chromosomes are stably paired in somatic cells. As with other aspects of genome organization, somatic homolog pairing plays important roles in gene regulation and genome stability. Over a century after its discovery, the mechanism underlying somatic homolog pairing remains unclear. In this study, I develop an image analysis pipeline for three-dimensional signals and use the pipeline to test the impact of several factors on the closeness of paired homologs in D. melanogaster embryos. I explore factors previously suggested to play a role in mediating pairing, including developmental time, insulator elements, and transcriptional activity, by testing whether manipulating these variables alters the distance between paired homologous chromosomes. My results suggest that pairing proximity remains consistent over developmental time and that the activity of a single element with insulator properties is insufficient to alter interhomolog distance. I present results indicating that regions with high transcriptional activity correspond to greater interhomolog distance when compared to regions with low transcriptional activity, supporting a model in which chromatin is locally decompacted to enable transcription. These results suggest that the interlaced relationship between nuclear organization and gene expression within the single chromosome may, in turn, impact the nuclear organization of homologs relative to each other. Ultimately, this study provides insight into the methods that can be used for analyzing 3D images, clarifies assumptions about factors involved in pairing, and suggests a role for transcriptional activity in pairing proximity.
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