<p>After finishing a human genome reference sequence in 2002, the genomics community has</p><p>turned to the task of interpreting it. A primary focus is to identify and characterize not only</p><p>protein-coding genes, but all functional elements in the genome. The effort has identified</p><p>millions of regulatory elements across species and in hundreds of human cell-types. Nearly</p><p>all identified regulatory elements are found in non-coding DNA, hypothesizing a function</p><p>for previously unannotated sequence. The ability to identify regulatory DNA genome-wide</p><p>provides a new opportunity to understand gene regulation and to ask fundamental questions</p><p>in diverse areas of biology.</p><p>One such area is the aim to understand the molecular basis for phenotypic differences</p><p>between humans and other primates. These phenotypic differences are partially driven</p><p>by mutations in non-coding regulatory DNA that alter gene expression. This hypothesis</p><p>has been supported by differential gene expression analyses in general, but we have not</p><p>yet identified specific regulatory variants responsible for differences in transcription and</p><p>phenotype. I have worked to identify regulatory differences in the same cell-type isolated</p><p>from human, chimpanzee, and macaque. Most regulatory elements were conserved among</p><p>all three species, as expected based on their central role in regulating transcription. How-</p><p>ever, several hundred regulatory elements were gained or lost on the lineages leading to</p><p>modern human and chimpanzee. Species-specific regulatory elements are enriched near</p><p>differentially expressed genes, are positively correlated with increased transcription, show</p><p>evidence of branch-specific positive selection, and overlap with active chromatin marks.</p><p>ivSpecies-specific sequence differences in transcription factor motifs found within this regu-</p><p>latory DNA are linked with species-specific changes in chromatin accessibility. Together,</p><p>these indicate that species-specific regulatory elements contribute to transcriptional and</p><p>phenotypic differences among primate species.</p><p>Another fundamental function of regulatory elements is to define different cell-types in</p><p>multicellular organisms. Regulatory elements recruit transcription factors that modulate</p><p>gene expression distinctly across cell-types. In a study of 112 human cell-types, I classified</p><p>regulatory elements into clusters based on regulatory signal tissue specificity. I then used</p><p>these to uncover distinct associations between regulatory elements and promoters, CpG-</p><p>islands, conserved elements, and transcription factor motif enrichment. Motif analysis</p><p>identified known and novel transcription factor binding motifs in cell-type-specific and</p><p>ubiquitous regulatory elements. I also developed a classifier that accurately predicts cell-</p><p>type lineage based on only 43 regulatory elements and evaluated the tissue of origin for</p><p>cancer cell-types. By correlating regulatory signal and gene expression, I predicted target</p><p>genes for more than 500k regulatory elements. Finally, I introduced a web resource to</p><p>enable researchers to explore these regulatory patterns and better understand how expression</p><p>is modulated within and across human cell-types.</p><p>Regulation of gene expression is fundamental to life. This dissertation uses identified</p><p>regulatory DNA to better understand regulatory systems. In the context of either evolution-</p><p>ary or developmental biology, understanding how differences in regulatory DNA contribute</p><p>to phenotype will be central to completely understanding human biology.</p> / Dissertation

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