Histone H3: Biological Overview | Evolutionary Homologs | Regulation | Developmental Biology | Effects of Mutation | References
Gene name - Histone H3

Synonyms - H3

Cytological map position -

Function - core histone

Keywords - chromatin

Symbol - His3

FlyBase ID: FBgn0001199

Genetic map position -

Classification - histone-fold/TFIID-TAF/NF-Y domain

Cellular location - nuclear



NCBI links: UniGene | Entrez Gene

Recent literature
Cabrera, J. R., Olcese, U. and Horabin, J. I. (2015). A balancing act: heterochromatin protein 1a and the Polycomb group coordinate their levels to silence chromatin in Drosophila. Epigenetics Chromatin 8: 17. PubMed ID: 25954320
Summary: Early in Drosophila development, Heterochromatin protein 1a (HP1a) collaborates with the Polycomb/trithorax groups of proteins to regulate gene expression and that the two chromatin systems do not act separately as convention describes. This study shows that HP1a affects the levels of both the Polycomb complexes and RNA polymerase II at promoters, as assayed by chromatin immunoprecipitation analysis. Deposition of both the repressive (H3K27me3) and activating (H3K4me3) marks promoted by the Polycomb/trithorax group genes at gene promoters is affected. Additionally, depending on which parent contributes the null mutation of the HP1a gene, the levels of the H3K27me3 and H3K9me3 silencing marks at both promoters and heterochromatin are different. Changes in levels of the H3K27me3 and H3K9me3 repressive marks show a mostly reciprocal nature. The time around the mid-blastula transition, when the zygotic genome begins to be actively transcribed, appears to be a transition/decision point for setting the levels. This study finds that HP1a affects the generation of the epigenetic marks of the Polycomb/trithorax groups of proteins, chromatin modifiers which are key to maintaining gene expression in euchromatin. At gene promoters, deposition of both the repressive H3K27me3 and activating H3K4me3 marks of histone modifications shows a dependence on HP1a. Around the mid-blastula transition, when the zygotic genome begins to be actively transcribed, a pivotal decision for the level of silencing appears to take place. This is also when the embryo organizes its genome into heterochromatin and euchromatin. A balance between the HP1a and Polycomb group silencing systems appears to be set for the chromatin types that each system will primarily regulate.

Lee, Y. C. (2015). The role of piRNA-mediated epigenetic silencing in the population dynamics of transposable elements in Drosophila melanogaster. PLoS Genet 11: e1005269. PubMed ID: 26042931.
Summary:
The piwi-interacting RNAs (piRNA) are small RNAs that target selfish transposable elements (TEs) in many animal genomes. Until now, piRNAs' role in TE population dynamics has only been discussed in the context of their suppression of TE transposition, which alone is not sufficient to account for the skewed frequency spectrum and stable containment of TEs. On the other hand, euchromatic TEs can be epigenetically silenced via piRNA-dependent heterochromatin formation and, similar to the widely known "Position-effect variegation", heterochromatin induced by TEs can "spread" into nearby genes. This study hypothesized that the piRNA-mediated spread of heterochromatin from TEs into adjacent genes has deleterious functional effects and leads to selection against individual TEs. Unlike previously identified deleterious effects of TEs due to the physical disruption of DNA, the functional effect investigated in this study is mediated through the epigenetic influences of TEs. The repressive chromatin mark, H3K9me, was found to be elevated in sequences adjacent to euchromatic TEs at multiple developmental stages in Drosophila melanogaster. Furthermore, the heterochromatic states of genes depend not only on the number of and distance from adjacent TEs, but also on the likelihood that their nearest TEs are targeted by piRNAs. These variations in chromatin status probably have functional consequences, causing genes near TEs to have lower expression. Importantly, stronger selection against TEs were found that lead to higher H3K9me enrichment of adjacent genes, demonstrating the pervasive evolutionary consequences of TE-induced epigenetic silencing. Because of the intrinsic biological mechanism of piRNA amplification, spread of TE heterochromatin could result in the theoretically required synergistic deleterious effects of TE insertions for stable containment of TE copy number. The indirect deleterious impact of piRNA-mediated epigenetic silencing of TEs is a previously unexplored, yet important, element for the evolutionary dynamics of TEs.

Shimaji, K., Konishi, T., Tanaka, S., Yoshida, H., Kato, Y., Ohkawa, Y., Sato, T., Suyama, M., Kimura, H. and Yamaguchi, M. (2015). Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis. Genes Cells 20(11):902-14. PubMed ID: 26334932
Summary:
Post-translational modification of the histone plays important roles in epigenetic regulation of various biological processes. Among the identified histone methyltransferases (HMTases), G9a is a histone H3 Lys 9 (H3K9)-specific example active in euchromatic regions. Drosophila G9a (dG9a) has been reported to feature H3K9 dimethylation activity in vivo. This study shows that the time required for hatching of a homozygous dG9a null mutant and heteroallelic combination of dG9a null mutants is delayed, suggesting that dG9a is at least partially responsible for progression of embryogenesis. Immunocytochemical analyses of the wild-type and the dG9a null mutant flies indicated that dG9a localizes in cytoplasm up to nuclear division cycle 7 where it is likely responsible for di-methylation of nucleosome-free H3K9. From cycles 8-11, dG9a moves into the nucleus and is responsible for di-methylating H3K9 in nucleosomes. RNA-sequence analysis utilizing early wild-type and dG9a mutant embryos showed that dG9a down-regulates expression of genes responsible for embryogenesis. RNA fluorescent in situ hybridization analysis further showed temporal and spatial expression patterns of these mRNAs did not significantly change in the dG9a mutant. These results indicate that dG9a controls transcription levels of some zygotic genes without changing temporal and spatial expression patterns of the transcripts of these genes.

Natsume-Kitatani, Y. and Mamitsuka, H. (2016). Classification of promoters based on the combination of core promoter elements exhibits different histone modification patterns. PLoS One 11: e0151917. PubMed ID: 27003446
Summary:
The associations between core promoter elements (CPEs) and histone modifications were systematically studied by integrating the Drosophila Core Promoter Database and time-series ChIP-seq data for histone modifications (H3K4me3, H3K27ac, and H3K27me3) during development in Drosophila via the modENCODE project. 96 core promoters were classified into four groups based on the presence or absence of the TATA box or DPE, calculated the histone modification ratio at the core promoter region, and transcribed region for each core promoter. Histone modifications found in TATA-less groups were static during development and the core promoters could be clearly divided into three types: 1) core promoters with continuous active marks (H3K4me3 and H3K27ac), 2) core promoters with a continuous inactive mark (H3K27me3) and occasional active marks, and 3) core promoters with occasional histone modifications. Linear regression analysis and non-linear regression by random forest showed that the TATA-containing groups included core promoters without histone modifications, for which the measured RNA expression values were not predictable accurately from the histone modification status. DPE-containing groups had a higher relative frequency of H3K27me3 in both the core promoter region and transcribed region. In summary, this analysis showed that there was a systematic link between the existence of the CPEs and the dynamics, frequency and influence on transcriptional activity of histone modifications.

Elnfati, A. H., Iles, D. and Miller, D. (2016). Nucleosomal chromatin in the mature sperm of Drosophila melanogaster. Genom Data 7: 175-177. PubMed ID: 26981400
Summary:
During spermiogenesis in mammals and many other vertebrate classes, histone-containing nucleosomes are replaced by protamine toroids, which can repackage chromatin at a 10 to 20-fold higher density than in a typical somatic nucleus. However, recent evidence suggests that sperm of many species, including human and mouse retain a small compartment of nucleosomal chromatin, particularly near genes important for embryogenesis. As in mammals, spermiogenesis in the fruit fly, Drosophila melanogaster has also been shown to undergo a programmed substitution of nucleosomes with protamine-like proteins. Using chromatin immunoprecipitation (ChIP) and whole-genome tiling array hybridization (ChIP-chip), supported by immunocytochemical evidence, this stuy shows that in a manner analogous to nucleosomal chromatin retention in mammalian spermatozoa, distinct domains packaged by the canonical histones H2A, H2B, H3 and H4 are present in the fly sperm nucleus. Evidence was also found for the retention of nucleosomes with specific histone H3 trimethylation marks characteristic of chromatin repression (H3K9me3, H3K27me3) and active transcription (H3K36me3).

Lee, H. G., Kahn, T. G., Simcox, A., Schwartz, Y. B. and Pirrotta, V. (2015). Genome-wide activities of Polycomb complexes control pervasive transcription. Genome Res 25: 1170-1181. PubMed ID: 25986499
Summary:
Polycomb group (PcG) complexes PRC1 and PRC2 are well known for silencing specific developmental genes. PRC2 is a methyltransferase targeting histone H3K27 and producing H3K27me3, essential for stable silencing. Less well known but quantitatively much more important is the genome-wide role of PRC2 that dimethylates approximately 70% of total H3K27. H3K27me2 occurs in inverse proportion to transcriptional activity in most non-PcG target genes and intergenic regions and is governed by opposing roaming activities of PRC2 and complexes containing the H3K27 demethylase UTX. Surprisingly, loss of H3K27me2 results in global transcriptional derepression proportionally greatest in silent or weakly transcribed intergenic and genic regions and accompanied by an increase of H3K27ac and H3K4me1. H3K27me2 therefore sets a threshold that prevents random, unscheduled transcription all over the genome and even limits the activity of highly transcribed genes. PRC1-type complexes also have global roles. Unexpectedly, a pervasive distribution of histone H2A ubiquitylated at lysine 118 (H2AK118ub) was found outside of canonical PcG target regions, dependent on the RING/Sce subunit of PRC1-type complexes. It was shown, however, that H2AK118ub does not mediate the global PRC2 activity or the global repression and is predominantly produced by a new complex involving L(3)73Ah, a homolog of mammalian PCGF3.
Kahn, T.G., Dorafshan, E., Schultheis, D., Zare, A., Stenberg, P., Reim, I., Pirrotta, V. and Schwartz, Y.B. (2016). Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements. Nucleic Acids Res [Epub ahead of print]. PubMed ID: 27557709
Summary:
Polycomb Group (PcG) proteins are epigenetic repressors essential for control of development and cell differentiation. They form multiple complexes of which PRC1 and PRC2 are evolutionary conserved and obligatory for repression. The targeting of PRC1 and PRC2 is poorly understood and has been proposed to be hierarchical and involve tri-methylation of histone H3 (H3K27me3) and/or monoubiquitylation of histone H2A (H2AK118ub). This study tested this hypothesis using the Drosophila model. It was discovered that neither H3K27me3 nor H2AK118ub is required for targeting PRC complexes to Polycomb Response Elements (PREs). PRC1 can bind PREs in the absence of PRC2 but at many PREs PRC2 requires PRC1 to be targeted. It was shown that one role of H3K27me3 is to allow PcG complexes anchored at PREs to interact with surrounding chromatin. In contrast, the bulk of H2AK118ub is unrelated to PcG repression. These findings radically change the view of how PcG repression is targeted and suggest that PRC1 and PRC2 can communicate independently of histone modifications.

Penke, T. J., McKay, D. J., Strahl, B. D., Matera, A. G. and Duronio, R. J. (2016). Direct interrogation of the role of H3K9 in metazoan heterochromatin function. Genes Dev [Epub ahead of print]. PubMed ID: 27566777
Summary:
A defining feature of heterochromatin is methylation of Lys9 of histone H3 (H3K9me), a binding site for heterochromatin protein 1 (HP1). Although H3K9 methyltransferases and HP1 are necessary for proper heterochromatin structure, the specific contribution of H3K9 to heterochromatin function and animal development is unknown. Using a recently developed platform to engineer histone genes in Drosophila, H3K9R mutant flies were generated, separating the functions of H3K9 and nonhistone substrates of H3K9 methyltransferases. Nucleosome occupancy and HP1a binding at pericentromeric heterochromatin are markedly decreased in H3K9R mutants. Despite these changes in chromosome architecture, a small percentage of H3K9R mutants complete development. Consistent with this result, expression of most protein-coding genes, including those within heterochromatin, is similar between H3K9R and controls. In contrast, H3K9R mutants exhibit increased open chromatin and transcription from piRNA clusters and transposons, resulting in transposon mobilization. Hence, transposon silencing is a major developmental function of H3K9.
Bahrampour, S. and Thor, S. (2016). Ctr9, a key component of the Paf1 complex affects proliferation and terminal differentiation in the developing Drosophila nervous system. G3 (Bethesda). PubMed ID: 27520958
Summary:
The Paf1 protein complex (Paf1C) promotes H3K4 and H3K36 trimethylation, H2BK123 ubiquitination, RNA Pol II transcriptional termination, and also RNA-mediated gene silencing. Paf1C contains five canonical protein components including Paf1 and Ctr9, that are critical for overall complex integrity, as well as , Leo1 and Cdc73/Hyrax. This study provide the first detailed phenotypic study of Ctr9 function in Drosophila. Ctr9 mutants die at late embryogenesis or early larval life, but can be partly rescued by nervous system re-expression of Ctr9. A number of phenotypes are observed in Ctr9 mutants, including increased neuroblast numbers, increased nervous system proliferation, as well as down-regulation of many neuropeptide genes. Analysis of cell cycle and regulatory gene expression reveals up-regulation of the E2f1 cell cycle factor, as well as changes in Antennapedia and Grainy head expression. Reduction of H3K4me3 modification was found in the embryonic nervous system. Genome-wide transcriptome analysis points to additional downstream genes that may underlie these Ctr9 phenotypes, revealing gene expression changes in Notch pathway target genes, cell cycle genes and neuropeptide genes. In addition, significant effects were found on the gene expression of metabolic genes. These findings reveal that Ctr9 is an essential gene that is necessary at multiple stages of nervous system development, and provides a starting point for future studies of the Paf1C in Drosophila.
McElroy, K. A., Jung, Y. L., Zee, B. M., Wang, C. I., Park, P. J. and Kuroda, M. I. (2017). upSET, the Drosophila homologue of SET3, Is required for viability and the proper balance of active and repressive chromatin marks. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 28064188
Summary:
Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). This study shows that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, S2 cells were generated that are mutant for upset. Loss of UpSET was tolerated in S2 cells, but heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone post-translational modification quantification. To test whether this finding was consistent in the whole organism, the upset coding sequence was deleted using CRISPR/Cas-9; it was found to be lethal in both sexes in flies. This lethality could be rescued using a tagged upSET transgene; UpSET protein was found to localizes to transcriptional start sites of active genes throughout the genome. Misregulated heterochromatin is apparent by suppressed position effect variegation of a wm4 allele in heterozygous upset-deleted flies. This result applies to heterochromatin genes generally using nascent-RNA sequencing in the upset-mutant S2 lines. These findings support a critical role for UpSET in maintaining heterochromatin, perhaps by delimiting the active chromatin environment.
Laprell, F., Finkl, K. and Muller, J. (2017). Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA. Science. PubMed ID: 28302792
Summary:
=Epigenetic inheritance models posit that during Polycomb repression, Polycomb Repressive Complex 2 (PRC2) propagates histone H3K27 tri-methylation (H3K27me3) independently of DNA sequence. This study shows that insertion of Polycomb Response Element (PRE) DNA into the Drosophila genome creates extended domains of H3K27me3-modified nucleosomes in the flanking chromatin and causes repression of a linked reporter gene. After excision of PRE DNA, H3K27me3 nucleosomes become diluted with each round of DNA replication and reporter gene repression is lost, whereas in replication-stalled cells, H3K27me3 levels stay high and repression persists. Hence, H3K27me3-marked nucleosomes provide a memory of repression that is transmitted in a sequence-independent manner to daughter strand DNA during replication. In contrast, propagation of H3K27 tri-methylation to newly incorporated nucleosomes requires sequence-specific targeting of PRC2 to PRE DNA (Laprell, 2017).
Laprell, F., Finkl, K. and Muller, J. (2017). Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA. Science [Epub ahead of print]. PubMed ID: 28302792
Summary:
Epigenetic inheritance models posit that during Polycomb repression, Polycomb Repressive Complex 2 (PRC2) propagates histone H3K27 tri-methylation (H3K27me3) independently of DNA sequence. This study shows that insertion of Polycomb Response Element (PRE) DNA into the Drosophila genome creates extended domains of H3K27me3-modified nucleosomes in the flanking chromatin and causes repression of a linked reporter gene. After excision of PRE DNA, H3K27me3 nucleosomes become diluted with each round of DNA replication and reporter gene repression is lost, whereas in replication-stalled cells, H3K27me3 levels stay high and repression persists. Hence, H3K27me3-marked nucleosomes provide a memory of repression that is transmitted in a sequence-independent manner to daughter strand DNA during replication. In contrast, propagation of H3K27 tri-methylation to newly incorporated nucleosomes requires sequence-specific targeting of PRC2 to PRE DNA.
BIOLOGICAL OVERVIEW

Distinct modifications of histone amino termini, such as acetylation, phosphorylation and methylation, have been proposed to underlie a chromatin-based regulatory mechanism that modulates the accessibility of genetic information. Histone lysine methylation occurs on lysines 4, 9, 27, 36, and 79 of Histone H3 and on lysine 20 of Histone H4. Biochemical and genetic studies indicate that methylation of different lysine residues, with the exception of H3-K79, is catalyzed by different SET domain-containing proteins. Histone H3 methylated at lysine 9 (H3-mLys9) is characteristic of the heterochromatic (genetically silent) state. Immunofluorescent staining of Drosophila polytene chromosomes shows that the bulk of the H3-mLys9 is present in the pericentric heterochromatin and in a banded pattern on the fourth chromosome, known sites of repetitive DNA. Similarly, chromatin immunoprecipitation experiments demonstrate that H3-mLys9 is a prominent component of the silent mating type locus in fission yeast (Schizosaccharomyces pombe), while essentially absent from flanking regions containing inducible genes. Methylation of histone H3-Lys9 has also been associated with the silencing of euchromatic genes (Richards, 2002 and references therein).

A key role for gene silencing and specification of heterochromatin is shown by the demonstration that mammalian homologs of Drosophila Su(var)3-9, including human SUV39H1 and murine Suv39h1, encode enzymes that specifically methylate histone H3 on lysine 9. Su(var)3-9 was originally identified as a suppressor of PEV in Drosophila, indicating that the wild-type gene product is involved in heterochromatin formation. A homolog in S. pombe, Clr4, is also a specific histone H3-Lys9 methyltransferase, suggesting that this activity is widely distributed and well conserved. clr4 mutants exhibit reduced heterochromatin formation at centromeres, with elevated mitotic chromosome loss and reduced silencing within both pericentromeric heterochromatin and the silent mating type locus. Similarly, mammalian Su(var)3-9-like proteins have been implicated in both centromere activity and gene silencing. Disruption of the murine Suv39h1 and Suv39h2 paralogs causes genome instability, chromosome missegregation, and male meiotic defects (Richards, 2002 and references therein).

Drosophila Polycomb Group (PcG) complexes are responsible for the maintenance of the repressed state of genes subject to their control. The best-known PcG targets are the homeotic genes, which are activated in the early embryo by the products of segmentation genes. At this stage, transient, localized activators and repressors determine the segmental domains of expression of each homeotic gene but, after gastrulation, epigenetic (genetically based non-heritable) mechanisms take over to maintain the segmental pattern of expression for the rest of development. These mechanisms are mediated by the Polycomb Response Elements (PREs), regulatory regions of several hundred base pairs, where two kinds of chromatin complexes are assembled. One kind, the PcG complexes, is repressive and can maintain a silent state. The other kind involves the Trithorax protein (Trx) and mediates the persistence of the active state. Which of the two predominates depends on the state of activity of the target promoter at the blastoderm stage of development. If the genes had been repressed by early regulators, the PcG silencing mechanisms maintain the repressed state throughout the rest of development. If the gene was active in the early embryo, the Trx function stimulates its expression and prevents later silencing by the PcG complexes. The gene remains then unrepressed and potentially active for the rest of development. Thus, early transcriptional activity of a target gene sets a mark that maintains transcriptional competence and prevents the establishment of PcG silencing, while early repression results in an antagonistic mark that ensures the maintenance of the silenced state in subsequent cell cycles (Czermin, 2002 and references therein).

Formally, therefore, the PRE mediates both the memory of the silent state and the memory of the derepressed state. The repressive memory is illustrated by the fact that, although PcG proteins are nearly ubiquitous, at every cell division they restore the repressed chromatin state only in cells in which their target genes had been previously repressed. The memory of the derepressed state is shown by the fact that if the target gene is active in the early embryo, or if derepression is forced by massive doses of activator, the derepressed state is inherited by the progeny cells. This memory is affected by trx mutations. In the absence of trx function, cells in which a PRE-containing construct had been activated in the early embryo may lose the derepressed state and become silenced again (Czermin, 2002 and references therein).

In the preblastoderm embryo, Polycomb complexes are assembled at the PREs, which contain consensus sequences for DNA binding proteins such as GAGA factor and Pleiohomeotic (Pho), the fly homolog of the mammalian YY1 factor. These, together with other, unidentified DNA binding proteins, recruit cooperatively a PcG complex that includes Pc, Ph, and GAGA factor but also Esc, E(z), Pho, and Rpd3. The E(z)/Esc/Pho complex dissociates from the Pc-containing complex after the blastoderm stage, and Esc ceases to be produced by the end of embryogenesis. However, the E(z) protein continues to be needed, at least intermittently, to maintain the silent state and is most likely recruited to the PRE by the Pho DNA binding protein. Experiments with Pc targeted to a reporter gene by the LexA DNA binding domain show that, while it can recruit the Esc/E(z) component to establish silencing in the early embryo, it can no longer recruit E(z) at later stages, when the early complex has dissociated. LexA-Pc repression continues in the embryo but the memory of the repressed state is then lost and the reporter gene becomes derepressed during larval stages. These results suggest that E(z) might mediate the creation of a chromatin mark necessary for repression and responsible for maintaining the memory of the silent state (Czermin, 2002 and references therein).

Trx and E(z) are therefore good candidates for the functions required for the positive and negative memories, respectively. Structurally, these two proteins share with Su(var)3-9 the SET domain, named after the three founding members Su(var)3-9, E(z), and Trx. Advances in the past years have shown that the SET domain in many proteins is responsible for a histone H3 methyltransferase (MTase) activity. With one exception, all reported histone MTases that methylate lysine residues contain a SET domain, which harbors the amino acids important for MTase function. Su(var)3-9 and its homologs, in particular, are necessary for the formation of heterochromatic complexes in mammals, flies, and fission yeast. Their activities methylate lysine 9 of histone H3, which becomes a binding site for the chromodomain of heterochromatin proteins such as Hp1 (Czermin, 2002 and references therein).

It was reasoned that Trithorax and Enhancer of zeste might reside in complexes that possess MTase activities. Pc contains a chromodomain whose structure and essential residues are homologous to those found in Hp1 and related methyl lysine binding proteins and might therefore recognize a nucleosomal methylation mark. Both Trx and E(z) complexes have now been shown to contain an H3 MTase activity. To study the Esc/E(z) complex, Drosophila nuclear extract was fractionated and it was asked if a MTase activity copurifies with E(z) and Esc. A complex containing E(z) and Esc trimethylates lysine 9 and methylates lysine 27 of histone H3 and the trimethylated lysine 9 mark is closely correlated with PcG binding sites on polytene chromosomes. The conjecture that the Esc/E(z) complex contains a histone MTase activity has been confirmed by the finding that the complex immunoprecipitated by anti-Esc or purified biochemically methylates in vitro histone H3 whether assembled in a nucleosome, as a free histone, or in the form of oligopeptides. The purified complex contains several components as predicted from previous studies: in addition to E(z), Su(z)12, Esc, p55, and Rpd3 are found. An additional component of approximately 168 kDa remains to be identified (Czermin, 2002).

The activity of the Esc/E(z) complex leads to trimethylation of lysine 9 and probably also of lysine 27 of H3. In vivo, an antibody directed against dimethylated H3 lysine (9me2K9 antibody) does not detectably stain chromosomal PcG sites while a me3K9 antibody directed against trimethylated H3 lysine decorates all chromosomal PcG sites. Whether three methyl groups are added processively or by independent events and whether lysine 9 and lysine 27 are targeted simultaneously remains to be elucidated. The partial ability of the complex to methylate the peptide acetylated at lysine 9 is accounted for by the presence of the Rpd3 deacetylase (Czermin, 2002).

The Su(var)3-9 product has been reported to dimethylate H3 lysine 9, constituting a mark for heterochromatic complexes (Rea, 2000; Lachner, 2001). However, antibody staining of polytene chromosomes detects abundant trimethyl lysine 9 in heterochromatin as well as most of chromosome 4, sites that do not contain PcG complexes. At least some of the heterochromatic me3K9 is lost in Su(var)3-9 mutants. A participation of E(z) in heterochromatic H3 methylation cannot be excluded. This function would be consistent with the report that E(z) mutations are also suppressors of heterochromatic position-effect variegation. However, a more distinct difference between the Su(var)3-9 mark and the E(z) mark is the methylation of H3 K27. In vitro, Su(var)3-9 does not methylate the K27 peptide. It will be important to test whether K27 methylation is present in heterochromatin, but it is likely that K27 methylation differentiates heterochromatic from PcG sites (Czermin, 2002).

Suvar3-9 methylation of lysine 9 of histone H3 is thought to stabilize or even target Hp1-containing heterochromatic complexes through binding of the Hp1 chromodomain to the methylated lysine 9 (Bannister, 2001; Lachner, 2001). The structure of the Hp1 chromodomain bound to histone H3 di- or tri-methylated at lysine 9 shows that either peptide fits in a groove and lodges the methyllysine in a hydrophobic pocket (Nielsen, 2002; Jacobs, 2002). This was confirmed by peptide binding experiments and makes it unlikely that H3 K9 methylation would be sufficient to discriminate between the heterochromatic methylation imprint and the PcG methylation imprint. The parallelism suggests that the chromodomain of Pc would recognize trimethyl lysine 9 H3. Pc has been shown to bind to histone H3 and to nucleosomes in vitro; however, the domain involved does not appear to be the chromodomain but the C-terminal region (Breiling, 1999). Binding experiments detected little increased affinity of Pc for the trimethyl K9 peptide compared to the unmethylated peptide. Instead, methyl K27 appears to make the major contribution to Pc affinity for methylated H3. The amino acid context of K27 (KAARKS) resembles that of K9 (QTARKS) but Hp1 binds weakly to a methylated K27 peptide (Nielsen, 2002; Jacobs, 2002). It remains to be seen which domain of Pc interacts with methylated H3 and whether Hp1 can bind to meK9 meK27 H3. Nevertheless, the presence of me3K9 at PcG sites, as well as in heterochromatin and chromosome 4, suggests that the meK27 or other factors must contribute to discriminate between heterochromatic and PcG sites (Czermin, 2002).

Specific recognition of the methylated histone H3 by Polycomb complexes might be facilitated by other PcG components or by other modifications of the histones. E(z)-dependent methylation might contribute to the stability of the PcG complex, particularly in the early stages of assembly at the PRE, for example, by permitting complex formation to spread to neighboring sequences for a distance of 2- 3 kb. However, the fact that in the E(z)S2 mutant chromosomes the trimethylation mark is lost well before the binding of PcG proteins indicates that methylation is not essential for the binding of the complex. Alternatively, the trimethyl mark might signify the difference between the mere recruitment of a PcG complex and its repressive function. Chromatin immunoprecipitation shows that PcG complexes are present at some PREs whether or not the corresponding gene is repressed, implying that, while recruitment of the complexes may be constitutive, the decision to repress or not depends on other features transmitted epigenetically. The methylation might then constitute the epigenetic mark triggering the silent state. It is interesting to note, therefore, that two polytenic sites that are strongly stained with anti-Psc antibody but very weakly with anti-me3K9 antibody are 2D and 49F, respectively, the sites of the PcG genes ph and Psc. These PcG genes are downregulated but not silenced by PcG mechanisms. If trimethylation of H3 lysine 9 signals strong silencing, these sites might be expected to be occupied by PcG complexes but only partly repressed (Czermin, 2002).

A role of H3 methylation in the assembly of stable PcG complexes is suggested by another observation. When the chromodomain in Hp1 is substituted by the chromodomain of Pc, the chimeric Hp1 is recruited to PcG binding sites on polytene chromosomes. This implies either that the chromodomain is sufficient to recognize and bind to the meK9 meK27 H3 or that the Pc chromodomain specifies critical interactions with other PcG components that are recruited to PcG sites. That the latter interpretation is correct is shown by the fact that the chimeric Hp1 also recruits PcG proteins to heterochromatin, where they are not normally found, and that this recruitment is dependent on E(z) function. Strong staining is observed with the anti-me3K9 antibody in the chromocenter and chromosome 4, implying that me3K9 H3 is widespread in heterochromatin. If this is, in fact, due to E(z) activity, it would explain the intervention of E(z) in the heterochromatic recruitment of PcG proteins mediated by the chimeric Hp1 (Czermin, 2002).

It would be important, therefore, to determine whether E(z) contributes to heterochromatic me3K9. Anti-E(z) antibody does not stain the chromocenter of salivary polytenic chromosomes. In E(z)S2 mutant larvae raised at nonpermissive temperature, me3K9 staining is still seen in heterochromatin although with very variable intensity. One possible explanation for these two observations is that since heterochromatin is very little replicated in polytene chromosomes, the methylated H3 produced before the temperature shift might perdure a long time at nonpermissive temperature (Czermin, 2002).

It is interesting to note that anti-me3K9 staining at telomeres is not affected in Su(var)3-9 null polytene chromosomes but is lost in the absence of E(z) function. Telomeres, particularly those of chromosome 2R and 2L, stain prominently with antibodies against PcG proteins but also against Hp1. A critical role has been attributed to telomeric Hp1 in 'capping' chromosome termini and preventing telomeric fusions, failure to segregate chromosomes, and chromosome breakage. The fact that Drosophila Su(var)3-9 null mutants are perfectly viable implies that this role of Hp1 is not dependent on Su(var)3-9. In contrast, embryos lacking both maternal and zygotic E(z) function are reported to have mitotic phenotypes similar to those attributed to Hp1 mutants. It is likely, therefore, that the recruitment of Hp1 to telomeric sites depends at least in part on E(z) and not on Su(var)3-9. Unfortunately, the evidence obtained with the E(z)S2 mutant is inconclusive (Czermin, 2002).

It is concluded that a combination of histone methylation marks could be a major factor in the establishment of stable patterns of homeotic gene expression and constitutes the molecular basis of a cellular memory system. The analysis of the existing methylation patterns in cells expressing different homeotic genes by chromatin immunoprecipitation will give further insight into how the MTases such as E(z) are targeted to different sites and how they are regulated at different developmental stages (Czermin, 2002).

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

Trimethylation of histone H3 lysine 27 (H3K27me3) by Polycomb repressive complex 2 (PRC2) is essential for transcriptional silencing of Polycomb target genes, whereas acetylation of H3K27 (H3K27ac) has recently been shown to be associated with many active mammalian genes. The Trithorax protein (TRX), which associates with the histone acetyltransferase CBP, is required for maintenance of transcriptionally active states and antagonizes Polycomb silencing, although the mechanism underlying this antagonism is unknown. This study shows that H3K27 is specifically acetylated by Drosophila CBP and its deacetylation involves RPD3. H3K27ac is present at high levels in early embryos and declines after 4 hours as H3K27me3 increases. Knockdown of E(Z) decreases H3K27me3 and increases H3K27ac in bulk histones and at the promoter of the repressed Polycomb target gene abd-A, suggesting that these indeed constitute alternative modifications at some H3K27 sites. Moderate overexpression of CBP in vivo causes a global increase in H3K27ac and a decrease in H3K27me3, and strongly enhances Polycomb mutant phenotypes. TRX is required for H3K27 acetylation. TRX overexpression also causes an increase in H3K27ac and a concomitant decrease in H3K27me3 and leads to defects in Polycomb silencing. Chromatin immunoprecipitation coupled with DNA microarray (ChIP-chip) analysis reveals that H3K27ac and H3K27me3 are mutually exclusive and that H3K27ac and H3K4me3 signals coincide at most sites. It is proposed that TRX-dependent acetylation of H3K27 by CBP prevents H3K27me3 at Polycomb target genes and constitutes a key part of the molecular mechanism by which TRX antagonizes or prevents Polycomb silencing (Tie, 2009).

The major findings of this work are: (1) that Drosophila CBP acetylates H3K27; (2) that this acetylation requires TRX; and (3) that it prevents H3K27 trimethylation by E(Z) at Polycomb target genes and antagonizes Polycomb silencing. The remarkably complementary developmental profiles of H3K27ac and H3K27me3 (but not H3K27me2) during embryogenesis suggest that the deposition of H3K27me3, which increases steadily after ~4 hours with the onset of Polycomb silencing, occurs at the expense of a substantial fraction of the H3K27ac already present. This suggests that the establishment of Polycomb silencing might require active deacetylation of this pre-existing H3K27ac. The reciprocal effects of knockdown and overexpression of CBP and E(Z) on H3K27 trimethylation and acetylation in bulk chromatin further suggest that the two modifications constitute alternative chromatin states associated with active and inactive genes. Consistent with this, ChIP-chip experiments revealed that H3K27me3 and H3K27ac are mutually exclusive genome wide. Moreover, in S2 cells, the inactive abd-A gene does not have the H3K27ac modification in its promoter region, but acquires it upon RNAi knockdown of E(Z). It will be important to determine whether such a modification switch occurs genome wide after loss of E(Z) (Tie, 2009).

The ability of E(Z) overexpression to suppress the small rough eye phenotype of CBP overexpressers further supports the conclusion that H3K27 trimethylation by E(Z) antagonizes H3K27 acetylation by CBP and suggests that deacetylation of H3K27 by RPD3, and possibly other deacetylases, might be a prerequisite for subsequent methylation by E(Z) and therefore important for reversal of an active state. Conversely, the ability of CBP and TRX overexpression to increase the global H3K27ac level at the expense of H3K27me3 suggests that either active demethylation of H3K27me3 by the H3K27-specific demethylase UTX (Agge, 2007; Lee, 2007b; Smith, 2008), or histone replacement (Ahmad, 2002), might be a prerequisite to acetylation by CBP. Indeed, depletion of Drosophila UTX in vivo using a GAL4-inducible UTX RNAi transgene line results in an increase in H3K27me3, as previously reported (Smith, 2008), and in a marked decrease in H3K27ac. These data, together with the evidence of developmentally programmed reversal of Polycomb silencing, now suggest that the widely accepted stability of Polycomb silencing during development might be more dynamically regulated than previously appreciated (Tie, 2009).

This is the first report that CBP/p300 acetylates H3K27. Recombinant Drosophila CBP acetylates H3K27 and K18 in vivo and in vitro. The greatly reduced H3K27ac levels in CBP-depleted S2 cells also strongly suggest that CBP is the major H3K27 acetylase in Drosophila. The conservation of H3K27 acetylation by human p300, together with the reported association of CBP with the TRX homolog MLL in humans (Ernst, 2001), suggest that it is likely to play a similar role in antagonizing Polycomb silencing in mammals (Tie, 2009).

The genome-wide distribution of H3K27ac, as estimated from human ChIP-chip experiments, appears very similar to that of H3K4me3. This suggests that H3K27ac is much more widely distributed than just at Polycomb target genes, which are estimated to number several thousand in mammalian cells and hundreds in Drosophila. Although these numbers could grow with the identification of additional Polycomb-silenced genes in additional cell types, the recently reported strong correlation of H3K27ac with active genes suggests that it plays an additional role(s) in promoting the transcription of active genes, including those that are never targets of Polycomb silencing. (Note that the H3K27ac at non-Polycomb target genes will not be directly affected by global changes in H3K27me3.) Interestingly, like H3K27me3, H3K27ac appears on the transcribed regions of Polycomb target genes, which might reflect a role for H3K27ac in facilitating transcriptional elongation, and, conversely, a role for H3K27me3 in inhibiting elongation. In addition to its anti-silencing role in preventing H3K27 trimethylation, H3K27ac may also serve as a signal for recruitment of other proteins with additional enzyme activities that alter local chromatin structure further to facilitate or promote transcription. Prime candidates are those containing a bromodomain, a conserved acetyl-lysine-binding module present in several dozen chromatin-associated proteins, including a number of TrxG proteins that also antagonize Polycomb silencing (Tie, 2009).

The results presented in this study provide new insight into how TRX and CBP function together to antagonize Polycomb silencing. Robust H3K27 acetylation by CBP is dependent on TRX, suggesting that H3K27ac plays a crucial role in the anti-silencing activity of TRX. Consistent with this, preliminary genetic evidence suggests that the Polycomb phenotypes caused by TRX overexpression are dependent on CBP, as they are suppressed by RNAi knockdown of CBP. The nature of this dependence is currently unknown, but could involve targeting of CBP by TRX or regulation of the H3K27 acetylation activity of CBP by TRX (Tie, 2009).

The physical association of TRX and CBP and the widespread coincidence of H3K27ac and H3K4me3 sites in the human ChIP-chip data further suggest that the two modifications might be coordinately executed by TRX and CBP. However, the results also raise the possibility that H3K4 trimethylation by TRX itself might be less important for antagonizing Polycomb silencing than H3K27 acetylation. This possibility is also suggested by the discovery of Polycomb-silenced genes in ES and human T cells that contain 'bivalent' marks (both H3K4me3 and H3K27me3) in their promoter regions (although the H3K4me3 levels at these inactive genes are typically lower, on average, than they are at active genes, hinting at the possible importance of quantitative effects of the two marks) (Tie, 2009).

A speculative model is proposed for the regulation of Polycomb silencing that incorporates the activities of TRX, CBP, E(Z), RPD3 and UTX. Repressed genes are marked with H3K27me3. H3K27 trimethylation by PRC2 (which can also control DNA methylation in mammals) requires RPD3 (and possibly other histone deacetylases) to deacetylate any pre-existing H3K27ac. H3K27me3 promotes binding of PC-containing PRC1 complexes, which may inhibit H3K27 acetylation and maintain silencing through 'downstream' events, including those promoted by the H2AK119 mono-ubiquitylation mediated by its RING subunit. Conversely, active genes are marked with H3K4me3 and H3K27ac. H3K27 acetylation by CBP is dependent on TRX and possibly other TrxG proteins, as suggested by the observation that H3K27me3 levels are significantly increased on salivary gland polytene chromosomes from trx, ash1 and kis mutants. The current results predict that this increase will be accompanied by a decrease in H3K27ac. Interestingly, ash1 encodes another HMTase that also interacts with CBP and antagonizes Polycomb silencing. Acetylation of H3K27 is likely to also require the K27-specific demethylase UTX when removal of pre-existing H3K27me3 is a prerequisite for acetylation, e.g. for developmentally regulated reversal of Polycomb silencing at the onset of differentiation. H3K27ac prevents H3K27 trimethylation and might also serve as a signal for recruitment of other TrxG proteins with additional chromatin-modifying activities that may protect the H3K27ac modification and also alter local chromatin structure to promote transcription and further inhibit Polycomb silencing (Tie, 2009).

Histone H3 Serine 28 is essential for efficient Polycomb-mediated gene repression in Drosophila

Trimethylation at histone H3K27 is central to the polycomb repression system. Juxtaposed to H3K27 is a widely conserved phosphorylatable serine residue (H3S28) whose function is unclear. To assess the importance of H3S28, a Drosophila H3 histone mutant was generated with a serine-to-alanine mutation at position 28. H3S28A mutant cells lack H3S28ph on mitotic chromosomes but support normal mitosis. Strikingly, all methylation states of H3K27 drop in H3S28A cells, leading to Hox gene derepression and to homeotic transformations in adult tissues. These defects are not caused by active H3K27 demethylation nor by the loss of H3S28ph. Biochemical assays show that H3S28A nucleosomes are a suboptimal substrate for PRC2 (containing Esc, Su(z)12, E(z) and Nurf55), suggesting that the unphosphorylated state of serine 28 is important for assisting in the function of polycomb complexes. Collectively, these data indicate that the conserved H3S28 residue in metazoans has a role in supporting PRC2 catalysis (Yung, 2015).

This report has established a H3S28A histone mutant in Drosophila. In theory, this mutation could have two different effects on the polycomb system. (1) It could be that PcG proteins are not evicted from H3K27me3-binding sites in the absence of H3S28ph, and thus, PcG target genes might become ectopically repressed or (2) the mutation at H3S28 or the absence of H3S28ph could compromise PcG functions, resulting in derepression of PcG target genes. No evidence was found for the first possibility, although it is formally possible that H3S28 is phosphorylated under certain developmental conditions or in response to particular stimuli to counteract polycomb silencing. Instead, the data point to an inhibition of PRC2 activity by the H3S28A mutation. This inhibition is independent of active H3K27 demethylation by dUtx. Besides, RNAi against Aurora B kinase and hence depletion of H3S28ph did not hamper polycomb silencing. On the other hand, H3S28A nucleosomes proved to be a suboptimal substrate for in vitro PRC2 HMT activity. Although a 3D structure of the human Ezh2 SET domain is available, the exact contribution of the hydroxyl group of H3S28 for H3K27 methylation is difficult to deduce from the available data. vSET, the only other protein capable of H3K27 methylation in the absence of PRC2 subunits, does not require H3S28 for catalysis, whereas it does use H3A29 to define substrate specificity. Clearly, more work will be required to determine the exact structural and biochemical role of H3S28 in PRC2 catalysis. Consistent with the in vitro HMT assays, in vivo the H3S28A mutant exhibits defects in H3K27 methylation and shows similar, though milder, Hox derepression profiles and transformation phenotypes to those observed in H3K27R mutant flies (Yung, 2015).

Interestingly, the 'KS' module is frequently found in Ezh2 substrates other than K27S28 of histone H3. These include K26S27 of human histone H1 variant H1b (H1.4), K38S39 of the nuclear orphan receptor RORα, and K180S181 of STAT3. Whether these serine residues act similarly to H3S28 to support methylation of the adjacent lysine residue remains unknown. Of note, some other Ezh2 substrates can be methylated despite the lack of a 'KS' module. These include K26 of mouse histone H1 variant H1e, K49 of STAT3, and K116 of Jarid2, where the lysine residue is followed by an alanine, glutamate, and phenylalanine, respectively. Moreover, the link between peptide sequence and enzymology of Ezh2 was shown to differ in non-histone substrates. Hence, the role of serine following the Ezh2 methylation target amino acid might not be extrapolated to all other Ezh2 substrates and should be tested individually (Yung, 2015).

Previous reports revealed discrepancies in Drosophila PcG protein localization on mitotic chromosomes depending on staining protocols and tissue types. Nonetheless, live imaging of Pc-GFP, Ph-GFP, and E(z)-GFP in early Drosophila embryos has suggested that the majority of these PcG components are dissociated from mitotic chromosomes. Because stress-induced H3S28ph evicts PcG complexes during interphase, one might expect rebinding of PcG proteins on mitotic chromosomes depleted of H3S28ph. Whereas loss of Ph from mitotic chromosomes was observed in WT background, significant Ph association was not observed in H3S28A mutant condition. The reduced levels of H3K27me3 in the H3S28A mutant could contribute to this observation. Alternatively, other mechanisms might operate to dissociate the majority of PcG proteins during mitosis (Yung, 2015).

The establishment of the histone replacement system in Drosophila has proven to be an important tool to complement functional characterization of chromatin modifiers. Whereas depletion of H3K27 methylation, either by mutation of the histone mark writer E(z) or by mutation of the histone itself in the H3K27R mutant, leads to similar loss of polycomb-dependent silencing, other histone mutations revealed different phenotypes than the loss of their corresponding histone mark writers. For example, H3K4R mutations in both H3.2 and H3.3, hence a complete loss of H3K4 methylation, did not hamper active transcription. Also, the loss of H4K20 methylation upon H4K20R mutation unexpectedly supports development and does not phenocopy cell cycle and gene silencing defects reported upon the loss of the H4K20 methylase PR-Set7. In this study, by comparing the phenotype of Aurora B knockdown and H3S28A mutation in vivo, together with in vitro HMT assay, the requirement of the unmodified H3S28 residue is specifically attributed to supporting PRC2 deposition of H3K27 methylation (Yung, 2015).

Whereas the published data suggest that H3S28 phosphorylation might be important for eviction of PcG components for derepression of PcG target genes upon stimulatory cues, the data reveal a so far unacknowledged function of the unphosphorylated state of H3S28. This study shows that serine 28 is required to enable proper methylation of H3K27 by PRC2 and thus to establish polycomb-dependent gene silencing. Serine 28 of histone H3 is universally conserved in species that display canonical PRC2-dependent silencing mechanisms. Given the fact that no major mitotic defects are found upon its mutation, it is proposed that the major role of this residue is to ensure optimal PRC2 function while facilitating the removal of polycomb proteins in response to signals that induce phosphorylation (Yung, 2015).


GENE STRUCTURE

4.8kb and 5.0kb repeats containing the histone genes His1, His2A, His2B, His3 and His4 were present in all of the more than 20 D. melanogaster strains studied. The strains differ in the relative amounts of the two repeat types, with the 5.0kb repeat always present in equal or greater amounts than the 4.8kb repeat. The strains also differ in a number of far less abundant fragments containing histone gene sequences. The expression of HIS-C genes, including His3, during oogenesis has been studied, and compared to periods of DNA synthesis and actin expression during this developmental stage. The D. virilis core histone genes (Dvir\His2B, Dvir\His3, Dvir\His4 and Dvir\His2A), are arranged in the same order and orientation as the D. melanogaster core histone genes (His2B, His3, His4 and His2A). However, the His1 gene that is located between His2B and His3 in D. melanogaster is not found between Dvir\His2B and Dvir\His3 in D. virilis. The genomic organization of the histone genes in D. hydei closely resembles that of D. melanogaster. The position of the homologous histone gene repeats within the nuclei of early embryo cells has been investigated. The two homologous histone gene clusters are distinct and separate through all stages of the cell cycle up to nuclear cycle 13. During interphase of cycle 14, the two clusters colocalize with high frequency, and move from near the midline of the nucleus towards the apical side. The codon bias of the histone genes from D. melanogaster and D. hydei illustrates that the generalization -- that abundantly expressed genes have a high codon bias and low rates of silent substitution -- does not hold for the histone genes. DNA replication of the 5kb histone gene repeating unit in tissue culture cells (Drosophila Kc cells) initiates at multiple sites located within the repeating unit. Several replication pause sites are located at 5' upstream regions of some histone genes. The TFIID complex interacts with the promoter of His3 making contacts at the TATA element, initiator, +18 and +28 regions. Distinct specific subsets of lysines are utilized during deposition-related His4 diacetylation (FlyBase record for His3 and references therein).


PROTEIN STRUCTURE

Amino Acids - 135

For information on H3 structure see Structures of Histone Proteins and Proteins Containing the Histone Fold Motif and associated links.


Histone H3: Evolutionary Homologs | Regulation | Developmental Biology | Effects of Mutation | References

date revised: 18 November 2002

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