Recognition of phosphorylated CTD of RNA Pol II by Nrd1

H. Cerna¹, K. Kubicek², R. Stefl¹

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno

²Dept. of Condensed Matter Physics, Faculty of Science, Masaryk University, 61137 Brno

stefl@chemi.muni.cz

The transcription by RNA polymerase II (Pol II) in Saccharomyces cerevisiae can be terminated via at least two pathways - the mRNA pathway and ncRNA pathway. Both of them require interaction of CTD domain of RNA poly II with CID domain of a specialized protein. The CTD domain of RNA polymerase II contains tandem repeats of a heptad sequence that are dynamically phosphorylated or dephosphorylated on Ser5 and Ser2 over the course of transcription. The Nrd1 protein acts in ncRNA pathway – where Nrd1 (in comlex with Nab3 and Sen1) is via its CID domain bound to CTD domain of RNA poly II. Depending on the extent of exosome degradation, this termination pathway can lead to either 3’end trimming or complete degradation. Unlike other factors of transcription termination, Nrd1 binds preferentially to CTD phosphorylated at Ser5, which has the highest levels of fosforylation in early elongation. We will present our NMR study of the Nrd1 CTD domain and its interaction with the Ser5-phosphorylated CTD of RNA Pol II.