Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae
© Verzijlbergen et al; licensee BioMed Central Ltd. 2009
Received: 20 February 2009
Accepted: 28 July 2009
Published: 28 July 2009
Methylation of lysine 79 on histone H3 by Dot1 is required for maintenance of heterochromatin structure in yeast and humans. However, this histone modification occurs predominantly in euchromatin. Thus, Dot1 affects silencing by indirect mechanisms and does not act by the recruitment model commonly proposed for histone modifications. To better understand the role of H3K79 methylation gene silencing, we investigated the silencing function of Dot1 by genetic suppressor and enhancer analysis and examined the relationship between Dot1 and other global euchromatic histone modifiers.
We determined that loss of H3K79 methylation results in a partial silencing defect that could be bypassed by conditions that promote targeting of Sir proteins to heterochromatin. Furthermore, the silencing defect in strains lacking Dot1 was dependent on methylation of H3K4 by Set1 and histone acetylation by Gcn5, Elp3, and Sas2 in euchromatin. Our study shows that multiple histone modifications associated with euchromatin positively modulate the function of heterochromatin by distinct mechanisms. Genetic interactions between Set1 and Set2 suggested that the H3K36 methyltransferase Set2, unlike most other euchromatic modifiers, negatively affects gene silencing.
Our genetic dissection of Dot1's role in silencing in budding yeast showed that heterochromatin formation is modulated by multiple euchromatic histone modifiers that act by non-overlapping mechanisms. We discuss how euchromatic histone modifiers can make negative as well as positive contributions to gene silencing by competing with heterochromatin proteins within heterochromatin, within euchromatin, and at the boundary between euchromatin and heterochromatin.
Post-translational modifications of histone proteins influence DNA transactions such as transcription, repair, recombination, and chromosome segregation. Many histone modifications affect local chromatin structure and function by recruitment of effector proteins that specifically recognize a modified state of a given residue [reviewed in [1–4]]. However, several histone modifications seem to act by alternative mechanisms. One such example is methylation of lysine 79 of histone H3 (H3K79) by Dot1. H3K79 methylation is required for heterochromatin formation in yeast and humans [5–10]. Paradoxically, methylation of H3K79 is low or absent from heterochromatic regions and is abundant in euchromatic regions of the genome [5, 7, 11–14]. Furthermore, methylation of H3K79, which causes small local changes of the nucleosome surface , negatively affects binding of the heterochromatin protein Sir3 in yeast [16–18]. Therefore, this histone modification most likely affects heterochromatin structure by mechanisms other than direct recruitment of repressive factors. We previously proposed that H3K79 methylation in yeast might act as an anti-binding signal to prevent non-specific binding of silencing proteins in euchromatin, thereby leading to efficient targeting of the limiting silencing proteins to the unmethylated heterochromatic regions of the genome [5, 19].
Heterochromatin in yeast, often referred to as silent chromatin, is found at telomeres, the silent mating type loci (HMLα and HMR a) and the ribosomal DNA repeats. At telomeres and HM loci, DNA elements called silencers recruit the Sir2/3/4 complex, which subsequently spreads along the chromosome to form a silent or heterochromatic domain [reviewed in ]. Besides H3K79 methylation, methylation of H3K4 and H3K36, histone acetylation, and deposition of the histone variant Htz1 (H2A.Z) in euchromatin have been shown to affect heterochromatin formation in yeast [reviewed in ]. Some euchromatic modifications have been suggested to act by (indirect) global effects, whereas others have been suggested to primarily act (directly) at the boundary between euchromatin and heterochromatin to prevent excessive spreading of the Sir2/3/4 complex. For example, loss of the histone variant Htz1, the H3K36 methyltransferase Set2, or the histone acetyltransferase Sas2 leads to loss of heterochromatin boundaries and excessive spreading at yeast telomeres [21–24], whereas in cells lacking Dot1 or the histone H3K4 methyltransferase Set1, Sir proteins become redistributed throughout the genome [5, 25, 26]. Methylation of H3K4 in euchromatin negatively affects binding of the C-terminus of Sir3, which led to the suggestion that Set1 enhances silencing by a mechanism similar to that of Dot1 .
Chromatin modifiers analyzed in this study
SAGA, SALSA, SLIK, HatB3.1
H3K9,14,18,23,36; H2B, Htz1K14, Rsc4
H4; H2A; Htz1
Rpd3L, Rpd3S (HDAC)
Rap1 interacting factor
Suppressor analysis of the silencing defect in strains lacking Dot1
First, Sir3 levels were increased by expression of SIR3 from a multi-copy plasmid. Overexpression of Sir3 partially suppressed the silencing defect of the dot1Δ strain (Figure 1B–C). Thus, Dot1 is not a critical component of heterochromatin. We note that Sir3 overexpression was not toxic for dot1Δ cells (Figure 1B and data not shown) indicating that an increase in Sir3 did not lead to ectopic silencing of essential genes.
Third, to test whether additional histone modifications are involved in Sir protein targeting, we investigated the consequences of inactivation of the histone deacetylase (HDAC) Rpd3. Acetylation of lysines in the histone tails negatively affects interactions between Sir3 and Sir4 with histones in vitro [35, 36]. We deleted RPD3 because cells lacking Rpd3 activity show increased global levels of histone acetylation in euchromatin [37–43]. Deletion of RPD3 enhanced silencing of ADE2 in wild-type cells, which is consistent with previous observations [40, 44–47], and suppressed the URA3 silencing defect of the dot1Δ strain (Figure 1D), suggesting that increased acetylation in euchromatin can compensate for the loss of H3K79 methylation. Analysis of URA3 mRNA levels confirmed that deletion of Rpd3 improved transcriptional silencing of telomeric URA3 in wild-type cells and suppressed the silencing defect of dot1Δ cells (Figure 1E). Deletion of Rpd3 also improved silencing of the ADE2 gene but did not improve transcriptional silencing of ADE2 in cells lacking Dot1 (Figure 1E), despite the similar dark red colony color of rpd3Δ and dot1Δrpd3Δ cells. We expect that red color development was near saturation in rpd3Δ and dot1Δrpd3Δ cells due to a combination of partial ADE2 silencing and slow growth of cells lacking Rpd3 and that a small reduction in silencing did not result in a color change in these slow growing cells. To investigate how Rpd3 enhanced silencing, binding of Sir3 was examined by ChIP. In wild-type cells, deletion of Rpd3 led to an increase in Sir3 binding at all three telomeres examined (Figure 1F), which supports the idea that global histone acetylation can promote targeting of Sir proteins to heterochromatin. However, in cells lacking Dot1, loss of Rpd3 did not lead to a detectable increase in Sir3 binding (Figure 1F), suggesting that the suppression of the dot1Δ silencing defect of telomeric URA3 was not caused by restoration of Sir3 binding.
Rpd3 is active in two multi-subunit complexes (see Table 1). The larger Rpd3L complex localizes to promoter regions. The smaller Rpd3S complex is active at transcribed coding regions and is recruited to these regions via the subunits Eaf3 and Rco1, which together bind methylated H3K36, a histone modification co-transcriptionally introduced by Set2 [48–51]. DEP1 deletion, which specifically eliminates the Rpd3L complex, phenocopied deletion of RPD3 (Figure 1G). In contrast, deletion of RCO1, which eliminates the Rpd3S complex, did not affect silencing, showing that the Rpd3L complex and not the Rpd3S promoted gene silencing (Figure 1G). A very recent study identified a third Rpd3 complex, containing Rpd3, Snt2 and Ecm5 . We expect that this complex is not involved in the silencing functions of Rpd3 that we identified here because deletion of ECM5 did not affect silencing (data not shown).
Together, the results shown in Figure 1A–G show that Dot1 modulates the strength of gene silencing and that the loss of this modifier can be compensated for by increased Sir3 dosage, strong silencers, and inactivation of Rpd3, a global HDAC.
Dot1 collaborates with histone acetyltransferases to promote gene silencing
To analyze the genetic relationship between DOT1 and other genes involved in euchromatic histone modification, we analyzed silencing of the reporter genes at different temperatures. Growth at high temperature enhances gene silencing in yeast by unknown mechanisms [33, 53] and was sufficient to suppress the dot1Δ silencing defect (Figure 2A). Perhaps non-specific association of Sir proteins with nucleosomes is decreased at higher temperatures, which improves binding at telomeres. This conditional silencing phenotype provided us with a genetic tool to identify enhancers of the silencing defect in dot1Δ strains. Having found that increased acetylation suppressed the dot1Δ silencing defect (Figure 1D–E), we examined which HAT might be responsible for the acetylation marks that promote gene silencing. We examined the non-essential HATs Elp3 , Gcn5 [55–60], Sas3 , and Sas2 [62–64], as well as Eaf1 , which encodes the only non-essential subunit of the NuA4 HAT complex (Table 1). Analysis of dot1Δ double and triple mutants showed that Elp3, Gcn5, and Sas2 were all required for efficient silencing in dot1Δ cells at high temperature (Figure 2B–F). These findings suggest that Gcn5 and Elp3, which have been shown to affect global levels of histone H3 acetylation [41, 66–68, 68–70], and Sas2, which has been shown to be the major H4K16 acetyltransferase [21, 62] all promote silencing in parallel to histone H3K79 methylation by Dot1. Analysis of sas2Δ in combination with elp3Δ or gcn5Δ showed that each double mutant had more severe silencing defects than either single mutant, suggesting that the three HATs affect silencing by redundant mechanisms (Figure 2E). Loss of Sas3, which affects bulk histone H3 acetylation when combined with loss of Gcn5 [70, 71], did not alter silencing in wild-type or dot1Δ cells (Figure 2C), whereas a single deletion of EAF1 was sufficient to disrupt telomeric silencing (Figure 2F), even at high temperature (Figure 2F). The histone variant Htz1 (H2A.Z), which is acetylated by NuA4 [72, 73] and of which the deposition into chromatin is dependent on Sas2 , was not critical for silencing in wild-type or dot1Δ strains (Figure 2G).
Dot1 and Set1 have distinct functions in silencing and cell division
Since the set1Δ silencing defect could be suppressed by increased histone acetylation by inactivation of Rpd3, we asked whether increased activity of Dot1 could also improve silencing and suppress the set1Δ silencing defect. To test this, wild type and set1Δ strains were transformed with a DOT1 multi-copy plasmid (Figure 4D). Under these conditions of Dot1 overexpression (Figure 4E) silencing of the telomeric URA3 gene was unaffected in wild-type strains and not or only slightly improved in set1Δ strains (Figure 4D). We conclude that the endogenous levels of H3K79 methylation are not limiting for silencing.
Sir2 and Sir3 expression in strains with silencing phenotypes
Our results and previous studies show that multiple euchromatic histone modifiers influence telomeric silencing and here we show that many of them seem to act by non-overlapping mechanisms. How might they affect gene silencing? Deletion of a histone modifier generally does not enhance silencing (e.g. Figures 2, 3 and 4). Therefore, they do not seem to weaken silencing by local competition with heterochromatin formation. Several factors might determine the importance of local competition. For example, euchromatic modifiers might not have access to the nucleosomal substrates in heterochromatin [17, 84], local disruption of silencing by histone modifiers might be counteracted by (indirect) positive silencing effects, or post-translational modification in heterochromatin might be counteracted by histone-demodifying activities such as the HDAC activity of Sir2 and the H2B deubiquitinating activity of UBP10, which is recruited to heterochromatin by Sir4 and negatively affects methylation by Dot1 and Set1 [85, 86]. We expect that Dot1, Set1, Gcn5, Elp3, and Sas2, which we investigated here, act at least in part by long-distance targeting effects because they deposit abundant histone modifications throughout the euchromatic genome and loss of the modifying enzymes leads to reduced silencing. Similarly, based on the phenotypes of rpd3Δ cells i.e. more spreading into flanking regions (Figure 1 and ) as well as increased silencing within wild-type heterochromatin regions (Figures 1 and 4), we propose that deletion of RPD3 leads to improved targeting of silencing proteins to heterochromatin domains, which can overrule the local boundary and lead to ectopic spreading. Set2 and Htz1 might act by a similar mechanism. Strains lacking Set2 show increased spreading  as well as increased silencing within existing heterochromatin regions in a set1Δ strain (Figure 4) and strains lacking Htz1 show increased spreading  without loss of silencing at wild-type heterochromatin loci (Figure 2). These silencing phenotypes suggest that Set2, Htz1, and Rpd3 might not act as local boundary factors, as has been proposed previously [23, 24, 31, 87], but instead affect the degree of spreading from a distance by reducing the targeting efficiency of Sir proteins to heterochromatin. Thus, these factors might set heterochromatin boundaries by weakening Sir-protein targeting to heterochromatin domains.
The mechanism by which Rpd3 weakens silencing is still unclear, however. Whereas increased gene silencing in rpd3Δ cells (Figure 1D+E) was accompanied by increased Sir3 binding (Figure 1F), deletion of Rpd3 in dot1Δ cells restored URA3 silencing without any detectable changes in Sir3 binding (Figure 1D–F). Although Sir3 is the major Sir protein that can spread along the chromosome over long distances, these results suggest that factors other than Sir3 restored silencing in rpd3Δdot1Δ cells. Whether Rpd3 affects binding of one of the other Sir proteins remains to be determined. Changes in silencing without detectable changes in Sir protein binding have been described previously, however . Therefore, it is also possible that Rpd3 might affect the activity of the Sir proteins, such as the deacetylase activity of Sir2, or targeting of repressor proteins that can act as heterochromatin factors but are normally not found in Sir-occupied heterochromatin domains, such as Sum1, Hst1, or Hda1 [89–94]. Interestingly, our results also indicate that the effect of Rpd3 on Sir3 targeting to telomeric heterochromatin requires the presence of Dot1. This suggests that targeting of Sir proteins to heterochromatin by increased histone acetylation might involve simultaneous recognition of methylated H3K79. The redundant roles of Dot1 and the histone H3 HATs Gcn5 and Elp3 in promoting gene silencing indicates that histone H3 acetylation and H3K79 methylation involve non-linked mechanisms. To fully understand the connection between Dot1 and Rpd3, it will be important to determine which of the many target lysines of Rpd3 affect Sir3 targeting in a Dot1-dependent manner and whether Rpd3 and Dot1 affect each others activity.
Targeting of the Sir complex to regions of heterochromatin in yeast is positively modulated by a range of euchromatic factors indicating that euchromatin and heterochromatin are interdependent. Our results and previous studies suggest that histone modifiers can compete with heterochromatin proteins at different locations and thereby make positive as well as negative contributions to heterochromatin formation. We expect that similar rules apply to histone modifications in higher eukaryotes, which might help to explain the paradoxical role of Dot1 in gene activation and repression in flies and mammals [8, 9, 11, 95–98].
Strains used in this study
Relevant genotype (all strains are isogenic to UCC7366)
MATa lys2Δ0 trp1Δ63 his3Δ200 ade2Δ::hisG ura3Δ0 leu2Δ0 met15Δ0 ADE2-TEL-VR URA3-TEL-VIIL
MATa/α ELP3/elp3Δ::KanMX GCN5/gcn5Δ::HphMX SET1/set1Δ::KanMX SIR3/sir3::HIS3
dot1Δ::NatMX set1Δ::KanMX set2Δ::HphMX
dot1Δ::NatMX gcn5Δ::HphMX elp3Δ::KanMX
Whole-cell extracts were obtained from approximately 5 × 107 cells by the classical glass beads breakage method using 200 μl of glass beads and SUMEB (1% SDS, 8 M Urea, 10 mM MOPS pH 6.8, 10 mM EDTA, 0.01% bromophenol blue, 1 mM DTT)  complemented with PMSF (1 mM), benzamidine (5 mM), pepstatin (1 μg/ml), leupeptin (1 μg/ml) and DTT (1 μM). Primary antibody incubations were performed in Tris-buffered saline-Tween with 2% dry milk. Antibodies used were Sir3 , Dot1 , Sir2 (Santa Cruz, Sc-6666), and Pgk1 (Invitrogen, A-6457).
Total yeast RNA was prepared from 5 × 107 cells of each of the indicated growth condition using the RNeasy kit (Qiagen) according to the manufacturer's protocol. RNA samples were treated with RNase free DNAse (Qiagen), and cDNA was made by using Super-Script II reverse transcriptase (Invitrogen).
ChIP was performed as described previously . Briefly, the chromatin was sheared using a bioruptor (Diagenode) for 6 minutes with 30 seconds intervals at high. The obtained fragments have an average size of 500 bp, as determined on a 2% TAE gel stained with ethidium bromide and quantified using TINA software. The isolated chromatin of the equivalent of 5 × 107 cells was immunoprecipitated overnight at 4°C using magnetic Dynabeads (Invitrogen) which were previously incubated with antibody o/n at 4°C.
qPCR primers used in this study
We thank E. Battaglia for help with strain constructions, J.M.M. den Haan for Sir3 antibody purification, and D.E. Gottschling, F. Frederiks, and M. Fornerod, for discussions and/or critical reading of the manuscript. This work was supported by the EU 6th framework program (NOE 'The Epigenome' LSHG-CT-2004-503433) and by a VIDI fellowship from NWO-ALW.
- Bhaumik SR, Smith E, Shilatifard A: Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol. 2007, 14: 1008-1016.PubMedGoogle Scholar
- Kouzarides T: Chromatin modifications and their function. Cell. 2007, 128: 693-705.PubMedGoogle Scholar
- Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ: How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol. 2007, 14: 1025-1040.PubMedGoogle Scholar
- Sims RJ, Reinberg D: Is there a code embedded in proteins that is based on post-translational modifications?. Nat Rev Mol Cell Biol. 2008, 9: 815-820.PubMedGoogle Scholar
- van Leeuwen F, Gafken PR, Gottschling DE: Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell. 2002, 109: 745-756.PubMedGoogle Scholar
- Ng HH, Feng Q, Wang H, Erdjument-Bromage H, Tempst P, Zhang Y, Struhl K: Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev. 2002, 16: 1518-1527.PubMed CentralPubMedGoogle Scholar
- Ng HH, Ciccone DN, Morshead KB, Oettinger MA, Struhl K: Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc Natl Acad Sci USA. 2003, 100: 1820-1825.PubMed CentralPubMedGoogle Scholar
- Gazin C, Wajapeyee N, Gobeil S, Virbasius CM, Green MR: An elaborate pathway required for Ras-mediated epigenetic silencing. Nature. 2007, 449: 1073-1077.PubMed CentralPubMedGoogle Scholar
- Jones B, Su H, Bhat A, Lei H, Bajko J, Hevi S, Baltus GA, Kadam S, Zhai H, Valdez R, et al: The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure. PLoS Genet. 2008, 4: e1000190-PubMed CentralPubMedGoogle Scholar
- Lacoste N, Utley RT, Hunter J, Poirier GG, Cote J: Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J Biol Chem. 2002, 30: 3-Google Scholar
- Krivtsov AV, Feng Z, Lemieux ME, Faber J, Vempati S, Sinha AU, Xia X, Jesneck J, Bracken AP, Silverman LB, et al: H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell. 2008, 14: 355-368.PubMed CentralPubMedGoogle Scholar
- Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K: High-resolution profiling of histone methylations in the human genome. Cell. 2007, 129: 823-837.PubMedGoogle Scholar
- Roh TY, Ngau WC, Cui K, Landsman D, Zhao K: High-resolution genome-wide mapping of histone modifications. Nat Biotechnol. 2004, 22: 1013-1016.PubMedGoogle Scholar
- Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O'Neill LP, Turner BM, Delrow J, et al: The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 2004, 18: 1263-1271.PubMed CentralPubMedGoogle Scholar
- Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K: The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat Struct Mol Biol. 2008, 15: 1122-1124.PubMed CentralPubMedGoogle Scholar
- Onishi M, Liou GG, Buchberger JR, Walz T, Moazed D: Role of the conserved Sir3-BAH domain in nucleosome binding and silent chromatin assembly. Mol Cell. 2007, 28: 1015-1028.PubMedGoogle Scholar
- Altaf M, Utley RT, Lacoste N, Tan S, Briggs SD, Cote J: Interplay of chromatin modifiers on a short basic patch of histone H4 tail defines the boundary of telomeric heterochromatin. Mol Cell. 2007, 28: 1002-1014.PubMed CentralPubMedGoogle Scholar
- Martino F, Kueng S, Robinson P, Tsai-Pflugfelder M, van Leeuwen F, Ziegler M, Cubizolles F, Cockell MM, Rhodes D, Gasser SM: Reconstitution of Yeast Silent Chromatin: Multiple Contact Sites and O-AADPR Binding Load SIR Complexes onto Nucleosomes In Vitro. Mol Cell. 2009, 33: 323-334.PubMedGoogle Scholar
- van Leeuwen F, Gottschling DE: Genome-wide histone modifications: gaining specificity by preventing promiscuity. Curr Opin Cell Biol. 2002, 14: 756-762.PubMedGoogle Scholar
- Rusche LN, Kirchmaier AL, Rine J: The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem. 2003, 72: 481-516.PubMedGoogle Scholar
- Kimura A, Umehara T, Horikoshi M: Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat Genet. 2002, 32: 370-377.PubMedGoogle Scholar
- Suka N, Luo K, Grunstein M: Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat Genet. 2002, 32: 378-383.PubMedGoogle Scholar
- Venkatasubrahmanyam S, Hwang WW, Meneghini MD, Tong AH, Madhani HD: Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proc Natl Acad Sci USA. 2007, 104: 16609-16614.PubMed CentralPubMedGoogle Scholar
- Meneghini MD, Wu M, Madhani HD: Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell. 2003, 112: 725-736.PubMedGoogle Scholar
- San Segundo PA, Roeder GS: Role for the silencing protein Dot1 in meiotic checkpoint control. Molecular Biology of the Cell. 2000, 11: 3601-3615.PubMed CentralPubMedGoogle Scholar
- Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T: Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol Cell. 2003, 12: 1325-1332.PubMedGoogle Scholar
- Santos-Rosa H, Bannister AJ, Dehe PM, Geli V, Kouzarides T: Methylation of H3 lysine 4 at euchromatin promotes Sir3p association with heterochromatin. J Biol Chem. 2004, 279: 47506-47512.PubMedGoogle Scholar
- Frederiks F, Tzouros M, Oudgenoeg G, van Welsem T, Fornerod M, Krijgsveld J, van Leeuwen F: Nonprocessive methylation by Dot1 leads to functional redundancy of histone H3K79 methylation states. Nat Struct Mol Biol. 2008, 15: 550-557.PubMedGoogle Scholar
- Wotton D, Shore D: A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisae. Genes Dev. 1997, 11329: 748-760.Google Scholar
- Marsellach FX, Huertas D, Azorin F: The multi-KH domain protein of Saccharomyces cerevisiae Scp160p contributes to the regulation of telomeric silencing. J Biol Chem. 2006, 281: 18227-18235.PubMedGoogle Scholar
- Raisner RM, Madhani HD: Genomewide screen for negative regulators of sirtuin activity in Saccharomyces cerevisiae reveals 40 loci and links to metabolism. Genetics. 2008, 179: 1933-1944.PubMed CentralPubMedGoogle Scholar
- Kyrion G, Liu K, Liu C, Lustig AJ: RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisae. Genes Dev. 1993, 7350: 1146-1159.Google Scholar
- van Welsem T, Frederiks F, Verzijlbergen KF, Faber AW, Nelson ZW, Egan DA, Gottschling DE, van Leeuwen F: Synthetic lethal screens identify gene silencing processes in yeast and implicate the acetylated amino terminus of Sir3 in recognition of the nucleosome core. Mol Cell Biol. 2008, 28: 3861-3872.PubMed CentralPubMedGoogle Scholar
- van Leeuwen F, Gottschling DE: Assays for gene silencing in yeast. Methods Enzymol. 2002, 350: 165-186.PubMedGoogle Scholar
- Hecht A, Laroche T, Strahl-Bolsinger S, Gasser SM, Grunstein M: Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell. 1995, 80: 583-592.PubMedGoogle Scholar
- Carmen AA, Milne L, Grunstein M: Acetylation of the yeast histone H4 N-terminus regulates its binding to heterochromatin protein SIR3. J Biol Chem. 2001, 190: 19-Google Scholar
- Vogelauer M, Wu JS, Suka N, Grunstein M: Global histone acetylation and deacetylation in yeast. Nature. 2000, 408: 495-498.PubMedGoogle Scholar
- Robyr D, Kurdistani SK, Grunstein M: Analysis of genome-wide histone acetylation state and enzyme binding using DNA microarrays. Methods Enzymol. 2004, 376: 289-304.PubMedGoogle Scholar
- Reid JL, Moqtaderi Z, Struhl K: Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol Cell Biol. 2004, 24: 757-764.PubMed CentralPubMedGoogle Scholar
- Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BM, Grunstein M: HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci USA. 1996, 93: 14503-14508.PubMed CentralPubMedGoogle Scholar
- Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD: A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev. 2008, 22: 2062-2074.PubMed CentralPubMedGoogle Scholar
- Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides T, Schreiber SL: Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci USA. 2002, 990: 8659-8700.Google Scholar
- Deckert J, Struhl K: Histone acetylation at promoters is differentially affected by specific activators and repressors. Mol Cell Biol. 2001, 21: 2726-2735.PubMed CentralPubMedGoogle Scholar
- Sun ZW, Hampsey M: A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics. 1999, 152: 921-932.PubMed CentralPubMedGoogle Scholar
- Bernstein BE, Tong JK, Schreiber SL: Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci USA. 2000, 97: 13708-13713.PubMed CentralPubMedGoogle Scholar
- De Rubertis F, Kadosh D, Henchoz S, Pauli D, Reuter G, Struhl K, Spierer P: The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature. 1996, 384: 589-591.PubMedGoogle Scholar
- Zhou J, Zhou BO, Lenzmeier BA, Zhou JQ: Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res. 2009, 37: 3699-3713.PubMed CentralPubMedGoogle Scholar
- Li B, Gogol M, Carey M, Lee D, Seidel C, Workman JL: Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science. 2007, 316: 1050-1054.PubMedGoogle Scholar
- Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, et al: Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005, 123: 593-605.PubMedGoogle Scholar
- Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, et al: Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell. 2005, 123: 581-592.PubMedGoogle Scholar
- Joshi AA, Struhl K: Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell. 2005, 20: 971-978.PubMedGoogle Scholar
- Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, Stewart AF: Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol. 2008, 9: R167-PubMed CentralPubMedGoogle Scholar
- Bi X, Yu Q, Sandmeier JJ, Elizondo S: Regulation of transcriptional silencing in yeast by growth temperature. J Mol Biol. 2004, 344: 893-905.PubMedGoogle Scholar
- Wittschieben BO, Otero G, de Bizemont T, Fellows J, Erdjument-Bromage H, Ohba R, Li Y, Allis CD, Tempst P, Svejstrup JQ: A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol Cell. 1999, 4: 123-128.PubMedGoogle Scholar
- Sendra R, Tse C, Hansen JC: The yeast histone acetyltransferase A2 complex, but not free Gcn5p, binds stably to nucleosomal arrays. J Biol Chem. 2000, 275: 24928-24934.PubMedGoogle Scholar
- Grant PA, Duggan L, Cote J, Roberts SM, Brownell JE, Candau R, Ohba R, Owen-Hughes T, Allis CD, Winston F, et al: Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 1997, 11: 1640-1650.PubMedGoogle Scholar
- Sterner DE, Belotserkovskaya R, Berger SL: SALSA, a variant of yeast SAGA, contains truncated Spt7, which correlates with activated transcription. Proc Natl Acad Sci USA. 2002, 99: 11622-11627.PubMed CentralPubMedGoogle Scholar
- Eberharter A, Sterner DE, Schieltz D, Hassan A, Yates JR, Berger SL, Workman JL: The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae. Mol Cell Biol. 1999, 19: 6621-6631.PubMed CentralPubMedGoogle Scholar
- Pray-Grant MG, Schieltz D, McMahon SJ, Wood JM, Kennedy EL, Cook RG, Workman JL, Yates JR, Grant PA: The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway. Mol Cell Biol. 2002, 22: 8774-8786.PubMed CentralPubMedGoogle Scholar
- Sklenar AR, Parthun MR: Characterization of yeast histone H3-specific type B histone acetyltransferases identifies an ADA2-independent Gcn5p activity. BMC Biochem. 2004, 5: 11-PubMed CentralPubMedGoogle Scholar
- John S, Howe L, Tafrov ST, Grant PA, Sternglanz R, Workman JL: The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex. Genes Dev. 2000, 14: 1196-1208.PubMed CentralPubMedGoogle Scholar
- Shia WJ, Osada S, Florens L, Swanson SK, Washburn MP, Workman JL: Characterization of the yeast trimeric-SAS acetyltransferase complex. J Biol Chem. 2005, 280: 11987-11994.PubMedGoogle Scholar
- Meijsing SH, Ehrenhofer-Murray AE: The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev. 2001, 15: 3169-3182.PubMed CentralPubMedGoogle Scholar
- Osada S, Sutton A, Muster N, Brown CE, Yates JR, Sternglanz R, Workman JL: The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 2001, 15: 3155-3168.PubMed CentralPubMedGoogle Scholar
- Auger A, Galarneau L, Altaf M, Nourani A, Doyon Y, Utley RT, Cronier D, Allard S, Cote J: Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants. Mol Cell Biol. 2008, 28: 2257-2270.PubMed CentralPubMedGoogle Scholar
- Winkler GS, Kristjuhan A, Erdjument-Bromage H, Tempst P, Svejstrup JQ: Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo. Proc Natl Acad Sci USA. 2002, 99: 3517-3522.PubMed CentralPubMedGoogle Scholar
- Kristjuhan A, Walker J, Suka N, Grunstein M, Roberts D, Cairns BR, Svejstrup JQ: Transcriptional inhibition of genes with severe histone h3 hypoacetylation in the coding region. Mol Cell. 2002, 10: 925-933.PubMedGoogle Scholar
- Choi JK, Grimes DE, Rowe KM, Howe LJ: Acetylation of Rsc4p by Gcn5p is essential in the absence of histone H3 acetylation. Mol Cell Biol. 2008, 28: 6967-6972.PubMed CentralPubMedGoogle Scholar
- Shahbazian MD, Grunstein M: Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem. 2007, 76: 75-100.PubMedGoogle Scholar
- Howe L, Auston D, Grant P, John S, Cook RG, Workman JL, Pillus L: Histone H3 specific acetyltransferases are essential for cell cycle progression. Genes Dev. 2001, 15: 3144-3154.PubMed CentralPubMedGoogle Scholar
- Durant M, Pugh BF: Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae. Mol Cell Biol. 2006, 26: 2791-2802.PubMed CentralPubMedGoogle Scholar
- Keogh MC, Mennella TA, Sawa C, Berthelet S, Krogan NJ, Wolek A, Podolny V, Carpenter LR, Greenblatt JF, Baetz K, et al: The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Genes Dev. 2006, 20: 660-665.PubMed CentralPubMedGoogle Scholar
- Babiarz JE, Halley JE, Rine J: Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev. 2006, 20: 700-710.PubMed CentralPubMedGoogle Scholar
- Shia WJ, Li B, Workman JL: SAS-mediated acetylation of histone H4 Lys 16 is required for H2A.Z incorporation at subtelomeric regions in Saccharomyces cerevisiae. Genes Dev. 2006, 20: 2507-2512.PubMed CentralPubMedGoogle Scholar
- Kristjuhan A, Wittschieben BO, Walker J, Roberts D, Cairns BR, Svejstrup JQ: Spreading of Sir3 protein in cells with severe histone H3 hypoacetylation. Proc Natl Acad Sci USA. 2003, 100: 7551-7556.PubMed CentralPubMedGoogle Scholar
- Jin Y, Rodriguez AM, Stanton JD, Kitazono AA, Wyrick JJ: Simultaneous mutation of methylated lysine residues in histone H3 causes enhanced gene silencing, cell cycle defects, and cell lethality in Saccharomyces cerevisiae. Mol Cell Biol. 2007, 27: 6832-6841.PubMed CentralPubMedGoogle Scholar
- VanDemark AP, Kasten MM, Ferris E, Heroux A, Hill CP, Cairns BR: Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol Cell. 2007, 27: 817-828.PubMed CentralPubMedGoogle Scholar
- Martin DG, Grimes DE, Baetz K, Howe L: Methylation of histone H3 mediates the association of the NuA3 histone acetyltransferase with chromatin. Mol Cell Biol. 2006, 26: 3018-3028.PubMed CentralPubMedGoogle Scholar
- Zhang K, Lin W, Latham JA, Riefler GM, Schumacher JM, Chan C, Tatchell K, Hawke DH, Kobayashi R, Dent SY: The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation. Cell. 2005, 122: 723-734.PubMed CentralPubMedGoogle Scholar
- Vernarecci S, Ornaghi P, Bagu A, Cundari E, Ballario P, Filetici P: Gcn5p plays an important role in centromere kinetochore function in budding yeast. Mol Cell Biol. 2008, 28: 988-996.PubMed CentralPubMedGoogle Scholar
- Singer MS, Kahana A, Wolf AJ, Meisinger LL, Peterson SE, Goggin C, Mahowald M, Gottschling DE: Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics. 1998, 150: 613-632.PubMed CentralPubMedGoogle Scholar
- Katan-Khaykovich Y, Struhl K: Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO J. 2005, 24: 2138-2149.PubMed CentralPubMedGoogle Scholar
- Ladurner AG, Inouye C, Jain R, Tjian R: Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol Cell. 2003, 11: 365-376.PubMedGoogle Scholar
- Fingerman IM, Li HC, Briggs SD: A charge-based interaction between histone H4 and Dot1 is required for H3K79 methylation and telomere silencing: identification of a new trans-histone pathway. Genes Dev. 2007, 21: 2018-2029.PubMed CentralPubMedGoogle Scholar
- Gardner RG, Nelson ZW, Gottschling DE: Ubp10/Dot4p regulates the persistence of ubiquitinated histone H2B: distinct roles in telomeric silencing and general chromatin. Mol Cell Biol. 2005, 25: 6123-6139.PubMed CentralPubMedGoogle Scholar
- Emre NC, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, Henry KW, Li K, Marmorstein R, Greenblatt JF, Shilatifard A, et al: Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing. Mol Cell. 2005, 17: 585-594.PubMedGoogle Scholar
- Tompa R, Madhani HD: Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complex. Genetics. 2007, 175: 585-593.PubMed CentralPubMedGoogle Scholar
- Yang B, Kirchmaier AL: Bypassing the catalytic activity of SIR2 for SIR protein spreading in Saccharomyces cerevisiae. Mol Biol Cell. 2006, 17: 5287-5297.PubMed CentralPubMedGoogle Scholar
- Lynch PJ, Rusche LN: A silencer promotes the assembly of silenced chromatin independently of recruitment. Mol Cell Biol. 2008, 29: 43-56.PubMed CentralPubMedGoogle Scholar
- Rusche LN, Rine J: Conversion of a gene-specific repressor to a regional silencer. Genes Dev. 2001, 15: 955-967.PubMedGoogle Scholar
- Robyr D, Suka Y, Xenarios I, Kurdistani SK, Wang A, Suka N, Grunstein M: Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell. 2002, 109: 437-446.PubMedGoogle Scholar
- Mead J, McCord R, Youngster L, Sharma M, Gartenberg MR, Vershon AK: Swapping the gene-specific and regional silencing specificities of the Hst1 and Sir2 histone deacetylases. Mol Cell Biol. 2007, 27: 2466-2475.PubMed CentralPubMedGoogle Scholar
- Sutton A, Heller RC, Landry J, Choy JS, Sirko A, Sternglanz R: A novel form of transcriptional silencing by Sum1-1 requires Hst1 and the origin recognition complex. Mol Cell Biol. 2001, 21: 3514-3522.PubMed CentralPubMedGoogle Scholar
- Halme A, Bumgarner S, Styles C, Fink GR: Genetic and epigenetic regulation of the FLO gene family generates cell-surface variation in yeast. Cell. 2004, 116: 405-415.PubMedGoogle Scholar
- Shanower GA, Muller M, Blanton JL, Honti V, Gyurkovics H, Schedl P: Characterization of the grappa gene, the Drosophila histone H3 lysine 79 methyltransferase. Genetics. 2005, 169: 173-184.PubMed CentralPubMedGoogle Scholar
- Okada Y, Feng Q, Lin Y, Jiang Q, Li Y, Coffield VM, Su L, Xu G, Zhang Y: hDOT1L links histone methylation to leukemogenesis. Cell. 2005, 121: 167-178.PubMedGoogle Scholar
- Zhang W, Xia X, Reisenauer MR, Hemenway CS, Kone BC: Dot1a-AF9 complex mediates histone H3 Lys-79 hypermethylation and repression of ENaCalpha in an aldosterone-sensitive manner. J Biol Chem. 2006, 281: 18059-18068.PubMed CentralPubMedGoogle Scholar
- Okada Y, Jiang Q, Lemieux M, Jeannotte L, Su L, Zhang Y: Leukaemic transformation by CALM-AF10 involves upregulation of Hoxa5 by hDOT1L. Nat Cell Biol. 2006, 8: 1017-1024.PubMed CentralPubMedGoogle Scholar
- Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD: Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast. 1998, 14: 115-132.PubMedGoogle Scholar
- Gardner R, Cronin S, Leader B, Rine J, Hampton R: Sequence determinants for regulated degradation of yeast 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell. 1998, 9: 2611-2626.PubMed CentralPubMedGoogle Scholar
- McConnell AD, Gelbart ME, Tsukiyama T: Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Mol Cell Biol. 2004, 24: 2605-2613.PubMed CentralPubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.