Genome-Wide Study of mRNA Isoform Half-Lives

In eukaryotes, RNA polymerase II-driven transcription and processing results in the formation of numerous mRNA 3' isoforms that for any given gene may differ from one another by as little as a single nucleotide. These 3' isoforms can vary in physical properties that may affect their function and stability. Here, we outline a systematic framework to measure individual mRNA 3' isoform half-lives on a genome-wide level in S. cerevisiae. Our approach utilizes the Anchor-Away system to sequester RNA polymerase II (Pol II) in the cytoplasm followed by direct single-molecule RNA sequencing to generate a highly detailed view of 3' isoform stability under most physiological conditions without many of the adverse effects associated with commonly used alternative approaches.