Large scale identification and analysis of human transcriptional regulatory elements

Almost every cell in the human body contains the same genetic information, yet we develop from a single-celled embryo into an organism comprised of many types of cells with diverse structures and functions. Transcription is one step at which the progress from DNA content to differentiated cell is regulated. My thesis focuses on the study of transcriptional regulatory elements in the human genome. The first part of the thesis is a study of how polymorphisms in a transcriptional regulatory element of a single important gene can heritably affect transcription and have significant links to disease susceptibility. Such studies reinforce the importance of identifying and understanding regulatory elements. The second part of this work focuses on multiple approaches for identifying and analyzing regulatory elements on a large scale. In the first approach, we relied on available mRNA sequences to predict the locations of human promoters; we followed with extensive experimental testing of those predictions and the behavior of the fragments identified. In addition to yielding more information about promoters in general, this data highlighted the abundance of a unique class of promoters: bidirectional promoters. We further explored of this unique group of elements. Finally, I had the opportunity to build on and optimize a promoter trapping technology previously developed in the lab, while I also built a new version of the trapping system for rapid isolation of long-range positive regulatory elements from random genomic fragments. I used both of these trapping technologies to identify new elements in the CFTR region of the human genome.