UCSF

The development of an organism from conception to adulthood requires the specification of cell types to distinct fates. In an adult organism, tissues can similarly undergo dramatic transformation, altering their structure, physiology, and overall biochemical properties. In both of these paradigms, the study of gene transcription and its contribution to protein content in the cells has been the primary focus. While clearly important, more recently, alternative splicing and microRNA regulation have been recognized as significant processes that can have crucial regulatory influences on the diversity of mRNAs produced and their over-all expression in the cell.

In this dissertation, I have set out to characterize the molecular changes that occur in two distinct cellular paradigms, muscle remodeling in the uterus throughout pregnancy and the differentiation of embryonic stem cells to distinct fates using DNA microarray technology. To achieve this goal, I developed several new software applications, designed specifically to assess the relevance of coordinated gene regulatory events along biological pathways (GenMAPP and GO-Elite) and characterize sequence level functional attributes of proteins and mRNAs regulated by alternative splicing (AltAnalyze).

Studies of the mouse uterus during gestation reveal novel coordinated transcriptional networks regulating quiescence, contraction, and involution when multiple time-points are considered. Analysis of alternative splicing in mouse and human embryonic stem cell differentiation uncovered novel mechanisms for the regulation of protein domain and microRNA binding site inclusion and at least for one gene, Tcf3, the requirement of splicing to properly promote the early steps of embryonic lineage commitment down multiple paths. In summary, I have used novel computational methods and genomic resources to uncover new regulatory networks and potential biological mechanisms from both differentiating and transitioning cells, that involve regulation at the level of transcription, alternative splicing, and translational regulation by micoRNAs.