Development of Genomics and Bioinformatics Tools to Elucidate Alternative Splicing and Gene Expression Networks in Human Embryonic Stem Cells
The hundreds of different cell types in the human body – each with its own functional characteristics – ultimately all derive from a single type of undifferentiated precursor cell in the embryo, the pluripotent human embryonic stem cell (hESC). hESCs can proliferate indefinitely while maintaining their capacity to give rise to all cell types in the body, a process known as self-renewal. Upon appropriate developmental triggers, hESCs differentiate to generate the more specialized cells of the body, such as blood cells or cells of the nervous system. Understanding the processes governing hESC self-renewal and differentiation are critical for understanding basic mechanisms of developmental biology, and moreover will illuminate the pathways that go awry in human developmental diseases. We hope to gain a comprehensive knowledge of such processes with the ultimate goal of identifying strategies for therapeutic intervention.
The genetic information in the human genome resides in units of DNA known as genes. Information from the DNA is converted to an intermediate called messenger RNA (mRNA), which in turn is used as a template for synthesizing the cell’s proteins. Almost all the approximately 25,000 genes in humans are composed of discontinuous building blocks known as exons. These exons are interleaved with intervening segments called introns. In a process known as RNA splicing, the exon segments are made continuous through the removal of the intervening introns. Alternative splicing refers to a mechanism by which the exons within a given gene are mixed and matched in any number of different combinations. This process of mixing and matching of exons results in an increase in the number and diversity of proteins encoded by the genes in the human genome. The pattern in which different exons of individual genes are spliced together in different cell types underlies the diversity and function of specialized cells and tissues of the body. Importantly, 30-40% of known mutations causing human diseases are thought to involve the mRNA splicing process. Thus, understanding the nature of alternative splicing events in human pluripotent stem cells is crucial not only for understanding how alternative splicing regulates cell differentiation, but also how defects in alternative splicing cause inherited human diseases.
We propose to develop new tools and computational methods for studying alternative splicing in human pluripotent stem cells. Our approach will leverage and apply the latest technological advances in studying gene expression in complex systems. The anticipated developments should be broadly applicable to a wide range of models of stem cell biology and human disease.
The proposed project will benefit the State of California in two major ways. First, the tools and technologies we plan to develop will allow new and fundamental insights into the biological processes underlying human stem cell biology. Second, these technological advances will place scientists in California in the unique and enviable position of applying this knowledge to elucidate the causes of certain inherited human diseases and devising novel strategies for their treatment.