Effects of the Paf1 Complex and Histone Modifications on snoRNA 3′-End Formation Reveal Broad and Locus-Specific Regulation

Abstract

Across diverse eukaryotes, the Paf1 complex (Paf1C) plays critical roles in RNA polymerase II transcription elongation and regulation of histone modifications. Beyond these roles, the human and Saccharomyces cerevisiae Paf1 complexes also interact with RNA 3′-end processing components to affect transcript 3′-end formation. Specifically, the Saccharomyces cerevisiae Paf1C functions with the RNA binding proteins Nrd1 and Nab3 to regulate the termination of at least two small nucleolar RNAs (snoRNAs). To determine how Paf1C-dependent functions regulate snoRNA formation, we used high-density tiling arrays to analyze transcripts in paf1Δ cells and uncover new snoRNA targets of Paf1. Detailed examination of Paf1-regulated snoRNA genes revealed locus-specific requirements for Paf1-dependent posttranslational histone modifications. We also discovered roles for the transcriptional regulators Bur1-Bur2, Rad6, and Set2 in snoRNA 3′-end formation. Surprisingly, at some snoRNAs, this function of Rad6 appears to be primarily independent of its role in histone H2B monoubiquitylation. Cumulatively, our work reveals a broad requirement for the Paf1C in snoRNA 3′-end formation in S. cerevisiae, implicates the participation of transcriptional proteins and histone modifications in this process, and suggests that the Paf1C contributes to the fine tuning of nuanced levels of regulation that exist at individual loci.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.01233-12.

ACKNOWLEDGMENTS

We thank members of the Nislow lab for their technical advice and assistance and Jeff Corden and David Brow for sharing reagents and information. We also thank Allen Ho, Sarah Hainer, Kristin Klucevsek, Peggy Shirra, and Joe Martens for comments on the manuscript.

This research was supported by National Institutes of Health grant R01-GM52593 to K.M.A. and by award number F32GM093383 to B.N.T. from the National Institute of General Medical Sciences. L.E.H., M.G., and C.N. are supported by grants from the Canadian Institutes of Health Research (MOP-84305).

The content of this article is solely the responsibility of the authors and does not represent the views of the funding institutions.