Laboratory Funding

ProjectYearProject TitleContact PI/Project
GM1257221GENOME-WIDE STRUCTURAL ORGANIZATION OF PROTEINS WITHIN HUMAN GENE REGULATORY COMPLEXESMahony, Shaun
ABSTRACT: The DNA sequence of the human genome informs us as to the composition of proteins that make up healthy cells, but also altered compositions that create diseased cells. How protein production is controlled through the regulation of the genes that encode them is of critical importance for healthy and diseased cells. Knowing precisely where gene regulatory proteins bind, and are organized throughout the genome, including their interactions with each other, informs us as to how genes are regulated and mis-regulated. Since there are potentially thousands of different kinds of regulatory proteins and thousands of different kinds of human cell types and environmental responses that are a product of various subsets of regulatory proteins, the entire “universe” of gene regulatory events is quite substantial and consequently, quite costly to identify. A subset of these events will likely be informative or diagnostic of diseases states. Therefore, an important goal is to define informative interactions using cost-enabling, high accuracy, and robust genome-wide assays.
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ProjectYearProject TitleContact PI/Project
ES01376812PROMOTER REGULATION IN RESPONSE TO ENVIRONMENTAL STRESSPUGH, B FRANKLIN
ABSTRACT: The regulation of eukaryotic genes involves many hundreds of proteins. How they work together at the many thousands of genes that comprise a genome is not known. In order to obtain a comprehensive understanding of how all genes are regulated, we need to know the precise spatial organization, structure, and occupancy levels of all involved proteins. We have developed a genome-wide assay, called ChIP-exo, to measure these aspects of genome regulation, and now propose to develop a higher-throughput version of the assay, and apply it to the mapping of hundreds of genome-binding proteins (aim 1). The goal of aim 2 will be to create a user-friendly, quickly-navigable, platform to execute scripts on ChIP-exo and related data, using our established pipeline. Public use utility of the ChIP-exo datasets will be enhanced with a dedicated platform.
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ProjectYearProject TitleContact PI/ Project Leader
GM05905518GENOME-WIDE REGULATION OF THE TATA BINDING PROTEINPUGH, B FRANKLIN
ABSTRACT: Human health is highly dependent upon proper gene expression. Understanding how genes are regulated is critical in our understanding how mis-regulation leads to diseases. One major point where genes are regulated is during the assembly of the transcription machinery. This project is focused on understanding the molecular events that govern the assembly of the transcription machinery at promoters.
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LINK TO PUBLICATIONS


ProjectYearProject TitleContact PI/Project
HG00416011HIGH RESOLUTION MAPPING OF FUNCTIONAL ELEMENTS IN THE YEAST GENOMEPUGH, B FRANKLIN
ABSTRACT: Eukaryotic DNA is packaged into chromatin, and this chromatin has a well-defined organization. Chromatin is composed of nucleosome building blocks, whose positioning along the DNA dictates the accessibility of gene regulatory elements, and ultimately the expression levels of genes. Nucleosomes occur in regular repeating intervals on genes. These arrays are highly regulated through many mechanisms including: post- translational modifications, deposition and eviction that are facilitated by chaperones, and re-positioning facilitated by chromatin remodeling complexes. We propose to further our understanding of nucleosomal arrays on a genomic scale.
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LINK TO PUBLICATIONS


Patent NumberPatent TitlePatent OwnerPrimary Agency
8367334Methods, systems and kits for detecting protein-nucleic acid interactionsPENNSYLVANIA STATE UNIVERSITYNIH