The dissection of VEGFA stimulus-responsive regulatory and transcriptional changes in angiogenesis

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.

Department dc:contributor.department

Harvard--MIT Program in Health Sciences and Technology.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2015

Author dc:creator

• Day, Daniel S. (Daniel Sindt)

Advisor dc:contributor.advisor

• Peter J. Park.

• Harvard--MIT Program in Health Sciences and Technology.

Statement dc:rights

• 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.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/98726

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/98726