Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Cell & Molecular Biology

First Advisor

Arjun Raj


A major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor binding events. In concert with RNA-sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short duration treatments with specific perturbations. Here, we used tandem, bulk ATAC-seq and RNA-seq measurements from MCF-7 breast carcinoma cells to systematically evaluate the concordance between changes in accessibility and changes in expression in response to retinoic acid and TGF-β. We found two classes of genes whose expression showed a significant change: those that showed some change in accessibility of nearby chromatin, and those that showed virtually no change despite strong changes in expression. The peaks associated with genes in the former group had a lower baseline accessibility prior to exposure to signal. Analysis of paired chromatin accessibility and gene expression data from distinct paths along the hematopoietic differentiation trajectory showed a much stronger correspondence, suggesting that the multifactorial biological processes associated with differentiation may lead to changes in chromatin accessibility that reflect rather than drive altered transcriptional status. Together, these results show many gene expression changes can happen independent of changes in accessibility of local chromatin in the context of a single-factor perturbation and suggest that some changes to accessibility changes may occur after changes to expression, rather than before.Furthermore, we establish the role of cell-intrinsic differences in clonal melanoma cell lines leading to a rare subpopulation of cells that demonstrate invasive behavior both in vitro and in vivo. This population is molecularly characterized by the high expression of SEMA3C, and knockout studies demonstrate that the formation of the invasives subpopulation is negatively regulated by the transcription factor NKX2.2. Overall, these results establish a role for non-genetic differences in important cancer attributes such as cellular invasion.

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