Transcriptional and structural control of cell identity genes

Mammals contain a wide array of cell types with distinct functions, yet nearly all cell types have the same genomic DNA. How the genetic instructions in DNA are selectively interpreted by cells to specify various cellular functions is a fundamental question in biology. This thesis work describes two genome-wide studies designed to study how transcriptional control of gene expression programs defines cell identity. Recent studies suggest that a small number of transcription factors, called "master" transcription factors, dominate the control of gene expression programs. These master transcription factors and the transcriptional regulatory circuitry they produce, however, are not known for all cell types. Ectopic expression of these factors can, in principle, direct transdifferentiation of readily available cells into medically relevant cell types for applications in regenerative medicine. Limited knowledge of these factors is a roadblock to generation of many medically relevant cell types. Chapter 2 presents a study in which a novel computational approach was undertaken to generate an atlas of candidate master transcriptional factors for 100+ human tissue/cell types. The candidate master transcription factors in retinal pigment epithelial (RPE) cells were then used to guide the investigation of the regulatory circuitry of RPE cells and to reprogram human fibroblasts into functional RPE-like cells. Master transcription factors define cell-type-specific gene expression through binding to enhancer elements in the genome. These enhancer-bound transcription factors regulate genes by contacting target gene promoters via the formation of DNA loops. It is becoming increasingly clear that transcription factors operate and regulate gene expression within a larger three-dimensional (3D) chromatin architecture, but these structures and their functions are poorly understood. Chapter 3 presents a study in which Cohesin ChIA-PET data was generated to identify the local chromosomal structures at both active and repressed genes across the genome in embryonic stem cells. The results led to the discovery of functional insulated neighborhood structures that are formed by two CTCF interaction sites occupied by Cohesin. The integrity of these looped structures contributes to the transcriptional control of super-enhancer-driven active genes and repressed genes encoding lineage-specifying developmental regulators.