Chromatin Modification and Pre-Messenger RNA Splicing

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Since the 2001 announcement of the sequence of the human genome, it has become evident that the next step toward understanding the genome is answering the fundamental questions: "How does the information contained within the genome get expressed, and how is the correct expression of each gene controlled?" Two features of the genome make this a particularly intriguing problem. First, human genes (and genes from other eukaryotic organisms) are interrupted by long stretches of non-coding DNA sequence. Once the DNA is "read" by the cellular machinery and transcribed to make "messenger RNA" (the intermediate information-containing genetic material that directs protein synthesis), these long stretches of non-coding RNA must be removed, and the remaining protein-coding regions must be joined. This cellular process, "pre-messenger RNA splicing," takes place with exquisite accuracy and is crucial for proper gene expression. The second notable feature of the genome is that the DNA is packaged in a compact protein/DNA structure called chromatin. In order for the DNA sequence to be transcribed to make messenger RNA, the chromatin must undergo extensive modification that alters the DNA packaging and makes the DNA accessible. This change in DNA accessibility plays a pivotal role in regulating RNA synthesis. While the reactions involved in gene expression have typically been studied independently, as isolated processes, recent studies have illustrated that RNA synthesis and splicing are, in fact, tightly coordinated: the splicing reaction occurs as the RNA is being synthesized. Consequently, the RNA synthesis reaction can affect the process of splicing, and pre-mRNA splicing can affect RNA synthesis. Given these connections between pre-mRNA splicing and RNA synthesis, one might expect connections between the RNA synthesis machinery's ability to navigate chromatin structure and synthesize messenger RNA, and the coordinated removal of introns by the splicing machinery. Using the biochemically and genetically tractable model organism, the yeast Saccharomyces cerevisiae, this project will explore the basic mechanisms underlying gene expression by analyzing the coordination between the pre-mRNA splicing machinery and the chromatin modifying and chromatin restructuring machineries.