The Regulation of Alternative Pre-mRNA Splicing

Our lab is interested in the regulation of pre-mRNA splicing and the biochemical mechanisms that control changes in mRNA structure and utilization. The sequences of metazoan genomes, with their relatively low gene numbers, have highlighted the question of how protein number can be expanded in complex organisms. Alternative splicing, which allows the generation of multiple mRNAs and hence multiple proteins from a single gene, is a major contributor to protein diversity. In mammals, most genes produce more than one functional protein through this process. Alternative splicing is particularly common in genes expressed in the mammalian nervous system, where it contributes to the enormous functional diversity of neuronal cells. Many genes important for neuronal differentiation and function express isoforms that are specific to neurons or to particular neuronal subtypes. However, despite playing key roles in the developmental control of gene expression, the mechanisms that alter splicing patterns are poorly understood.

Our lab works on a range of projects related to the control of pre-mRNA splicing in neurons and other cells. We aim to determine the mechanisms of action of splicing regulators, as well as to understand their roles in neural development and mature neuronal function. We have long-standing projects focused on two families of regulatory factors: the polypyrimidine tract–binding proteins (PTBP1 and PTBP2), and the Rbfox proteins (1, 2 and 3). Each of these RNA binding proteins alters the splicing of a specific set of gene transcripts in neurons, and each can induce different splicing outcomes depending on its binding context.

Mechanism

In mechanistic studies, we use biochemical methods, tissue culture, and in vitro splicing systems to examine the molecular interactions of splicing regulators and analyze how they can alter spliceosome assembly.

Biology

To understand the biological roles of splicing regulators and their impact on neuronal development and function, we have developed conditional knock out mice for multiple proteins.

Genomewide Analysis

In support of both our mechanistic and biological interests, we make extensive use of genomewide methods to assess the broad programs of gene regulation mediated by RNA binding proteins.