Investigating the coordination of transcription and RNA splicing via chromatin modification

Abstract

All cells need to be able to respond to changes in their environment. The process that cells use to respond to environmental stimuli is gene expression, in which certain genes are expressed to generate the proteins required to mount the response. There are several steps in the gene expression pathway and we are interested in understanding how these steps are coordinated to allow for fast and accurate expression of genes. Transcription is the step where an RNA copy of the DNA (gene) is produced. Another critical step is RNA splicing, where the non-protein coding introns are removed from the RNA molecule an the protein-coding exons are fused together. Splicing can happen cotranscriptionally, which raises the question can transcription impact splicing. Transcription happens in context of chromatin that consists of the DNA wrapped around histone. These histones can be methylated in a process known as chromatin modification, and this modification of the chromatin facilitates transcription. We are interested in investigating whether transcription and RNA splicing can be coordinated via chromatin modification. Although there are many different sites that can be methylated, we are looking at histone3 on lysine 36 (H3K36). Our lab has already implicated the Set2 histone methylase in RNA splicing. There are two main demethylases, Jhd1 and Rph1. Our current work is testing whether histone demethylation is important for splicing. Here we show that there is a modest positive genetic interaction between the splicing gene ISY1 and both RPH1 and JHD1, which indicates they are impacting the same function. To test the hypothesis that Jhd1 and Rph1 might be substituting for each other (e.g. Rph1 can demethylate histone when Jhd1 is absent) we have created triple mutant yeast that are missing the ISY1 gene as well as RPH1 and JHD1. In this triple mutant we observe a stronger positive genetic interaction, which supports our hypothesis. We plan to test for changes in RNA splicing in this triplemutant in the future.. In addition, we tested the hypothesis that interfering with RNA splicing can alter the rate of transcription. Our preliminary finding show that deletion of ISY1 can speed up transcription rate. Thus, we provide evidence that histone methylation is linked to RNA splicing and that RNA splicing can regulatetranscription.