2 research outputs found
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Utilizing cell-specific chromatin accessibility states to understand appendage patterning and diversification in Drosophila Melanogaster
During development DNA-binding transcription factors are deployed downstream of patterning events to enable specific gene regulatory programs that define diverse cell identities. Within a given eukaryotic cell only a subset of potential binding targets in the genome, called cis-regulatory modules, are available due to the distribution of nucleosomes which restrict access to the underlying DNA. The accessible landscape of cells is highly dynamic over time and across different cell types, although how this process is regulated and influences the function of transcription factors in patterning of complex tissues is not well understood. In this thesis I focused on dissecting the cell type-specific chromatin accessibility landscapes that distinguishes different cell populations within the Drosophila dorsal appendages. The patterning of this system is extremely well characterized allowing for a detailed understanding of how transcription factors at the top of cell fate hierarchies influence, or respond to, the chromatin landscape during development.
In Chapter 2 I describe the differences in chromatin accessibility along the proximal-distal axis of the wing imaginal disc which gives rise to distinct populations of the thoracic body wall and appendage in the second thoracic segment (T2). I found that a major driver of chromatin differences in these populations is the repressive input of the conserved insect wing marker Nubbin, whose function in the appendage is associated with decreasing accessibility of select chromatin regions relative to their conformation in body wall cells. In Chapter 3 I characterized the serially homologous body wall and appendage cells in the adjacent third thoracic body segment (T3), which diverge extensively in morphology from the T2 state due to influence of a single gene, Ultrabithorax (Ubx). Ubx is a member of the Hox gene family which functions to provide cells with spatial identity along the anterior-posterior axis. I show this function for Ubx in specifying T3 cells coincides with widespread changes to chromatin accessibility which contribute to a segment and cell type-specific regulatory program
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Accurate and sensitive quantification of protein-DNA binding affinity
Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes