Functional genomics in mouse embryonic stem cells

Embryonic stem (ES) cells have unique capacities of self-renewal and differentiation into other cell types. ES cells are widely used for studies of development processes and thought to provide a system for design of novel transplantation therapies. Perspective biomedical and research applications require an understanding of mechanisms that maintain the unique properties of these cells. Here we present development and application of novel methods for large-scale functional analyses in ES cells.;In Chapter 1, we describe a novel method of genome-wide functional analysis that combines gain-of-function genetic screen and microarray detection. Using this method, we identify a number of genes that regulate self-renewal and differentiation of mouse ES cells. The identified genes encode a variety of regulatory proteins and their function in ES cells was previously unknown. The results of these studies establish a novel method of genome-wide functional analysis and provide an insight into the regulatory mechanisms of ES cells.;In Chapter 2, we combine computational and experimental methods to identify splice variants in embryonic and hematopoietic stem cells on a genome-wide scale. We also analyze the distribution of splice variants across different classes of genes. We find that tissue-specific genes have a higher tendency to undergo alternative splicing than ubiquitously expressed genes. Furthermore, the patterns of alternative splicing are only weakly conserved between orthologous genes in human and mouse. Our studies provide an insight into its overall role of alternative splicing as a mechanism of generating genomic diversity.;In Chapter 3, we describe a novel computational method for a comprehensive identification of transcription factor (TF) binding sites in the genome of Saccharomyces cerevisiae. These studies provide a methodology for identification of cis-regulatory elements from computational comparison of evolutionarily close genomes. The common theme of the presented studies is obtaining systematic knowledge of different aspects of gene function and regulation. Further development of these methods will enable comprehensive description of biological mechanisms, which is necessary for a deep understanding of development processes and design of future therapies.