Functional and Mechanistic Analyses of Neural-regulated Alternative Splicing

Recent applications of genome-wide approaches to profile the transcriptomes of cells and tissues have provided novel insights into the regulatory principles governing the dynamic control of gene expression. Such global analyses have revealed that alternative splicing (AS) of precursor messenger RNAs, a fundamental process by which cells can expand their transcriptomic diversity from a limited number of genes, occurs in ~95% of human multi-exon genes with the highest frequency observed in the brain. A current goal in the field is to determine how these alternative exon networks are coordinated and contribute to neural functions. Previously, we identified the vertebrate and neural-specific Ser/Arg-related protein of 100 kDa (nSR100/SRRM4) as a novel splicing factor that promotes the inclusion of a subset of brain-specific exons with critical functions in nervous system development. In this thesis, I describe an in-depth investigation of the roles of individual nSR100-dependent splice variants, and the mechanisms by which nSR100 activates its target exon network during neurogenesis. My results uncover an important nSR100-dependent neural AS event in the transcription factor REST/NRSF that modulates its activity and influences the expression of REST targets. I further discuss how the coordination of the AS and transcriptional regulatory layers impact neuronal differentiation. Finally, I describe how I combined multiple experimental and bioinformatic analyses to elucidate important mechanistic features underlying positive and negative regulation of the nSR100-dependent exon network. At the heart of this regulation is an intronic cis-element that can contribute to exon skipping and inclusion depending on the cellular context. Collectively, these studies have advanced our understanding of the functions of nSR100 and its target exons in neural development.Ph.D