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Peter J. Park. Day, Daniel S. (Daniel Sindt) Harvard--MIT Program in Health Sciences and Technology. Harvard University--MIT Division of Health Sciences and Technology 2015-09-17T19:07:45Z 2015-09-17T19:07:45Z 2015 2015 http://hdl.handle.net/1721.1/98726 920873071 Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015. Cataloged from PDF version of thesis. Includes bibliographical references (pages 133-147). Several studies over the past decade have transformed our understanding of the regulatory elements and mechanisms utilized by a human cell to drive cell type identity. In particular, epigenomic studies have revealed recurrent epigenetic signatures at enhancers and other regulatory regions, as well as their role in cellular lineage specification. However, these studies generally focused on steady-state cellular states where much of the lifespan of adult cells involves responding to extracellular cues. To better understand the gene expression changes that occur in response to stimuli, I studied a time-course stimulation of human umbilical vascular endothelial cells (HUVECs) with vascular endothelial growth factor A (VEGFA) as a model system. Using data collected from multiple genome-wide assays I modeled the dynamic changes in epigenetic, transcriptional, and transcription factor binding profiles in regulation of angiogenesis, the formation of new blood vessels. First, I identify regulatory elements involved in VEGFA-response through focal, temporal changes in chromatin structure and that p300 activity is mechanistically required for this response. Secondly, I analyze changes in combinatorial binding of transcription factors linked with VEGFA-responsive enhancers. These studies highlight general strategies to study stimulus-responsive regulatory systems, and reveal new insights into angiogenesis, human disease and therapeutic targets. Finally, I show that VEGFA-responsive genes are regulated by promoter-proximal RNA Polymerase II pausing and extend it to comprehensive analysis of gene expression and chromatin regulation by promoter-proximal pausing across cell types. by Daniel S. Day. Ph.D. 147 pages eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Harvard--MIT Program in Health Sciences and Technology. The dissection of VEGFA stimulus-responsive regulatory and transcriptional changes in angiogenesis Dissection of vascular endothelial growth factor stimulus-responsive regulatory and transcriptional changes in angiogenesis Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="70f8354b-e48e-4336-9d61-ac7a5395444e"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>The dissection of VEGFA stimulus-responsive regulatory and transcriptional changes in angiogenesis</Title> <Subtitle>Dissection of vascular endothelial growth factor stimulus-responsive regulatory and transcriptional changes in angiogenesis</Subtitle> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2015</PublicationDate> <Authors> <Author> <DisplayName>Day, Daniel S. (Daniel Sindt)</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Harvard--MIT Program in Health Sciences and Technology.</Keyword> <Abstract>Several studies over the past decade have transformed our understanding of the regulatory elements and mechanisms utilized by a human cell to drive cell type identity. In particular, epigenomic studies have revealed recurrent epigenetic signatures at enhancers and other regulatory regions, as well as their role in cellular lineage specification. However, these studies generally focused on steady-state cellular states where much of the lifespan of adult cells involves responding to extracellular cues. To better understand the gene expression changes that occur in response to stimuli, I studied a time-course stimulation of human umbilical vascular endothelial cells (HUVECs) with vascular endothelial growth factor A (VEGFA) as a model system. Using data collected from multiple genome-wide assays I modeled the dynamic changes in epigenetic, transcriptional, and transcription factor binding profiles in regulation of angiogenesis, the formation of new blood vessels. First, I identify regulatory elements involved in VEGFA-response through focal, temporal changes in chromatin structure and that p300 activity is mechanistically required for this response. Secondly, I analyze changes in combinatorial binding of transcription factors linked with VEGFA-responsive enhancers. These studies highlight general strategies to study stimulus-responsive regulatory systems, and reveal new insights into angiogenesis, human disease and therapeutic targets. Finally, I show that VEGFA-responsive genes are regulated by promoter-proximal RNA Polymerase II pausing and extend it to comprehensive analysis of gene expression and chromatin regulation by promoter-proximal pausing across cell types.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>