Speaker: Dr Matthew Simon, Associate Professor - Department of Molecular Biophysics and Biochemistry, Yale University

Title: Chemical tools to study the dynamics of the transcriptome

Abstract: The expression of different cellular RNAs is regulated by controlling the rates of synthesis and decay. This regulation occurs at many steps in RNA metabolism, starting with the accessibility of transcription start sites in chromatin and extending to polymerase dynamics, RNA processing, transport and degradation. Teasing apart the different strategies a cell uses to regulate gene expression requires methods to monitor the flux of RNAs through these many regulated steps. Cellular RNAs can be monitored through metabolic labeling using thiolated nucleosides including 4-thiouridine (s4U) and 6-thioguanosine (s6G). We have developed chemistry in two areas to provide new insight into RNA metabolism. First, we have developed improved methods to biochemically enrich these metabolically labeled transcripts, reducing bias and increasing yields. Second, we have developed chemistry to recode the hydrogen bonding pattern of s4U and s6G nucleotides in metabolically labeled RNA, converting them into cytosine and adenosine analogues, respectively. This TimeLapse-seq approach allows the identification of newly transcribed RNAs directly in a sequencing experiment without the need for biochemical enrichment. Together these approaches can be used to study RNA metabolism across a wide range of time scales providing new insight into regulated gene expression.