Cells and organisms function based on the expression patterns, actions, and interactions of thousands of genes and their products. A tremendous amount of work has gone into  dissecting the transcriptional regulatory and protein interaction networks that drive cell function. However, one important aspect of gene regulation is often overlooked in these studies - alternative splicing. Alternative splicing is the process by which exons can be joined together in different patterns to generate multiple mRNAs from a single gene. Alternative splicing is a tremendously important mechanism by which eukaryotes regulate gene expression and is the primary means of enhancing the diversity of proteins encoded by the genome. It is currently estimated that as many as 75% of human genes encode pre-mRNAs that are alternative spliced to generate multiple mRNAs, each of which can potentially encode a protein with a distinct function. Thus, just like transcription regulation, alternative splicing can function as a developmental switch.

    A number of microarray studies have been conducted to identify a set of “stemness” genes - genes that are expressed in and define the core gene regulatory program for all types of stem cells. While these studies have led to the identification of a number of genes that play important roles in controlling various aspects of stem cell biology, they have not examined alternative splicing in stem cells. Thus, a crucial aspect of the gene regulatory programs of all types of human stem cells have been overlooked.

    The goal of our work is to fill this gap by performing expression profiling experiments of hES cells in their undifferentiated state and as they differentiate down different lineage pathways using microarrays that can monitor alternative splicing and to elucidate the role of specific RNA binding proteins in controlling alternative splicing in hES cells. These experiments should lead to a more complete understanding of the gene expression programs of hES cells which is critical to our ability to guide stem cells down different lineage pathways and to realizing the full therapeutic potential of hES cells.