Histone H3


Table of contents

Histone H3 and gene repression in yeast

Repression of yeast mating-type regulated genes by the global repressor Ssn6/Tup1 has been linked to a specific organization of chromatin. Tup1 directly interacts with the amino-terminal tails of histones H3 and H4, providing a molecular basis for this connection. This interaction appears to be required for Tup1 function because amino-terminal mutations in H3 and H4 that weaken interactions with Tup1 cause derepression of both cell-specific genes and DNA damage-inducible genes. Moreover, the Tup1 histone-binding domain coincides with the previously defined Tup1 repression domain. Tup1/histone interactions are negatively influenced by high levels of histone acetylation, suggesting a mechanism whereby the organization of chromatin may be modulated in response to changing environmental signals (Edmondson, 1996).

The Saccharomyces cerevisiae alpha2 repressor controls two classes of cell-type-specific genes in yeast through association with different partners. alpha2-Mcm1 complexes repress a cell-specific gene expression in haploid alpha cells and diploid a/alpha cells, while a1-alpha2 complexes repress haploid-specific genes in diploid cells. In both cases, repression is mediated through Ssn6-Tup1 corepressor complexes that are recruited via direct interactions with alpha2 (Tup1 is a yeast homolog of Groucho). Nucleosomes are positioned adjacent to the alpha2-Mcm1 operator under conditions of repression and Tup1 interacts directly with histones H3 and H4. An examination was carried out of the role of chromatin in a1-alpha2 repression to determine if chromatin is a general feature of repression by Ssn6-Tup1. Mutations in the amino terminus of histone H4 cause a 4- to 11-fold derepression of a reporter gene under a1-alpha2 control, while truncation of the H3 amino terminus has a more modest (3-fold or less) effect. Strikingly, combination of the H3 truncation with an H4 mutation causes a 40-fold decrease in repression, clearly indicating a central role for these histones in a1-alpha2-mediated repression. However, in contrast to the ordered positioning of nucleosomes adjacent to the alpha2-Mcm1 operator, nucleosomes are not positioned adjacent to the a1-alpha2 operator in diploid cells. These data indicate that chromatin is important to Ssn6-Tup1-mediated repression but that the degrees of chromatin organization directed by these proteins differ at different promoters (Huang, 1997).

Position-dependent gene silencing in yeast involves many factors, including the four HIR genes and nucleosome assembly proteins Asf1p (see Drosophila Asf1) and chromatin assembly factor I (CAF-I, a heterotrimeric protein complex encoded by the CAC1-3 genes). CAF-I performs the first step of nucleosome formation, deposition of the histone (H3/H4)2 tetramer onto DNA. CAF-I delivers histones to DNA molecules that have been recently replicated either bidirectionally or during DNA repair; it is targeted to replicated DNA via a direct interaction with proliferating cell nuclear antigen (PCNA), the DNA polymerase processivity factor. Both cacDelta asf1Delta and cacDelta hirDelta double mutants display synergistic reductions in heterochromatic gene silencing. However, the relationship between the contributions of HIR genes and ASF1 to silencing has not previously been explored. Biochemical and genetic studies of yeast Asf1p have revealed links to Hir protein function. In vitro, an active histone deposition complex is formed from recombinant yeast Asf1p and histones H3 and H4 that lack a newly synthesized acetylation pattern. This Asf1p/H3/H4 complex generates micrococcal nuclease-resistant DNA in the absence of DNA replication and stimulates nucleosome assembly activity by recombinant yeast CAF-I during DNA synthesis. Also, Asf1p binds to the Hir1p and Hir2p proteins in vitro and in cell extracts. In vivo, the HIR1 and ASF1 genes contribute to silencing the heterochromatic HML locus via the same genetic pathway. Deletion of either HIR1 or ASF1 eliminates telomeric gene silencing in combination with pol30-8, encoding an altered form of the DNA polymerase processivity factor PCNA that prevents CAF-I from contributing to silencing. Conversely, other pol30 alleles prevent Asf1/Hir proteins from contributing to silencing. It is concluded that yeast CAF-I and Asf1p cooperate to form nucleosomes in vitro. In vivo, Asf1p and Hir proteins physically interact and together promote heterochromatic gene silencing in a manner requiring PCNA. This Asf1/Hir silencing pathway functionally overlaps with CAF-I activity (Sharp, 2001).

Posttranslational modifications of histone tails regulate chromatin structure and transcription. Global analyses are presented of histone acetylation and histone H3 Lys 4 methylation patterns in yeast. A significant correlation is observed between acetylation of histones H3 and H4 in promoter regions and transcriptional activity. In contrast, dimethylation of histone H3 Lys 4 in coding regions correlates with transcriptional activity. The histone methyltransferase Set1 is required to maintain expression of these active, promoter-acetylated, and coding region-methylated genes. Global comparisons reveal that genomic regions deacetylated by the yeast enzymes Rpd3 and Hda1 overlap extensively with Lys 4 hypo- but not hyper-methylated regions. In the context of recent studies showing that Lys 4 methylation precludes histone deacetylase recruitment, it is concluded that Set1 facilitates transcription, in part by protecting active coding regions from deacetylation (Bernstein, 2002).

Histone methylation has emerged as an important mechanism for regulating the transcriptional accessibility of chromatin. Several methyltransferases have been shown to target histone amino-terminal tails and mark nucleosomes associated with either euchromatic or heterochromatic states. However, the biochemical machinery responsible for regulating histone methylation and integrating it with other cellular events has not been well characterized. The Set1 protein complex that is necessary for methylation of histone H3 at lysine residue 4 in Saccharomyces cerevisiae has been purified, molecularly identified, and genetically and biochemically characterized. The seven-member 363-kDa complex contains homologs of Drosophila melanogaster proteins Ash2 and Trithorax and Caenorhabditis elegans protein DPY-30, which are implicated in the maintenance of Hox gene expression and regulation of X chromosome dosage compensation, respectively. Mutations of Set1 protein comparable to those that disrupt developmental function of its Drosophila homolog Trithorax abrogate histone methylation in yeast. These studies suggest that epigenetic regulation of developmental and sex-specific gene expression are species-specific readouts for a common chromatin remodeling machinery associated mechanistically with histone methylation (Nagy, 2002).

Histone 3 lysine 4 (H3 Lys4) methylation in Saccharomyces cerevisiae is mediated by the Set1 complex (Set1C) and is dependent upon ubiquitinylation of H2B by Rad6. Mutually exclusive methylation of H3 at Lys4 or Lys9 is central to chromatin regulation; however, S. cerevisiae lacks Lys9 methylation. Furthermore, a different H3 Lys4 methylase, Set 7/9, has been identified in mammals, thereby questioning the relevance of the S. cerevisiae findings for eukaryotes in general. The majority of Lys4 methylation in Schizosaccharomyces pombe, like in S. cerevisiae, is mediated by Set1C and is Rad6-dependent. S. pombe Set1C mediates H3 Lys(4) methylation in vitro and contains the same eight subunits found in S. cerevisiae, including the homologue of the Drosophila trithorax Group protein, Ash2. Three additional features of S. pombe Set1C each involve PHD fingers. Notably, the Spp1 subunit is dispensable for H3 Lys(4) methylation in budding yeast but required in fission yeast, and Sp_Set1C has a novel proteomic hyperlink to a new complex that includes the homologue of another trithorax Group protein, Lid (Little imaginal discs). Thus, it is inferred that Set1C is highly conserved in eukaryotes but observed that its links to the proteome are not (Roguev, 2003).

Changes in histone acetylation at promoters correlate with transcriptional activation and repression, but whether acetylation of histones in the coding region of genes is important for transcription is less clear. Cells lacking the histone acetyltransferases Gcn5 and Elp3 have widespread and severe histone H3 hypoacetylation in chromatin. Surprisingly, severe hypoacetylation in the promoter does not invariably affect the ability of TBP to bind the TATA element, or transcription of the gene. By contrast, similar hypoacetylation of the coding region correlates with inhibition of transcription, and inhibition correlates better with the overall charge of the histone H3 tail than with hypoacetylation of specific lysine residues. These data provide insights into the effects of histone H3 hypoacetylation in vivo and underscore the importance of the overall charge of the histone tail for transcription (Kristjuhan, 2002).

These data suggest that only very severe H3 hypoacetylation in the coding region of an active gene correlates with effects on transcription. For example, reducing the average overall acetylation level in the coding region to about half of that of wild-type did not show a relationship with reduced transcription, while the 4- to 5-fold reduction introduced at some genes invariably correlated with a dramatic transcription effect. Interestingly, similarly severe reductions in histone H3 promoter acetylation did not always correlate with reduced transcription, and the levels of promoter acetylation and coding region acetylation did not change together. For example, transcription at genes such as FAB1 and TRA1 was not significantly affected, yet their average promoter acetylation was reduced 5-fold. In contrast to the promoter, acetylation in the coding region of these genes was only slightly reduced. This suggests that histone H3 acetylation in the promoter and coding region can be deposited independently and that it can differentially affect the initial association of TBP with promoters and 'postrecruitment events' such as, for example, the movement of RNAPII through DNA (Kristjuhan, 2002).

Gene silencing in eukaryotes is associated with the formation of heterochromatin, a complex of proteins and DNA that block transcription. Heterochromatin is characterized by the methylation of cytosine nucleotides of the DNA, the methylation of histone H3 at lysine 9 (H3 Lys 9), and the specific binding of heterochromatin protein 1 (HP1) to methylated H3 Lys 9. Although the relationship between these chromatin modifications is generally unknown, in the fungus Neurospora crassa, DNA methylation acts genetically downstream of H3 Lys 9 methylation. Kryptonite, a methyltransferase gene specific to H3 Lys 9, was identified in a mutant screen for suppressors of gene silencing at the Arabidopsis thaliana Superman (Sup) locus. Loss-of-function kryptonite alleles resemble mutants in the DNA methyltransferase gene Chromomethylase3 (Cmt3), showing loss of cytosine methylation at sites of CpNpG trinucleotides (where N is A, C, G or T) and reactivation of endogenous retrotransposon sequences. Cmt3 interacts with an Arabidopsis homolog of HP1, which in turn interacts with methylated histones. These data suggest that CpNpG DNA methylation is controlled by histone H3 Lys 9 methylation, through interaction of Cmt3 with methylated chromatin (Jackson, 2002).

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. dim-2 encodes a DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora crassa. Another Neurospora gene, dim-5, is required for DNA methylation, as well as for normal growth and full fertility. dim-5 was mapped and identified by transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a gene related to histone methyltransferases that is involved in heterochromatin formation in other organisms. Transformation of a wild-type strain with a segment of dim-5 reactivated a silenced hph gene, apparently by 'quelling' of dim-5. Recombinant DIM-5 protein specifically methylates histone H3 and replacement of lysine 9 in histone H3 with either a leucine or an arginine phenocopies the dim-5 mutation. It is concluded that DNA methylation depends on histone methylation (Tumaru, 2003).

Centromeric domains often consist of repetitive elements that are assembled in specialized chromatin, characterized by hypoacetylation of histones H3 and H4 and methylation of lysine 9 of histone H3 (K9-MeH3). Perturbation of this underacetylated state by transient treatment with histone deacetylase inhibitors leads to defective centromere function, correlating with delocalization of the heterochromatin protein Swi6/HP1. Likewise, deletion of the K9-MeH3 methyltransferase Clr4/Suvar39 causes defective chromosome segregation. Fission yeast strains retaining one histone H3 and H4 gene have been created; the creation of these strains allows mutation of specific N-terminal tail residues and their role in centromeric silencing and chromosome stability to be investigated. Reduction of H3/H4 gene dosage to one-third does not affect cell viability or heterochromatin formation. Mutation of lysines 9 or 14 or serine 10 within the amino terminus of histone H3 impairs centromere function, leading to defective chromosome segregation and Swi6/HP1 delocalization. Surprisingly, silent centromeric chromatin does not require the conserved lysine 8 and 16 residues of histone H4. To date, mutation of conserved N-terminal residues in endogenous histone genes has only been performed in budding yeast, which lacks the Clr4/Suvar39 histone methyltransferase and Swi6/HP1. This study demonstrated the importance of conserved residues within the histone H3 N terminus for the maintenance of centromeric heterochromatin in fission yeast. In sharp contrast, mutation of two conserved lysines within the histone H4 tail has no impact on the integrity of centromeric heterochromatin. These data highlight the striking divergence between the histone tail requirements for the fission yeast and budding yeast silencing pathways (Mellone, 2003).

The presence of Set2-mediated methylation of H3K36 (K36me) correlates with transcription frequency throughout the yeast genome (see Drosophila Set2). K36me targets the Rpd3S complex to deacetylate transcribed regions and suppress cryptic transcription initiation at certain genes. Using a genome-wide approach, this study reports that the Set2-Rpd3S pathway is generally required for controlling acetylation at coding regions. When using acetylation as a functional readout for this pathway, longer genes and, surprisingly, genes transcribed at lower frequency exhibit a stronger dependency. Moreover, a systematic screen using high-resolution tiling microarrays allowed identification of a group of genes that rely on Set2-Rpd3S to suppress spurious transcripts. Interestingly, most of these genes are within the group that depend on the same pathway to maintain a hypoacetylated state at coding regions. These data highlight the importance of using the functional readout of histone codes to define the roles of specific pathways (Li, 2007).

Active genes are tri-methylated at K4 of histone H3 in Yeast

Lysine methylation of histones in vivo occurs in three states: mono-, di- and tri-methyl. Histone H3 has been found to be di-methylated at lysine 4 (K4) in active euchromatic regions but not in silent heterochromatic sites. The Saccharomyces cerevisiae Set1 protein can catalyse di- and tri-methylation of K4 and stimulate the activity of many genes. Using antibodies that discriminate between the di- and tri-methylated state of K4 it has been shown that di-methylation occurs at both inactive and active euchromatic genes, whereas tri-methylation is present exclusively at active genes. It is therefore the presence of a tri-methylated K4 that defines an active state of gene expression. These findings establish the concept of methyl status as a determinant for gene activity and thus extend considerably the complexity of histone modifications (Santos-Rosa, 2002).

The role of di-methylated K4 H3 may be to determine a transcriptionally 'permissive' chromatin environment whereas the tri-methylated state may allow for an 'active' chromatin conformation. Whether a similar change in methyl status at K4 is operational in the instances where Set1 acts as a repressor is still to be determined. Given that Set1 is the only K4 methylating enzyme in yeast, it is worthwhile noting that di-methylation can take place in the absence of tri-methyl. This suggests that a mechanism exists that prohibits Set1 from adding a third methyl group to di-methylated K4. This may involve, for example, methyl-binding proteins protecting the di-methylated state, a distinct modification preventing the transition of di- to tri-methylated K4 or the action of a demethylase acting on the tri-methylated state (Santos-Rosa, 2002).

Methylation at K4 (both di-methyl and tri-methyl) can be detected in both the promoter and the coding region of genes. This finding is consistent with genome-wide position location analysis, which established that di-methylated K4 is present in promoter and coding regions of genes in yeast but with a bias towards the coding region. The ChIP analysis of specific genes does not allow a determination of the relative amounts of methylation in promoters versus coding regions. However, the fact that tri-methyl is present in the coding region, along with the enrichment of di-methylated K4 in the coding region, suggests a role for K4 methylation in events associated with transcription elongation (Santos-Rosa, 2002).

These findings uncover a new level of regulation of K4 H3 function, by virtue of methylation status, and indicate that Set1 facilitates transcriptional activation. Given that there are many methylated lysines on histones H3 and H4, these observations suggest that the combinatorial potential for covalent modification on histones is far larger than previously suspected. It is no longer possible to surmise the transcriptional state of a gene based on whether a given lysine within its histones is methylated or not. The precise methylation state of the lysine is the true indicator of activity (Santos-Rosa, 2002).

Set1 (Drosophila homolog: Host cell factor), the yeast histone H3-lysine 4 (H3-K4) methylase, is recruited by the Pol II elongation machinery to a highly localized domain at the 5' portion of active mRNA coding regions. Set1 association depends upon the TFIIH-associated kinase that phosphorylates the Pol II C-terminal domain (CTD) and mediates the transition between initiation and elongation, and Set1 interacts with the form of Pol II whose CTD is phosphorylated at serine 5 but not serine 2. The Rtf1 and Paf1 components of the Pol II-associated Paf1 complex are also important for Set1 recruitment. Although the level of dimethylated H3-K4 is fairly uniform throughout the genome, the pattern of trimethylated H3-K4 strongly correlates with Set1 occupancy. Hypermethylated H3-K4 within the mRNA coding region persists for considerable time after transcriptional inactivation and Set1 dissociation from the chromatin, indicating that H3-K4 hypermethylation provides a molecular memory of recent transcriptional activity (Ng, 2003b).

The transition between transcriptional initiation and elongation results in a dramatic change in the factors that associate with Pol II in vivo. During the process of initiation at the promoter, Pol II associates with general transcription factors and mediator proteins. After TFIIH-dependent phosphorylation of Pol II, these initiation factors dissociate from Pol II and are replaced by a variety of so-called elongation factors, such as the Spt4,5, TREX, and Paf complexes. These elongation factors associate with the entire mRNA coding region, and in some cases it has been shown that they travel with elongating Pol II (Ng, 2003b and references therein).

The striking localization of Set1 to the 5' end of the mRNA coding region is distinct from all previously described proteins involved in elongation and other postinitiation processes. Thus, Set1 is recruited by, but does not travel with, the elongating Pol II machinery. Set1 recruitment to mRNA coding regions depends on TFIIH-dependent phosphorylation of the Pol II CTD at serine 5, and Set1 interacts with Pol II that is phosphorylated at CTD-serine 5. However, TFIIH-dependent phosphorylation of the Pol II CTD at serine 5 can occur at the promoter and hence is not sufficient for Set1 recruitment, which is restricted to the mRNA coding region. Set1 recruitment to mRNA coding regions also involves the Rtf1 and Paf1 components of the Pol II-associated Paf complex. However, the Paf complex associates with essentially the entire active mRNA coding region, indicating that the presence of the Paf complex on an active gene does not necessarily result in Set1 association. Thus, Set1 is recruited by a specific and heretofore undescribed form of the elongating Pol II complex (Ng, 2003b and references therein).

The simplest model is that Set1 recruitment occurs specifically with elongating Pol II during the exchange of the associated initiation and elongation factors. It is suggested that Set1 association occurs after dissociation of the mediator complex from Pol II and around the time or after association of the Paf complex (and possibly other factors that travel with elongating Pol II). Although TFIIH-dependent phosphorylation of CTD-serine 5 at the promoter initiates this transition, it is presumed that mediator dissociation and/or Paf complex association occur downstream of the promoter. In this view, Set1 association would depend on a form of Pol II that is phosphorylated at CTD-serine 5 and contains the Paf complex (and perhaps other elongation factors), and Set1 association with Pol II might be inhibited by the mediator complex. It is further suggested that continued Set1 association with the mRNA coding region does not occur because CTD-serine 5 phosphorylation is strongly biased to the 5' coding region, presumably reflecting the activity of a CTD-serine 5 phosphatase. Consistent with this idea, Set1 does not associate with Pol II phosphorylated at serine 2 of the CTD, and Ctk1-mediated phosphorylation of serine 2 occurs preferentially at downstream portions of mRNA coding regions. It is also possible that Set1 association might be actively inhibited by CTD-serine 2 phosphorylation or by the full complement of associated factors that travel with Pol II throughout the entire gene. Although the molecular details remained to be determined, the results clearly demonstrate that Set1 recruitment defines a distinct, and previously undescribed, stage of the Pol II transcription process that occurs after initiation (Ng, 2003b and references therein).

Targeted H3-K4 trimethylation (and induced dimethylation) constitutes a molecular memory within the mRNA coding region for recent transcriptional activity. Specifically, H3-K4 trimethylation in the mRNA coding region occurs only during the act of transcription, yet this specific and localized chromosomal mark persists for considerable time after transcriptional inactivation and Set1 dissociation. In other words, H3-K4 trimethylation within a given mRNA coding region informs the cell that transcription of that gene occurred in the recent past but is not necessarily happening at the present time. Thus, by the definition of memory, during the time period when a gene contains a localized mark of H3-K4 trimethylation yet is transcriptionally inactive, the cell remembers that this gene was transcribed recently (Ng, 2003b and references therein).

This molecular memory clearly lasts for a significant portion of an individual cell cycle, and the induced modifications might be transmitted to new progeny after cell division. However, this memory of recent transcriptional activity is not faithfully transmitted to all daughter cells and hence is mechanistically distinct from long-term epigenetic memory as occurs in transcriptional silencing and position-effect variegation. Of particular interest, the relatively short-term memory described here is different from the long-term memory during Drosophila development mediated by the Set1-like Trithorax protein or from epigenetic silencing in yeast heterochromatin which is affected by Set1 itself. Thus, H3-K4 methylation is involved in biologically and mechanistically distinct short-term and long-term memories of transcriptional activity (Ng, 2003b and references therein).

In principle, loss of H3-K4 trimethylation (and induced dimethylation) upon transcriptional inactivation can be due to nontransmission of the modification to both sister chromosomes during DNA replication and/or to nonreplicative exchange of histones (or, less likely, active histone demethylation). The loss of H3-K4 trimethylation (and induced dimethylation) occurs somewhat more rapidly than can be accounted for solely by dilution upon cell division, suggesting that nonreplicative histone exchange contributes to removal of the memory mark. Histone exchange during this time would favor dimethylated H3-K4 over the trimethylated form, and this (and perhaps also incomplete dissociation of Set1 at the early time points) might explain why dimethylated H3-K4 levels decrease more slowly than trimethylated H3-K4 levels upon transcriptional inactivation (Ng, 2003b and references therein).

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. 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. 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, these results suggest that the Paf1 complex is required for histone H3 methylation, therefore linking transcriptional elongation to chromatin methylation (Krogan, 2003b).

Hypoacetylated histones are a hallmark of heterochromatin in organisms ranging from yeast to humans. Histone deacetylation is carried out by both NAD+-dependent and NAD+-independent enzymes. In the budding yeast Saccharomyces cerevisiae, deacetylation of histones in heterochromatic chromosomal domains requires Sir2, a phylogenetically conserved NAD+-dependent deacetylase. In the fission yeast Schizosaccharomyces pombe, NAD+-independent histone deacetylases are required for the formation of heterochromatin, but the role of Sir2-like deacetylases in this process has not been evaluated. spSir2, the S. pombe Sir2-like protein that is the most closely related to the S. cerevisiae Sir2, has been shown to be an NAD+-dependent deacetylase that efficiently deacetylates histone H3 lysine 9 (K9) and histone H4 lysine 16 (K16) in vitro. In sir2delta cells, silencing at the donor mating-type loci, telomeres, and the inner centromeric repeats (imr) is abolished, while silencing at the outer centromeric repeats (otr) and rDNA is weakly reduced. Furthermore, Sir2 is required for hypoacetylation and methylation of H3-K9 and for the association of Swi6 with the above loci in vivo. These findings suggest that the NAD+-dependent deacetylase Sir2 plays an important and conserved role in heterochromatin assembly in eukaryotes (Shankaranarayana, 2003).

Transcription by RNA polymerase II (polII) is accompanied by dramatic changes in chromatin structure. Numerous enzymatic activities contribute to these changes, including ATP-dependent nucleosome remodeling enzymes and histone modifying enzymes. Recent studies in budding yeast document a histone modification pathway associated with polII transcription, whereby ubiquitylation of histone H2B leads to methylation of histone H3 on specific lysine residues. Although this series of events appears to be highly conserved among eukaryotes, its mechanistic function in transcription is unknown. This study documents a significant functional divergence between ubiquitylation of H2B and methylation of Lys 4 on histone H3 in the fission yeast Schizosaccharomyces pombe. Loss of H2B ubiquitylation results in defects in cell growth, septation, and nuclear structure, phenotypes not observed in cells lacking H3 Lys 4 methylation. Consistent with these results, gene expression microarray analysis reveals a greater role for H2B ubiquitylation in gene regulation than for H3 Lys 4 methylation. Chromatin immunoprecipitation (ChIP) experiments demonstrate that loss of H2B ubiquitylation alters the distribution of polII and histones in gene coding regions. It is proposed that ubiquitylation of H2B impacts transcription elongation and nuclear architecture through its effects on chromatin dynamics (Tanny, 2007).

Histone H3 methylation and recruitment of silencing factors and cohesin to yeast centromeres

Metazoan centromeres are generally composed of large repetitive DNA structures packaged in heterochromatin. Similarly, fission yeast centromeres contain large inverted repeats and two distinct silenced domains that are both required for centromere function. The central domain is flanked by outer repetitive elements coated in histone H3 methylated on lysine 9 and bound by conserved heterochromatin proteins. This centromeric heterochromatin is required for cohesion between sister centromeres. Defective heterochromatin causes premature sister chromatid separation and chromosome missegregation. A deletion strategy was used to identify centromeric sequences that allow heterochromatin formation in fission yeast. Fragments from the outer repeats are sufficient to cause silencing of an adjacent gene when inserted at a euchromatic chromosomal locus. This silencing is accompanied by the local de novo methylation of histone H3 on lysine 9, recruitment of known heterochromatin components, Swi6 and Chp1, and the provision of a new strong cohesin binding site. In addition, it has been demonstrated that the chromodomain of Chp1 binds to MeK9-H3 and that Chp1 itself is required for methylation of histone H3 on lysine 9. It is concluded that a short sequence, reiterated at fission yeast centromeres, can direct silent chromatin assembly and cohesin recruitment in a dominant manner. The heterochromatin formed at the euchromatic locus is indistinguishable from that found at endogenous centromeres. Recruitment of Rad21-cohesin underscores the link between heterochromatin and chromatid cohesion and indicates that these centromeric elements act independently of kinetochore activity to recruit cohesin (Partridge, 2002).

Interaction of RanGAP with H3 in yeast

Although the Ran GTPase-activating protein RanGAP (see Drosophila Ran) mainly functions in the cytoplasm, several lines of evidence indicate a nuclear function of RanGAP. Schizosaccharomyces pombe RanGAP, SpRna1, binds the core of histone H3 (H3) and enhances Clr4-mediated H3-lysine 9 (K9) methylation. This enhancement is not observed for methylation of the H3-tail containing K9 and is independent of SpRna1-RanGAP activity, suggesting that SpRna1 itself enhances Clr4-mediated H3-K9 methylation via H3. Although most SpRna1 is in the cytoplasm, some cofractionates with H3. Sprna1(ts) mutations causes decreases in Swi6 localization and H3-K9 methylation at all three heterochromatic regions of S. pombe. Thus, nuclear SpRna1 seems to be involved in heterochromatin assembly. All core histones bind SpRna1 and inhibit SpRna1-RanGAP activity. In contrast, Clr4 abolishes the inhibitory effect of H3 on the RanGAP activity of SpRna1 but partially affects the other histones. SpRna1 forms a trimeric complex with H3 and Clr4, suggesting that nuclear SpRna1 is reciprocally regulated by histones, especially H3, and Clr4 on the chromatin to function for higher order chromatin assembly. It was also found that SpRna1 forms a stable complex with Xpo1/Crm1 plus Ran-GTP, in the presence of H3 (Nishijima, 2006).

Heterochromatin formation involves changes in histone modifications over multiple cell generations

Stable, epigenetic inactivation of gene expression by silencing complexes involves a specialized heterochromatin structure, but the kinetics and pathway by which euchromatin is converted to the stable heterochromatin state are poorly understood. Induction of heterochromatin in Saccharomyces cerevisiae by expression of the silencing protein Sir3 results in rapid loss of histone acetylation, whereas removal of euchromatic histone methylation occurs gradually through several cell generations. Unexpectedly, Sir3 binding and the degree of transcriptional repression gradually increase for 3-5 cell generations, even though the intracellular level of Sir3 remains constant. Strains lacking Sas2 histone acetylase or the histone methylases that modify lysines 4 (Set1) or 79 (Dot1) of H3 display accelerated Sir3 accumulation at HMR or its spreading away from the telomere, suggesting that these histone modifications exert distinct inhibitory effects on heterochromatin formation. These findings suggest an ordered pathway of heterochromatin assembly, consisting of an early phase, driven by active enzymatic removal of histone acetylation and resulting in incomplete transcriptional silencing, followed by a slower maturation phase, in which gradual loss of histone methylation enhances Sir association and silencing. Thus, the transition between euchromatin and heterochromatin is gradual and requires multiple cell division cycles (Katan-Khaykovich, 2004).

Unlike the rapid loss of histone acetylation via the action of Sir2 and possibly other histone deacetylases, loss of H3-K79 and H3-K4 methylation in the course of heterochromatin formation is gradual and relatively slow due to the relative stability of these modifications. The dynamics of the different H3-K4 methylation marks at HMRa1/a2 reveal consecutive peaks of tri-, di-, and mono-methylation, with the latter decreasing substantially only after more than three generations. Importantly, the decline of a given methylation mark correlates with rising levels of the mark with one fewer methyl groups. This observation cannot be explained simply by passive dilution through DNA replication. Instead, the observation suggests that, during heterochromatin assembly, histones are exchanged and Set1 action on newly deposited histones is gradually reduced to favor tri-, then di-, then mono-methylation, with complete inhibition occurring at later times. The progressive association of Sir proteins is likely to progressively restrict access of Set1 to chromatin, and, in this view, the shift between the different methylated H3-K4's represents another indication that the transition between euchromatin and heterochromatin is gradual and takes multiple cell generations. An alternative mechanism, which is considered less likely, is direct conversion of tri- to di- to mono-methylation by an unknown histone demethylase. As indicated by the slow and gradual changes in H3-K4 methylation marks, such a hypothetical histone demethylase would be inefficient in the context of heterochromatin assembly (Katan-Khaykovich, 2004).

Unlike the case for H3-K4 methylation, both the kinetic analysis and synthetic silencer experiments suggest that replication-coupled histone deposition serves as the major (though not exclusive) removal mechanism for H3-K79 methylation. Four possibilities for why H3-K4 and H3-K79 methylation is lost with different kinetics during heterochromatin formation are considered. (1) Replication-independent histone exchange might preferentially occur on H3-K4-methylated nucleosomes. (2) Histone tail cleavage would preferentially remove H3-K4 methylation, although such a mechanism would have to be coupled with re-methylation of newly deposited histones to account for the consecutive peaks of different H3-K4 methylated forms. (3) The more rapid disappearance of H3-K4 methylation might be due to an H3-K4-specific histone demethylase: such an enzyme has been described recently in mammalian cells. (4) The extent of histone exchange, inferred from the pattern of H3-K4 methylation, might be masked by efficient H3-K79 methylation of newly deposited histones. In this regard, >90% of H3 is methylated at K79 (considering all three forms), whereas only 35% is methylated at K4 (Katan-Khaykovich, 2004).

Various histone modifications were examined across the promoter and the coding regions of constitutively active hepatic genes in G0/G1-enriched, mitotically arrested and alpha-amanitin-blocked cells. Gene activation correlates with localized histone hyperacetylation, H3-K4 tri- or di-methylation and H3-K79 dimethylation and localized nucleosome remodeling at the promoter and the 5' portion of the coding regions. Nucleosomes at more downstream locations are monomethylated at H3-K4. CBP, PCAF (see Drosophila Pcaf), Brg-1, SNF2H and FACT are recruited to the coding regions in a gene-specific manner, in a similarly restricted promoter-proximal pattern. Elongator, however, associates with the more downstream regions. While all factors are dissociated from the chromatin after transcriptional inactivation by alpha-amanitin, the histone modifications remain stable. In mitotic cells, histone modifications on parental nucleosomes are preserved and are regenerated in a transcription-dependent manner at the newly deposited nucleosomes, as the cells entered the next G1 phase. The findings suggest that histone modifications may function as molecular memory bookmarks for previously active locations of the genome, thus contributing to the maintenance of active chromatin states through cell division (Kouskouti, 2005).

Methylation of histone H3 targets programmed DNA elimination in Tetrahymena

Histone H3 lysine 9 methylation [Me(Lys9)H3] is an epigenetic mark for heterochromatin-dependent gene silencing, mediated by direct binding to chromodomain-containing proteins such as Heterochromatin Protein 1. In the ciliate Tetrahymena, two chromodomain proteins, Pdd1p and Pdd3p, are involved in the massive programmed DNA elimination that accompanies macronuclear development. Both proteins bind H3(Lys9)Me in vitro. In vivo, H3(Lys9)Me is confined to the time period and location where DNA elimination occurs, and associates with eliminated sequences. Loss of parental Pdd1p expression drastically reduces H3(Lys9)Me. Finally, tethering Pdd1p is sufficient to promote DNA excision. These results extend the range of H3(Lys9)Me involvement in chromatin activities outside transcriptional regulation and also strengthen the link between heterochromatin formation and programmed DNA elimination (Taverna, 2002).

How are the methylated regions targeted for degradation? It has been estimated that about 6000 DNA elimination events may occur during Tetrahymena macronuclear development. Coordinated excision of these elements must require a marking mechanism of considerable specificity. One possibility is that non-coding RNA molecules play a role in IES recognition. Increasing evidence points to the involvement of non-coding RNAs in the regulation of chromatin structure. Several lines of evidence suggest a possible involvement of RNA in ciliate programmed DNA elimination as well. Bidirectional transcription of internal eliminated sequences (IESs) occurs between approximately three and nine hours of conjugation. Inhibiting this transcription perturbs IES excision. Although the transcripts apparently vanish prior to DNA elimination, it is possible they have become digested into small fragments undetectable by the blotting methods used, as routinely found with small interfering RNAs. In addition, numerous studies have documented the ability of the parental macronuclei to influence processing of DNAs in the developing anlagen. Because this influence is sequence-specific and transmissible through the cytoplasm, an RNA component has been hypothesized to be involved. Indeed, evidence has been provided that small, specific RNAs play a role in programmed DNA elimination, and that accumulation of these RNAs is Pdd1p-dependent. It is interesting to note that some chromodomains have RNA binding activity and that Pdd1p's third globular domain, characterized in one study as a divergent chromodomain , shares sequence similarity with an RNA binding region of the protein SUI1. If an RNA/Pdd1p association (direct or indirect) between three and seven hours of conjugation is required for targeting of methyltransferase activity to IESs, this would explain the drastic loss of Me(Lys9)H3 in mating cells carrying a parental PDD1 knockout, these cells completely lack Pdd1p during this period (Taverna, 2002).

Methylated H3K27 is an important mark for Polycomb group (PcG) protein-mediated transcriptional gene silencing (TGS) in multicellular eukaryotes. Drosophila E(z) homolog, EZL1 has been characterized in the ciliated protozoan Tetrahymena thermophila and is shown to be responsible for H3K27 methylation associated with developmentally regulated heterochromatin formation and DNA elimination. Importantly, Ezl1p-catalyzed H3K27 methylation occurs in an RNA interference (RNAi)-dependent manner. H3K27 methylation also regulates H3K9 methylation in these processes. Furthermore, an 'effector' of programmed DNA elimination, the chromodomain protein Pdd1p, is shown to bind both K27- and K9-methylated H3. These studies provide a framework for an RNAi-dependent, Polycomb group protein-mediated heterochromatin formation pathway in Tetrahymena and underscore the connection between the two highly conserved machineries in eukaryotes (Liu, 2007).

Extensive studies, most notably in the fission yeast Schizosaccharomyces pombe, have established RNA interference (RNAi)-dependent H3K9 methylation as a central process for formation of constitutive heterochromatin, by which genes are silenced in pericentromeric regions and other regions containing repetitious DNA sequences. In this pathway, small interfering RNAs (siRNAs) homologous to the repeated sequences are generated by Dicer and associate with an Argonaute homolog. Via mechanisms not yet fully defined, these siRNAs target histone-modifying activities, in particular, Clr4, a H3K9-specific histone lysine methyltransferase (HKMT), to homologous loci. Methylated H3K9 recruits effectors like Swi6 and Chp1, through direct interaction with the chromodomains of these HP1-like proteins, leading eventually to the formation of condensed heterochromatin structures. These conserved mechanisms are important for maintaining genome integrity as well as transcriptional gene silencing (TGS) in a wide range of eukaryotes (Liu, 2007).

Important insights into RNAi-dependent heterochromatin formation have also been gained from studying developmentally regulated DNA elimination in Tetrahymena thermophila. Like most ciliates, Tetrahymena contains a transcriptionally active somatic macronucleus and a transcriptionally inactive germline micronucleus in the same cytoplasmic compartment. Dramatic genome reorganization occurs when macronuclei develop from micronuclei during conjugation, the sexual phase of the Tetrahymena life cycle. During a precisely programmed developmental window, ~15% of the micronuclear genome, mostly moderately repeated sequences, are compacted into cytologically distinct, heterochromatic structures in developing macronuclei (anlagen) and eventually eliminated from the mature macronuclei. This genome streamlining process functions arguably as the ultimate form of TGS (Liu, 2007).

In keeping with mechanisms underlying RNAi-mediated heterochromatin formation, an RNAi mechanism is also involved in DNA elimination. A special class of siRNAs enriched in micronuclear-limited sequences accumulates during conjugation. These siRNAs are produced from double-stranded transcripts synthesized during early conjugation, by the action of DCL1, a Dicer homolog, and their accumulation depends on TWI1, an Argonaute/PIWI homolog. Both DCL1 and TWI1 are required for appropriate deposition of methylated H3K9, which associates specifically with micronuclear-limited sequences. Pdd1p and Pdd3p, both abundant conjugation-specific chromodomain-containing proteins, bind methylated H3K9, associate with micronucleus-limited sequences, and are key components of the heterochromatic structures in which DNA elimination occurs. These observations point to a pathway in which siRNAs target H3K9 methylation and heterochromatin formation to specific chromatin regions (Liu, 2007).

Another type of heterochromatin, referred to as facultative heterochromatin, is associated with developmentally regulated TGS and mediated by Polycomb group (PcG) proteins. Among the most conserved PcG proteins are SET domain-containing E(z) and homologous HKMTs, which are responsible for H3K27 methylation in Caenorhabditis elegans, Drosophila, mammals, and Arabidopsis. Methylated H3K27, especially in the trimethylated form (H3K27me3), has since been identified as an important mark for facultative heterochromatin, involved in diverse processes like maintenance of the silent state of Hox genes in Drosophila and mammals, X-chromosome inactivation in female mammals, and vernalization in Arabidopsis. Polycomb (Pc) and homologous chromodomain proteins specifically interact with H3K27me3. This interaction plays an important role in recruiting and stabilizing PcG proteins at the target loci, leading to formation of facultative heterochromatin crucial for TGS (Liu, 2007).

Recently, evidence has accumulated that hints at a connection between RNAi and H3K27 methylation. Cosuppression at the transcriptional level in Drosophila is Polycomb-dependent and affected RNAi-deficient mutants . RNAi components are also required for nuclear clustering of Polycomb group response elements. In mammalian cells, Ago1 has been linked with PcG-regulated silencing and Ezh2 [a mammalian E(z) homolog]-catalyzed H3K27me3. While these results suggest that TGS and facultative heterochromatin formation mediated by H3K27me3 may be RNAi dependent, underlying mechanisms remain poorly understood. This study reports the characterization in Tetrahymena of a conjugation-specific H3K27 HKMTs (EZL1) homologous to Drosophila E(z). It is further demonstrated that EZL1-dependent H3K27 methylation is required for developmentally regulated DNA elimination and is connected to the RNAi pathway that leads to H3K9 methylation and DNA elimination. Evidence is presented that H3K27 methylation may regulate H3K9 methylation, and that both marks are specifically recognized by Pdd1p, a chromodomain protein associated with the DNA elimination heterochromatic structures. These findings lend support to the general view that a highly conserved mechanism underlies diverse heterochromatin-based epigenetic phenomena ranging from DNA elimination in ciliates to developmentally regulated TGS in higher eukaryotes (Liu, 2007).

DNA methylation controls histone H3 methylation and heterochromatin assembly in Arabdopsis

Several mutants with reduced DNA methylation levels have been isolated in Arabidopsis. The strongest effects on DNA methylation were found in the recessive mutants decrease in DNA methylation1 (ddm1) and methyltransferase1 (met1). DDM1 encodes a SWI/SNF-like protein, presumably a chromatin remodeling factor, while MET1 encodes a maintenance methyltransferase. They are the plant homologs of the mammalian Lsh and Dnmt1 genes, respectively. In both ddm1 and met1 mutants, repetitive and single-copy sequences become hypomethylated, causing a reduction in methylation level by ~70%. Remethylation of hypomethylated sequences is extremely slow or absent when ddm1 is backcrossed to the wild type. The mutants are further characterized by release of transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS) and by reactivation of some transposons. Morphological phenotypes of ddm1 and met1 include altered flower morphology and leaf shape, sterility and late flowering, and appear in the first homozygous mutant generation in met1, but only after several generations of inbreeding in ddm1 (Soppe, 2002 and references therein).

A model for heterochromatin assembly is proposed that links DNA methylation with histone methylation and DNA replication. The hypomethylated Arabidopsis mutants ddm1 and met1 were used to investigate the relationship between DNA methylation and chromatin organization. Both mutants show a reduction of heterochromatin due to dispersion of pericentromeric low-copy sequences away from heterochromatic chromocenters. DDM1 and MET1 control heterochromatin assembly at chromocenters by their influence on DNA maintenance (CpG) methylation and subsequent methylation of histone H3 lysine 9. In addition, DDM1, is required for deacetylation of histone H4 lysine 16. Analysis of F1 hybrids between wild-type and hypomethylated mutants revealed that DNA methylation is epigenetically inherited and represents the genomic imprint that is required to maintain pericentromeric heterochromatin (Soppe, 2002).

The decrease in DNA methylation in both hypomethylated mutants is paralleled by reduced methylation of H3K9 at chromocenters. Because only maintenance DNA methyl ation (mainly at CpG sites) is disturbed in the met1 mutant, the primary cause of reduction of H3K9 methylation should be the reduction in DNA methylation. In agreement with this assumption, in F1 plants heterozygous for ddm1, only chromocenters that have reduced DNA methylation also have reduced methylation of H3K9. Therefore, it is proposed that maintenance CpG methylation directs histone H3K9 methylation. This seems to contradict previous results in Neurospora crassa and Arabidopsis, which show that DNA methylation is dependent on H3K9 methylation, and disagrees with the suggestion that the loss of DNA methylation in ddm1 might be a consequence of reduced H3K9 methylation in heterochromatin. This discrepancy might be explained by a difference in function between the methylases involved because the histone methylation-dependent chromomethylase (CMT3) of Arabidopsis specifically methylates non-CpG sites. If CpG DNA methylation induces H3K9 methylation and this, in turn, induces CpNpG methylation, the positive feedback might induce spreading of heterochromatin from high-copy repeats to low-copy pericentromeric sequences (Soppe, 2002 and references therein).

Genomic DNA methylation patterns are maintained immediately after replication by the activities of DNA methyltransferase(s) with a high preference for hemimethylated DNA. The high level of H4 acetylation at this stage might facilitate this process. The additive effect of ddm1 and met1 on chromocenter size reduction in the double mutant ddm1 met1 implies that each gene controls DNA maintenance methylation by different mechanisms. Methylation of DNA by MET1 is probably supported by chromatin remodeling factors such as DDM1. This support might be more important for highly repetitive sequences in strongly condensed heterochromatic regions than for single-copy genes in euchromatic regions, since, in ddm1 mutants, high-copy sequences have already become hypomethylated in the first generation, whereas the single-copy sequences yielding phenotypes may become hypomethylated only in later generations (Soppe, 2002 and references therein).

Immunolabeling of nuclei from F1 hybrids heterozygous for ddm1 or met1 revealed the inability of DDM1 and MET1 to re-establish DNA methylation of chromocenters once it has been lost. This confirms the stable inheritance of DNA hypomethylation by ddm1, and is consistent with a role of DDM1and MET1 in maintenance methylation. The inability to remethylate repetitive sequences does not prevent de novo methylation of multicopy transgenes and endogenous genes in ddm1 and met1. It is possible that such repetitive genes require transcription to be methylated de novo in the process of TGS or PTGS. Transcription is lacking for most hypomethylated centromeric and pericentromeric repetitive sequences, thus preventing their de novo methylation (Soppe, 2002 and references therein).

The increased number of nuclei with H4K16 acetylation at chromocenters of ddm1 plants indicates that DDM1, in addition to its role in DNA methylation, is also involved in histone deacetylation, presumably after completion of maintenance DNA methylation. Similarly, a DDM1-like factor (ISWI) of Drosophila has been found (Corona, 2002) to counteract H4K16 acetylation (Soppe, 2002).

The characteristics of constitutive heterochromatin need to be preserved through cell divisions. A central role is proposed for DDM1, MET1, a H3K9-specific histone methylase (KYP) and a histone deacetylase (H4K16-specific in Arabidopsis) in the reassembly of heterochromatin, directly after DNA replication. DNA maintenance methylation at CpG sites is performed when newly replicated nucleosomes are still accessible due to acetylated H4K16. During or after maintenance methylation of DNA, H3K9 methylation, directed by methylated DNA, might complete heterochromatin assembly, including binding of HP1-like proteins to H3K9. Then DDM1 could mediate deacetylation of H4K16. When either DDM1 or MET1 is lacking, DNA methylation is reduced, causing reduced H3K9 methylation. At pericentromeric regions with low-copy sequences, DNA methylation and H3K9 methylation can fall below a critical threshold. As a consequence, these regions acquire euchromatin features (e.g. H3methylK4) and disperse from chromocenters. If DDM1 is lacking, deacetylation of H4K16 is prevented additionally (Soppe, 2002).

Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and tri-methylation

Transcriptional initiation is a key step in the control of mRNA synthesis and is intimately related to chromatin structure and histone modification. The ubiquitylation of H2A (ubH2A) correlates with silent chromatin and regulates transcriptional initiation. The levels of ubH2A vary during hepatocyte regeneration, and based on microarray expression data from regenerating liver, USP21, a ubiquitin-specific protease was identified that catalyzes the hydrolysis of ubH2A. When chromatin is assembled in vitro, ubH2A, but not H2A, specifically represses the di- and trimethylation of H3K4. USP21 relieves this ubH2A-specific repression. In addition, in vitro transcription analysis revealed that ubH2A represses transcriptional initiation, but not transcriptional elongation, by inhibiting H3K4 methylation. Notably, ubH2A-mediated repression was not observed when H3 Lys 4 was changed to arginine. Furthermore, overexpression of USP21 in the liver up-regulates a gene that is normally down-regulated during hepatocyte regeneration. These studies revealed a novel mode of trans-histone cross-talk, in which H2A ubiquitylation controls the di- and trimethylation of H3K4, resulting in regulation of transcriptional initiation (Nakagawa, 2008).

The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes

The chromatin landscape is key for gene regulation, but little is known about how it differs between sexes or between species. This paper examines the sex-specific chromatin landscape of Drosophila miranda, a species with young sex chromosomes, and compares it with Drosophila melanogaster. Six histone modifications were examined in male and female larvae of D. miranda (H3K4me1, H3K4me3, H3K36me3, H4K16ac, H3K27me3, and H3K9me2), and seven biologically meaningful chromatin states were defined that show different enrichments for transcribed and silent genes, repetitive elements, housekeeping, and tissue-specific genes. The genome-wide distribution of both active and repressive chromatin states differs between males and females. In males, active chromatin is enriched on the X, relative to females, due to dosage compensation of the hemizygous X. Furthermore, a smaller fraction of the euchromatic portion of the genome is in a repressive chromatin state in males relative to females. However, sex-specific chromatin states appear not to explain sex-biased expression of genes. Overall, conservation of chromatin states between male and female D. miranda is comparable to conservation between D. miranda and D. melanogaster, which diverged >30 MY ago. Active chromatin states are more highly conserved across species, while heterochromatin shows very low levels of conservation. Divergence in chromatin profiles contributes to expression divergence between species, with approximately 26% of genes in different chromatin states in the two species showing species-specific or species-biased expression, an enrichment of approximately threefold over null expectation. These data suggest that heteromorphic sex chromosomes in males (that is, a hypertranscribed X and an inactivated Y) may contribute to global redistribution of active and repressive chromatin marks between chromosomes and sexes (Brown, 2014).

Evolutionary homologs: Table of contents

Histone H3: Biological Overview | Regulation | Developmental Biology | Effects of Mutation | References

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