Regulation of Histone Modification and Transcription by the Yeast Paf1 Complex

Abstract

The Paf1 complex associates with RNA pol II and couples histone modification to transcription elongation. The Rtf1 subunit of the complex is essential for H2B K123 ubiquitylation and H3 K4 and K79 methylation. We have identified a conserved histone modification domain (HMD) in Rtf1 that is essential for these modifications. Specific amino acid substitutions in the HMD cause differential effects on H2B ubiquitylation and H3 K4 methylation, indicating that the functions of Rtf1 in directing these marks are genetically separable. Interestingly, expression of the isolated HMD in yeast cells is sufficient to promote histone modification. Microarray experiments have revealed broad effects of the Paf1 complex on transcription patterns, including many genes where the Paf1 complex functions as a repressor. Northern analyses demonstrated that Paf1 and Ctr9, and to a lesser extent Rtf1, are required for repression of the model gene ARG1. Analysis of ARG1 expression in single and double mutant strains indicated that Paf1 directs repression through a pathway that operates in parallel to known ARG1 regulators. The Paf1 complex localizes to ARG1 in both repressing and activating conditions, suggesting that it directly regulates ARG1 transcription. Replacement of the ARG1 coding sequence with that of a heterologous gene revealed that the Paf1 complex functions through the promoter or early transcribed region of ARG1. Our results suggest that the Paf1 complex inhibits transcription of ARG1 and potentially other genes by establishing a repressive chromatin structure at the promoters or 5' ends of these genes. Funding source: NIH.