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Nuclear Organization And The Epigenetic Landscape Of The Mus Musculus X-Chromosome, Alicia Liu

Doctoral Dissertations

X-linked imprinted genes have been hypothesized to contribute parent-of-origin influences on social cognition. A cluster of imprinted genes Xlr3b, Xlr4b, and Xlr4c, implicated in cognitive defects, are maternally expressed and paternally silent in the murine brain. These genes defy classic mechanisms of autosomal imprinting, suggesting a novel method of imprinted gene regulation. Using Xlr3b and Xlr4c as bait, this study uses 4C-Seq on neonatal whole brain of a 39,XO mouse model, to provide the first in-depth analysis of chromatin dynamics surrounding an imprinted locus on the X-chromosome. Significant differences in long-range contacts exist between X^M and X …

Linear Methods For Joint Analysis Of Multivariate Genomics Data, M. Henry Linder

Doctoral Dissertations

The rise of Big Data has enabled sophisticated analysis of the human genome in unprecedented detail. Large datasets are now collected as a matter of routine, and their scope spans multiple data types and multiple functional units at the molecular level of the cell. The breadth and depth of these data offer the opportunity for complex experiments and extensive structural modeling. But, given the intricacies of these data and the nuanced challenges they pose, robust and rigorous methods are essential to ensure the value and validity of the resulting scientific research. In this dissertation, we consider statistical methods for networks, …

Assembling The Puzzle Of An Enigmatic Shark Tapeworm: A Comparative Genomic And Transcriptomic Approach, Kaitlin Gallagher

Doctoral Dissertations

The evolution of novelty among closely related taxa is a phenomenon that has occurred repeatedly within parasitic clades, however, the mechanisms that underlie the evolution of such innovations is not fully understood. This dissertation explores one example of this phenomenon that occurs in a monogeneric order of tapeworms, the Litobothriidea, that infect lamniform sharks. The most recently described member of this group, Litobothrium aenigmaticum, lacks all the characters typically demonstrated by members of this group, yet it robustly nests within the genus Litobothrium with the barcoding gene 28S rDNA (D1-D3). The aim of this dissertation was to investigate which …

3d Genome Organization And Transcriptional Regulation In Mammalian Cells, Emaly Piecuch

Doctoral Dissertations

Remarkably, cell types sharing the same linear genome sequence express different genes and have distinct functions. 3D genomic arrangement has been demonstrated to play a critical role in this process. Fine scale organization of genes and regulatory elements within active and inactive domains underlie gene expression and disruption of this process has been shown to influence development and disease. Yet, the precise dynamics of cell type specific 3D genomic interactions mediating mammalian gene expression, such as those between enhancers and promoters, remain lacking on a genome wide level.

Neurons represent a specialized cell type known to respond to a myriad …