Characterization of snoRNA 3’‐end formation in Saccharomyces cerevisiae reveals a broad role for the Paf1 complex and locus‐specific roles for histone post‐translational modifications

Abstract

One eukaryotic protein complex involved in regulating RNA polymerase II transcription is the Paf1 complex (Paf1C), which has well‐characterized roles in promoting histone modifications and transcription elongation. Beyond these roles, the human and yeast Paf1 complexes also interact with RNA 3’‐end processing components to affect RNA formation. Specifically, the S. cerevisiae Paf1C is known to promote the proper 3’‐end formation of at least two small nucleolar RNAs (snoRNAs). To determine how Paf1C‐dependent functions regulate formation of these non‐coding RNAs, we used high‐density tiling arrays to analyze transcripts in cells lacking PAF1 and uncover new snoRNA targets of Paf1. Increased levels of RNA polymerase II seen downstream of snoRNA genes in the absence of PAF1 suggest that these snoRNA 3’‐end defects reflect impaired transcription termination. Examination of Paf1‐regulated snoRNA genes revealed locus‐specific requirements for post‐translational histone modifications and for other transcriptional regulators. Cumulatively, our work reveals a broad requirement for Paf1C in snoRNA 3’‐end formation and suggests that Paf1C contributes to the fine‐tuning of transcriptional regulation at individual loci.