Matteo Ruggiu

Associate Professor

The genetic information of an organism is stored in genes, the functional units of the genome that are encoded in the DNA of that organism. This information is transcribed from DNA into messenger RNA (mRNA) and then translated into proteins. In eukaryotes, however, the noncoding parts of a transcript — called introns —  need to be excised and the coding parts — called exons — need to be joined together to produce a mature mRNA. This trimming process is called splicing, and it is regulated by proteins called splicing factors that bind to specific regulatory sequences on the precursor mRNA. Splicing of the same transcript in different ways is referred to as alternative splicing, and alternative splicing allows a single gene to code for many proteins, thus generating complexity in organisms, as well as tissue and cell specificity. That is, how to generate a nerve cell and a muscle cell starting from the same set of genes.

The sequencing of the human genome revealed that humans have about the same number of genes as less complex organisms such as worms and flies and that, unexpectedly, the number of genes does not correlate with organismal complexity. To generate organismal complexity, it is not the amount of information of a genome that matters, but rather its functional information capacity: how that information is used, and how the flow of information is regulated. Alternative splicing —the inclusion or skipping of different exons in mRNA— has evolved as a versatile strategy of gene regulation, modulating the expression of various protein isoforms with distinctive new functions in different tissues and/or at different developmental times without the need to increase the number of genes and without affecting existing proteins.

Tissue-specific splicing patterns require direct interaction between cis-acting RNA sequences —enhancers and silencers— and trans-acting protein factors to promote inclusion or skipping of alternatively spliced exons. Interestingly, the number of alternative splicing events in eukaryotes has steadily increased during evolution and is strongly associated with organism complexity, suggesting that alternative splicing is critical in generating proteome diversity and tissue specificity. Consistent with this view, ~90% of human genes undergo alternative splicing, and disruption of splicing can cause disease. In fact, as many as 50% of disease-causing point mutations in humans affect alternative splicing, and an unexpectedly large fraction of exonic mutations cause disease by affecting the splicing code, and not by interfering with the protein code.

The central nervous system comprises the tissues and cells with the highest rate of alternative splicing in the body, and RNA-binding proteins play a major functional role in neurons in both normal conditions and in disease. To better understand the contribution of RNA processing to nerve cell biology, and to help elucidate the function that RNA processing regulators play in neuron physiology and neurologic disorders it is necessary to identify which RNA-binding proteins are involved in these biological pathways, and to characterize how they work at the molecular level.

In my lab we are studying protein-RNA networks that control alternative splicing, and how they relate to neurons and to diseases of the nervous system. Our long-term goal is to understand the molecular mechanisms regulating protein-RNA networks that control alternative splicing, and how they relate to neuron biology, and to disease of the nervous system. Given the universality of alternative splicing and the central role it plays in controlling gene expression, it is critical that we acquire a better understanding of the mechanisms regulating alternative splicing. In turn, a better understanding of how the splicing code is fine-tuned may hold promise for treating many types of diseases.

This work is funded by a grant from the National Institutes of Health.