Briefly, 50 ml of yeast cells were grown to a final OD600of 0.81.0 in YPD media and cross-linked with 1% formaldehyde. on yeast gene expression. Intriguingly, these expression changes are preferentially associated with chromosomal regions in which histone H3 lysine residues are hypoacetylated and hypomethylated. Finally, we show that the acetylated and methylated lysine mutants have strikingly different effects on the binding of Sir4 to yeast telomeres, suggesting that histone H3 acetylated lysine residues regulate yeast silencing through a mechanism independent of SIR binding. POST-translationally modified residues in histone proteins, such as acetylated or methylated lysine residues, play critical roles in the regulation of gene transcription and silencing (Shilatifard2006;Shahbazianand Grunstein2007). Acetylation of the -amino group of lysine residues in histone proteins is catalyzed by histone acetyltransferases (HATs) (Leeand Workman2007) and expunged by histone deacetylases (HDACs) (Yangand Seto2008). In the N-terminal Borussertib domain of histone H3 the lysine residues K9, K14, K18, K23, and K27 are acetylated. These residues are acetylated predominately by Gcn5 and Sas3 (Howeet al.2001;Sukaet al.2001), and are deacetylated by Hda1, Hos2, and Rpd3 (Millarand Grunstein2006). Histone H3 acetylation occurs both in the promoter and coding region of actively transcribed genes (Kurdistaniand Grunstein2003;Millarand Grunstein2006). The functional consequences of eliminating histone H3 acetylation are varied: mutation or deletion of histone H3 acetylated lysine residues causes a significant increase in the transcription of many genes (Sabetet al.2003), includingGAL1(Mannand Grunstein1992;Wanet al.1995) and genes located in telomeric and subtelomeric heterochromatin (Thompsonet al.1994;Martinet al.2004). In contrast, deletion of Gcn5 causes a reduction in the transcription of many genes (Holstegeet al.1998;Leeet al.2000;Durantand Pugh2006). Histone acetylation also regulates other DNA metabolic processes, Borussertib including DNA replication (Vogelaueret al.2002;Aparicioet al.2004) and repair (Grothet al.2007;Escargueilet al.2008). Histone lysine residues are also methylated by histone methyltransferase enzymes. InSaccharomyces cerevisiae, histone H3 K4, K36, and K79 are methylated by Set1, Set2, and Dot1, respectively. Histone methylation occurs predominately in transcriptionally active chromosomal regions, and the methylation marks are deposited on chromatin during the transcription cycle through the recruitment of the cognate histone methyltransferase (Hampseyand Reinberg2003;Shilatifard2006;Liet al.2007a). Mutations in methylated lysine residues or histone methyltransferase enzymes disrupt epigenetic silencing in yeast (Briggset al.2001;Bryket al.2002;Kroganet al.2002;Nget al.2002;vanLeeuwenand Gottschling2002;Tompaand Madhani2007), and can affect yeast viability (Jinet al.2007). Accumulating evidence suggests there is considerable interplay between acetylated and methylated lysine residues in histone H3. For example, methylation of H3 K4 is strongly correlated with acetylation of histone H3 N-terminal lysine residues (Zhanget al.2004;Millarand Grunstein2006;Tavernaet al.2007). Methylation of H3 K4 recruits the Gcn5 and Sas3 histone acetyltransferase complexes, as these complexes contain subunits (Chd1 and Yng1, respectively) that interact with methylated H3 K4 (Pray-Grantet al.2005;Martinet al.2006a,b;Tavernaet al.2006;Leeand Workman2007). Hence, abrogation of H3 K4 methylation alters the acetylation pattern of adjacent histone H3 lysine residues (Tavernaet al.2006;Jianget al.2007). Intriguingly, acetylation of histone H3 N-terminal lysine residues also affects the methylation state of H3 K4 (Jianget al.2007). There is evidence that H3 K36 methylation directs the recruitment of the H3-specific Sas3 complex (Martinet al.2006b). Set2-catalyzed histone H3 K36 methylation also recruits the Rpd3S histone deacetylase complex, CSH1 which deacetylates histones in the coding regions of actively transcribed genes (Carrozzaet al.2005;Joshiand Struhl2005;Keoghet al.2005). Taken together, these studies argue that Borussertib histone H3 acetylated and methylated lysine residues often function in interdependent molecular pathways to regulate gene transcription (Leeand Workman2007). There is considerable genetic evidence, however, suggesting that histone H3 acetylated and methylated lysine residues may regulate gene expression via redundant molecular mechanisms. In a previous study, we found that a significantly greater number of genes were differentially expressed when both a methylated (H3 K4) and Borussertib acetylated (H3 K9, K14, K18, K23, K27) lysine residues were mutated in combination as opposed to when these residues were mutated individually (Martinet al.2004). These results suggest that acetylated and methylated lysine residues may act in a redundant manner to regulate gene transcription. In this study, we have employed a genetic approach to investigate the functional interplay between histone H3 acetylated and methylated lysine residues. We have constructed yeast mutants lacking acetylated lysine residues (H3 K9,14,18,23,27G), methylated lysine residue (H3 K4,36,79G), or both acetylated and methylated lysine residues (H3 K4,9,14,18,23,27,36,79G). Surprisingly, yeast strains harboring each of these mutants were viable. Indeed, mutations in histone H3 acetylated lysine residues rescued the slow growth and other phenotypes (e.g., hydroxyurea sensitivity) exhibited by the H3 methylated lysine mutants. To investigate the interplay between histone H3 acetylation and methylation in gene expression, we used DNA microarrays to profile the noticeable changes in transcription in every histone H3 mutant strain. Surprisingly, our outcomes usually do not support either the redundant or interdependent versions, but indicate that mutations in acetylated and methylated lysine residues possess rather.