Genome‐Wide Mapping of RNA Polymerase II Termination Sites

Abstract

We have used in vivo RNA cross‐linking to map the position of RNA polymerase II (Pol II) in the yeast S. cerevisiae. Pol II terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non‐coding transcripts through the non‐polyadenylation (non‐pA) pathway. Using PAR‐CLIP we have mapped the position of Pol II genome‐wide in living yeast cells after depletion of components of either the pA or non‐pA termination complexes. The results indicate that depletion Nrd1, a non‐poly(A) termination factor leads to widespread read through of non‐pA terminators. Depletion of the RNA helicase Sen1 also leads to read through at non‐pA terminators. In contrast to Nrd1 this read through appears more susceptible to pausing. These results provide a map of in vivo Pol II non‐pA termination regions and reveal sequences that signal termination of different classes of non‐pA transcripts. Ysh1 is a component of the cleavage and polyadenylation machinery and is responsible for cleavage at the pA site and subsequent removal of Pol II from the template. When Ysh1 is depleted from the nucleus Pol II does not read through the termination site but rather accumulates just downstream of the polyadenylation site. We will discuss possible mechanisms that distinguish termination of pA and non‐pA transcripts.