UC Berkeley

Enhancers are non-coding DNA elements found throughout the genome that, in concert with transcription factors, coactivators, and general transcriptional machinery, activate cell-type specific gene expression. Initial studies on enhancers demonstrated these regulatory elements contained clusters of transcription factor binding sites to recruit endogenous transcription factors and drive elevated expression of a target gene . These early works highlighted that theirregulatory activity was maintained despite alterations in their orientation and/or positioning relative to the targeted gene. Nearly half a century later, enhancers are center stage in efforts to characterize the regulatory components and mechanisms behind development and disease. This dissertation is a study on mammalian enhancers, the genome-wide approaches for their identification, and their contributions in early developmental processes. Chapter 1 provides an overview of the enhancer properties uncovered from various experimental systems and how these properties are harnessed to predict and further dissect enhancer activity. Chapters 2 and 3 comprise two separate projects that involve 1) an extensive in vivo assessment of active enhancers that are hidden from canonical biochemical-based methods for enhancer identification and 2) the characterization of tissue-specific enhancers across the Shox2 locus that regulate early heart, face, and limb development. Altogether these works demonstrate the critical roles of enhancers for normal organismal development and the ongoing challenge of mapping increasingly large datasets to insights on enhancer prediction and function.