The coordinated regulation of gene expression in a condition- and cell type-specific fashion is fundamental to all organisms and vital to human development and homeostasis. Genome-wide measurements of differential gene expression and transcription factor (TF) binding in vivo have provided important information about how such condition-specific gene regulation is accomplished. However, the condition-specific functions of many TFs, even in the extensively studied unicellular yeast Saccharomyces cerevisiae , remain uncharacterized, and even locating potential regulatory regions in the larger genomes of multicellular organisms presents a formidable challenge. Here, I present work predicting and analyzing condition-specific TF-mediated gene regulation in yeast and exploring the importance of distal regulatory regions in human gene regulation.
I present an algorithm, CRACR, to predict condition-specific functions and target genes of yeast TFs by integrating comprehensive in vitro TF binding specificity data from protein binding microarrays (PBMs) with gene expression data. With CRACR, I predicted novel target genes and condition-specific functions of both poorly annotated and well-characterized factors in a set of 89 yeast TFs. Several of these target genes and functions were experimentally verified. By comparing PBM data with ChIP-chip in vivo TF binding data, I inferred which in vivo bound regions are direct targets of TFs, and investigated yeast TF preferences for single sites or homotypic clusters of binding sites in vivo. Integrating other genomic datasets, I found that biological functions and regulatory mechanisms of TFs are sometimes shared within DNA binding domain structural classes.
To further our understanding of regulatory regions in larger genomes, I analyzed potential cases of distal regulation in human muscle differentiation. I observed myogenic TF binding at predicted cis-regulatory modules (CRMs) distant from gene promoters. With the chromosome conformation capture (3C) method, I found differentiation-specific interactions between two of these distant CRMs and the PDLIM3 and ACTA1 gene promoters. I describe experiments currently underway to characterize the genome-wide interactions of these distal regulatory regions. In the future, combining approaches developed in yeast for detailed analysis of condition-specific TF binding with newly discovered distal regulatory regions in human will lead to a better understanding of gene regulatory mechanisms across organisms.
|Advisor:||Bulyk, Martha L.|
|School Location:||United States -- Massachusetts|
|Source:||DAI-B 71/07, Dissertation Abstracts International|
|Subjects:||Genetics, Bioinformatics, Biophysics|
|Keywords:||DNA sequence specificity, DNA-binding proteins, Data integration, Distant enhancers, Gene regulation, Genomics, Transcription factor|
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