RNA-binding protein Nrd1 directs poly(A)-independent 3 '-end formation of RNA polymerase II transcripts

A eukaryotic chromosome contains many genes, each transcribed separately by RNA polymerase (pol) I, II or III. Transcription termination between genes prevents the formation of polycistronic RNAs and anti-sense RNAs, which ar e generally detrimental to the correct expression of genes. Terminating the transcription of protein-coding genes by pol II requires a group of protei ns that also direct cleavage and polyadenylation of the messenger RNA in re sponse to a specific sequence element, and are associated with the carboxyl -terminal domain of the largest subunit of pol II (refs 1-6). By contrast, the cis-acting elements and trans-acting factors that direct termination of non-polyadenylated transcripts made by pol II, including small nucleolar a nd small nuclear RNAs, are not known. Here we show that read-through transc ription from yeast small nucleolar RNA and small nuclear RNA genes into adj acent genes is prevented by a cis-acting element that is recognized, in par t, by the essential RNA-binding protein Nrd1. The RNA-binding protein Nab3, the putative RNA helicase Sen1, and the intact C-terminal domain of pol II are also required for efficient response to the element. The same proteins are required for maintaining normal levels of Nrd1 mRNA, indicating that t hese proteins may control elongation of a subset of mRNA transcripts.