Methylation of histone proteins is one of their many modifications that affect chromatin structure and regulate gene expression. Methylation of histone H3 on lysines 4 and 79, catalyzed by the Set1-containing complex COMPASS and Dot1p, respectively, is required for silencing of expression of genes located near chromosome telomeres in yeast. We report that the Paf1 protein complex, which is associated with the elongating RNA polymerase II, is required for methylation of lysines 4 and 79 of histone H3 and for silencing of expression of a telomere-associated gene. We show that the Paf1 complex is required for recruitment of the COMPASS methyltransferase to RNA polymerase II and that the subunits of these complexes interact physically and genetically. Collectively, our results suggest that the Paf1 complex is required for histone H3 methylation, therefore linking transcriptional elongation to chromatin methylation.

Ubiquitination of histone H2B catalyzed by Rad6 is required for methylation of histone H3 by COMPASS. We identified Bre1 as the probable E3 for Rad6's role in transcription. Bre1 contains a C3HC4 (RING) finger and is present with Rad6 in a complex. The RING finger of Bre1 is required for ubiquitination of histone H2B, methylation of lysine 4 and 79 of H3 and for telomeric silencing. Chromatin immunoprecipitation experiments indicated that both Rad6 and Bre1 are recruited to a promoter. Bre1 is essential for this recruitment of Rad6 and is dedicated to the transcriptional pathway of Rad6. These results suggest that Bre1 is the likely E3 enzyme that directs Rad6 to modify chromatin and ultimately to affect gene expression.

. To learn about the mechanism of histone methylation, we surveyed the genome of the yeast Saccharomyces cerevisiae for genes necessary for this process. By analyzing ϳ4800 mutant strains, each deleted for a different non-essential gene, we discovered that the ubiquitin-conjugating enzyme Rad6 is required for methylation of lysine 4 of histone H3. Ubiquitination of histone H2B on lysine 123 is the signal for the methylation of histone H3, which leads to silencing of genes located near telomeres.

Monoubiquitination of histone H2B, catalyzed byRad6-Bre1, is required for methylation of histone H3 on lysines 4 and 79, catalyzed by the Set1-containing complex COMPASS and Dot1p, respectively. The Paf1 protein complex, which associates with RNA polymerase II, is known to be required for these histone H3 methylation events. During the early elongation stage of transcription, the Paf1 complex is required for association of COMPASS with RNA polymerase II, but the role the Paf1 complex plays at the promoter has not been clear. We present evidence that the Paf1 complex is required for monoubiquitination of histone H2B at promoters. Strains deleted for several components of the Paf1 complex are defective in monoubiquitination of histone H2B, which results in the loss of methylation of lysines 4 and 79 of histone H3. We also show that Paf1 complex is required for the interaction of Rad6 and COMPASS with RNA polymerase II. Finally, we show that the Paf1 complex is required for Rad6-Bre1 catalytic activity but not for the recruitment of Rad6-Bre1 to promoters. Thus, in addition to its role during the elongation phase of transcription, the Paf1 complex appears to activate the function but not the placement of the Rad6-Bre1 ubiquitinprotein ligase at the promoters of active genes.The DNA of eukaryotic organisms assembles around histone proteins in nucleosomes to form highly organized structures known as chromatin (1). Alterations in chromatin structure play a major role in regulating gene expression, and for this reason much attention has been focused recently on the covalent modifications of histone proteins and their outcomes in transcriptional elongation (1-4). Essential to this process are the N-terminal tails of histone proteins. Because they protrude from the globular body of the nucleosome and are available for interactions with other proteins, the tails are the site of many covalent modifications that alter nucleosome structure. A myriad of modifications, such as acetylation, phosphorylation, ubiquitination, and methylation, decorate each histone tail (2, 5) The combinatorial effects of such modifications can produce an array of different responses involved in transcriptional activation and repression (1-6).One histone modification of major consequence is the methylation of histone H3 at lysines 4 and 79, catalyzed by the Set1-containing complex COMPASS 1 and Dot1p, respectively (7)(8)(9)(10)(11)(12)(13)(14). It has been shown that methylation of both lysine residues impacts the expression of genes within the rDNA loci and telomeric regions of DNA in Saccharomyces cerevisiae (7-8, 15, 16). It has been demonstrated that some of the components of the Paf1 complex, a complex that associates with the initiating and elongating RNA polymerase II, is also required for histone H3 methylation on lysines 4 and 79 (17, 18). Accordingly, previous studies have demonstrated a role for the Paf1 complex in transcriptional elongation and initiation (19 -22). A further requirement for the methylation of both lysines 4 and 79 of hi...

The Set1-containing complex COMPASS, which is the yeast homolog of the human MLL complex, is required for mono-, di-, and trimethylation of lysine 4 of histone H3. We have performed a comparative global proteomic screen to better define the role of COMPASS in histone trimethylation. We report that both Cps60 and Cps40 components of COMPASS are required for proper histone H3 trimethylation, but not for proper regulation of telomere-associated gene silencing. Purified COMPASS lacking Cps60 can mono- and dimethylate but is not capable of trimethylating H3(K4). Chromatin immunoprecipitation (ChIP) studies indicate that the loss subunits of COMPASS required for histone trimethylation do not affect the localization of Set1 to chromatin for the genes tested. Collectively, our results suggest a molecular requirement for several components of COMPASS for proper histone H3 trimethylation and regulation of telomere-associated gene expression, indicating multiple roles for different forms of histone methylation by COMPASS.