Date of Award

Spring 5-15-2012

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Computational & Systems Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Using yeast S. cerevisiae GAL1-10 intergenic region as a model, I systematically introduced point mutations to the entire ~630 bp regulatory region and implemented a dual-color reporter gene assay which detects expression variation as small as 10%. Using this system, I quantitatively analyzed the relationship between sequence conservation and expression variation at single nucleotide resolution, and found that most (81%) rSNPs reside in conserved regions. I discovered a previously underappreciated regulatory signal-- upstream AUG (uAUG) in the 5'UTR. Using combined computational and experimental approaches, I demonstrated that uAUG is a potent and universal regulator of gene expression in yeast genome.

To identify rare variants enriched genes associated with neonatal respiratory distress syndrome (RDS), I applied the "candidate gene, pooling-sample" approach using next generation sequencing. By deep sequencing 27 genes involved in physiologically-relevant pathways in 843 RDS-affected and unaffected newborns, I identified enrichment patterns of rare variants that implicated several genes, including ABCA3, SCNN1D, SFTPB and SFTPD. Genotyping validation on ABCA3 in an African American population further confirmed our sequencing results. Interestingly, the directionality of SNP enrichment ¬ - deleterious or protective - was, in some cases, opposite in different populations; suggesting the complex effects of rare variants on disease association. This dissertation presents both novel methodology and novel biological insights furthering our understanding of molecular mechanisms of complex human diseases.


English (en)

Chair and Committee

Robi D Mitra

Committee Members

F Sessions Cole, Justin C Fay, John E Majors, Elaine R Mardis, Gary D Stormo


Permanent URL:

Available for download on Sunday, May 15, 2112

Included in

Biology Commons