Overlapping pathways dictate termination of RNA polymerase II transcription.

While it has long been appreciated that regulation of transcription initiation is vital to sustain dynamic gene expression, recent findings suggest that the control of transcription termination is equally important. Besides serving to avoid interference with downstream genes, transcription termination is a crucial determinant for the fate of the newly synthesized transcript through its intimate coupling to RNA 3'-end formation. This makes termination of eukaryotic RNA polymerase II transcription an interesting case since this enzyme is capable of generating very heterogenous transcripts ranging from protein coding mRNAs over small and stable non-coding RNAs to so-called cryptic unstable transcripts. Recent discoveries in the yeast S. cerevisiae have established that 3'-end formation of these functionally distinct molecules is carried out by a set of both shared and specific transcription termination and 3'-end processing factors that concurrently travel along with the transcribing polymerase. The choice of termination mode depends on sequences in the transcribed RNA, as well as on the distance of the termination signal to the promoter. The apparent ability of RNA polymerase II to switch between termination systems suggests hitherto unappreciated commonalities between the biosynthesis pathways of protein coding and non-coding transcripts.