Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

Methylated lysine 27 on histone H3 (H3K27me) marks repressed “facultative heterochromatin,” including developmentally regulated genes in plants and animals. The mechanisms responsible for localization of H3K27me are largely unknown, perhaps in part because of the complexity of epigenetic regulatory networks. We used a relatively simple model organism bearing both facultative and constitutive heterochromatin, Neurospora crassa, to explore possible interactions between elements of heterochromatin. In higher eukaryotes, reductions of H3K9me3 and DNA methylation in constitutive heterochromatin have been variously reported to cause redistribution of H3K27me3. In Neurospora, we found that elimination of any member of the DCDC H3K9 methylation complex caused massive changes in the distribution of H3K27me; regions of facultative heterochromatin lost H3K27me3, while regions that are normally marked by H3K9me3 became methylated at H3K27. Elimination of DNA methylation had no obvious effect on the distribution of H3K27me. Elimination of HP1, which “reads” H3K9me3, also caused major changes in the distribution of H3K27me, indicating that HP1 is important for normal localization of facultative heterochromatin. Because loss of HP1 caused redistribution of H3K27me2/3, but not H3K9me3, these normally nonoverlapping marks became superimposed. Indeed, mass spectrometry revealed substantial cohabitation of H3K9me3 and H3K27me2 on H3 molecules from an hpo strain. Loss of H3K27me machinery (e.g., the methyltransferase SET-7) did not impact constitutive heterochromatin but partially rescued the slow growth of the DCDC mutants, suggesting that the poor growth of these mutants is partly attributable to ectopic H3K27me. Altogether, our findings with Neurospora clarify interactions of facultative and constitutive heterochromatin in eukaryotes.It has become increasingly clear that covalent modifications of chromatin, such as methylation of specific histone residues and methylation of DNA, can have profound effects on genome functions. In animals, even partial disruption of DNA methylation leads to developmental defects and disease states (Robertson 2005). Similarly, methylation of histone H3 lysine 27 (H3K27me) by the Polycomb Repressive Complex 2 (PRC2) is critical for normal development in flies, plants, and other systems (Schwartz and Pirrotta 2007), and recent work implicates perturbation of H3K27me in a high fraction of pediatric gliomas (Schwartzentruber et al. 2012; Sturm et al. 2012; Wu et al. 2012; Chan et al. 2013; Lewis et al. 2013). It is of obvious interest to understand the normal regulation of epigenetic features such as methylation of DNA and H3K27, which normally mark constitutive and facultative heterochromatin, respectively. Unfortunately, despite numerous studies in a variety of systems, little is understood about how these chromatin modifications are controlled.Epigenetic marks frequently influence one another, confounding analyses. For example, Schmitges et al. (2011) demonstrated that the amino terminus of histone H3 is recognized by the Nurf55-Suz12 submodule of PRC2 and that this binding is blocked by marks of active chromatin, namely, K4me3 and K36me2/3. Although the mechanism of such “crosstalk” is sometimes reasonably obvious, more often it is not, as illustrated by observations of H3K27me3 redistribution in response to defects in constitutive heterochromatin. More than a decade ago, Peters et al. (2003) noticed that mouse cells defective in both of the SUV39H methyltransferases, which are responsible for the trimethylation of histone H3 lysine 9 (H3K9me3) characteristic of pericentric heterochromatin, show redistribution of H3K27me3; both cytological and molecular analyses suggested that this Polycomb mark “relocated” to the neighborhood abandoned by H3K9me3. DNA methylation typically colocalizes with H3K9me3 but not with H3K27me3 (Rose and Klose 2014). Because DNA methylation can depend on H3K9me, and vice versa (Tariq and Paszkowski 2004), it was of interest to determine whether loss of DNA methylation would also result in redistribution of H3K27me. In early studies with mouse embryonic stem cells, reduced DNA methylation resulting from mutation of either the maintenance methyltransferase gene dnmt1 or the de novo DNA methyltransferase genes dmnt3a and dnmt3b did not result in an obvious change in the distribution of H3K27me (Martens et al. 2005). However, subsequent studies with Arabidopsis (Mathieu et al. 2005; Deleris et al. 2012), mouse embryonic fibroblasts (Lindroth et al. 2008; Reddington et al. 2013), embryonic stem cells (Hagarman et al. 2013), and neural stem cells (Wu et al. 2010) revealed that loss of DNA methylation, caused by disruption of DNA methyltransferase genes or treatment with the demethylating agent 5-azacytidine, provided the most potent trigger of H3K27me3 redistribution.Considering that DNA methylation has been reported to stimulate H3K9 methylation, in both plants (Tariq and Paszkowski 2004) and animals (Jin et al. 2011), and that both of these epigenetic marks are tied to additional nuclear processes, interpretation of these fascinating results is problematic. We took advantage of a relatively simple system to explore possible relationships between marks of constitutive and facultative heterochromatin. Specifically, we used the filamentous fungus Neurospora crassa, which unlike many other simple model eukaryotes (e.g., budding and fission yeasts, Drosophila and Caenorhabditis elegans) has both DNA methylation and H3K27me (Aramayo and Selker 2013; Jamieson et al. 2013). The pathway for formation of constitutive heterochromatin in Neurospora is relatively well understood and essentially unidirectional, as illustrated in Figure 1A. Constitutive heterochromatin, which is primarily in centromere regions, is characterized by AT-rich (GC-poor) DNA resulting from the action of the genome defense system RIP (repeat-induced point mutation) operating on transposable elements (Selker 1990; Aramayo and Selker 2013). DIM-5, in the DIM-5/DIM-7/DIM-9/DDB1/CUL4 complex (DCDC) (Fig. 1B), methylates H3K9 associated with RIP''d DNA (Lewis et al. 2010a,b). Heterochromatin Protein 1 (HP1) specifically binds the resulting H3K9me3 (Freitag et al. 2004) and recruits the DNA methyltransferase DIM-2 (Honda and Selker 2008). Consequently, the genomic distribution of 5mC, HP1, H3K9me3, AT-rich DNA, and repeated sequences correlate almost perfectly (Fig. 1A). Importantly, mutation of dim-2 does not affect the distributions of H3K9me3 and HP1, unlike the situation in plants (Tariq and Paszkowski 2004) and animals (Espada et al. 2004; Gilbert et al. 2007). Similarly, mutation of the gene encoding HP1 (hpo) has almost no effect on the distribution of H3K9me3 (Lewis et al. 2009). Although mutations in genes encoding DCDC proteins render the organism slow-growing and sensitive to certain drugs (Lewis et al. 2010a), neither the components of the DNA methylation/constitutive heterochromatin machinery nor the components of the H3K27me2/3/facultative heterochromatin machinery are essential for viability of the organism, allowing us to test knockouts of genes for components of these processes for possible epigenetic interactions.Open in a separate windowFigure 1.Heterochromatin formation in Neurospora crassa. (A) An ∼500-kb region, including the centromere of LG III, is shown to illustrate the pathway leading to constitutive heterochromatin in Neurospora. During the sexual phase of the life cycle, the genome defense system RIP (repeat-induced point mutation) recognizes repeated DNA (e.g., transposons and other repeated DNA shown as black rectangles) and litters them with C:G-to-T:A mutations (Selker 1990). In vegetative cells, lysine 9 of histone H3 (H3K9) associated with G:C-poor DNA is methylated by DIM-5, generating H3K9me3 (orange track), which is bound by the HP1-DIM-2 complex (yellow track) and catalyzes DNA methylation (green track). Perturbation of any step in the pathway eliminates the downstream steps without significantly influencing earlier steps. (B) Key proteins required to form constitutive (left) or facultative (right) heterochromatin. Methylation of H3K9 by DIM-5 depends on all five members of the DCDC (DIM-5/-7/-9, CUL4/DDB1 complex) (Lewis et al. 2010a). HP1 directly binds to H3K9me3 (cluster of three red hexagons labeled “Me”) and recruits the DNA methyltransferase DIM-2 (Honda and Selker 2008), resulting in a genome-wide correlation between H3K9me3 and DNA methylation (orange hexagons labeled “Me”) (Lewis et al. 2009). HP1 is also involved in the HCHC deacetylase silencing complex (Honda et al. 2012) and the DMM (Honda et al. 2010) complex, which limits spreading of constitutive heterochromatin. Methylation of H3K27 (cluster of three blue hexagons labeled “Me”) is carried out by the PRC2 complex consisting of SET-7, EED, SU(Z)12, and NPF (Jamieson et al. 2013).     

Evaluation of Histone 3 Lysine 27 Trimethylation (H3K27me3) and Enhancer of Zest 2 (EZH2) in Pediatric Glial and Glioneuronal Tumors Shows Decreased H3K27me3 in H3F3A K27M Mutant Glioblastomas

H3F3A mutations are seen in ～30% of pediatric glioblastoma (GBMs) and involve either the lysine residue at position 27 (K27M) or glycine at position 34 (G34R/V). Sixteen genes encode histone H3, each variant differing in only a few amino acids. Therefore, how mutations in a single H3 gene contribute to carcinogenesis is unknown. H3F3A K27M mutations are predicted to alter methylation of H3K27. H3K27me3 is a repressive mark critical to stem cell maintenance and is mediated by EZH2, a member of the polycomb‐group (PcG) family. We evaluated H3K27me3 and EZH2 expression using immunohistochemistry in 76 pediatric brain tumors. H3K27me3 was lowered/absent in tumor cells but preserved in endothelial cells and infiltrating lymphocytes in six out of 20 GBMs. H3K27me3 showed strong immunoreactivity in all other tumor subtypes. Sequencing of GBMs showed H3F3A K27M mutations in all six cases with lowered/absent H3K27me3. EZH2 expression was high in GBMs, but absent/focal in other tumors. However, no significant differences in EZH2 expression were observed between H3F3A K27M mutant and wild type GBMs, suggesting that EZH2 mediated trimethylation of H3K27 is inhibited in GBM harboring K27M mutations. Our results indicate that H3F3A K27M mutant GBMs show decreased H3K27me3 that may be of both diagnostic and biological relevance.     

Global mapping of H3K4me3 and H3K27me3 reveals chromatin state-based regulation of human monocyte-derived dendritic cells in different environments

Depending on the environment, dendritic cells (DCs) may become active or tolerogenic, but little is known about whether heritable epigenetic modifications are involved in these processes. Here, we have found that epigenetic histone modifications can regulate the differentiation of human monocyte-derived DCs (moDCs) into either activated or tolerized DCs. The inhibition or silencing of methyltransferases or methylation-associated factors affects the expression of multiple genes. Genome mapping of transforming growth factor (TGF-β)- or lipopolysaccharide (LPS)-associated H3K4 trimethylation (H3K4me3) and H3K27 trimethylation (H3K27me3) demonstrated the presence of histone modification of gene expression in human TGF-β- or LPS-conditioned moDCs. Although the upregulated or downregulated genes were not always associated with H3K4me3 and/or H3K27me3 modifications in TGF-β-conditioned (tolerized) or LPS-conditioned (activated) moDCs, some of these genes may be regulated by the increased and/or decreased H3K4me3 or H3K27me3 levels or by the alteration of these epigenetic marks, especially in TGF-β-conditioned moDCs. Thus, our results suggested that the differentiation and function of moDCs in tumor and inflammation environments are associated with the modification of the H3K4me3 and K3K27me3 epigenetic marks.     

Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates

In invertebrates that harbor functional DNA methylation enzymatic machinery, gene-bodies are the primary targets for CpG methylation. However, virtually all other aspects of invertebrate DNA methylation have remained a mystery until now. Here, using a comparative methylomics approach, we demonstrate that Nematostella vectensis, Ciona intestinalis, Apis mellifera, and Bombyx mori show two distinct populations of genes differentiated by gene-body CpG density. Genome-scale DNA methylation profiles for A. mellifera spermatozoa reveal CpG-poor genes are methylated in the germline, as predicted by the depletion of CpGs. We find an evolutionarily conserved distinction between CpG-poor and GpC-rich genes: The former are associated with basic biological processes, the latter with more specialized functions. This distinction is strikingly similar to that recently observed between euchromatin-associated genes in Drosophila that contain intragenic histone 3 lysine 36 trimethylation (H3K36me3) and those that do not, even though Drosophila does not display CpG density bimodality or methylation. We confirm that a significant number of CpG-poor genes in N. vectensis, C. intestinalis, A. mellifera, and B. mori are orthologs of H3K36me3-rich genes in Drosophila. We propose that over evolutionary time, gene-body H3K36me3 has influenced gene-body DNA methylation levels and, consequently, the gene-body CpG density bimodality characteristic of invertebrates that harbor CpG methylation.     

H3K27me3 and VEGF is associated with poor prognosis in patients with synovial sarcoma

Purpose

Previous studies have shown a correlation between the expression of H3K27me3 and pathological characteristics of malignant tumors. This study aimed to investigate the association of H3K27me3 and VEGF expression with clinical outcomes of synovial sarcoma patients.

H3K27me3去甲基化酶Jmjd3调节胎鼠肺上皮细胞增殖和分化

目的分析H3K27me3特异去甲基化酶Jmjd3(KDM6B)在胎鼠肺生长发育过程中的作用。方法 HE染色、PAS染色和免疫组化方法检测E19.5 Jmjd3基因敲除胎鼠肺生长发育情况。结果与野生型(Jmjd3+/+)胚胎比较,杂合型敲除(Jmjd3+/-)胚胎的肺发育稍差,但纯合型敲除(Jmjd3-/-)胚胎肺发育明显不良,支气管的纤毛上皮细胞和Clara细胞以及肺泡的Ⅰ型和Ⅱ型上皮细胞分化不良。Jmjd3-/-胚胎肺上皮细胞增殖指数高于野生型和Jmjd3+/-组,未发现Jmjd3-/-胚胎肺上皮细胞凋亡异常。结论 Jmjd3对胎鼠肺上皮细胞的增殖和分化具有重要调节作用。     

H3K27me3 demethylase UTX regulates the differentiation of a subset of bipolar cells in the mouse retina

Di‐ and trimethylation of lysine 27 on histone 3 (H3K27me2/3) is a critical gene repression mechanism. We previously showed that down‐regulation of the H3K27 demethylase, Jumonji domain‐containing protein 3 (JMJD3), resulted in a reduced number of protein kinase C (PKC)α‐positive rod ON‐bipolar cells. In this work, we focused on the role of another H3K27 demethylase, ubiquitously transcribed tetratricopeptide repeat X chromosome (UTX), in retinal development. UTX was expressed in the retinal progenitor cells of the embryonic mouse retina and was observed in the inner nuclear layer during late retinal development and in the mature retina. The short hairpin RNA‐mediated knockdown of Utx in a mouse retinal explant led to a reduced number of PKCα‐positive rod ON‐bipolar cells. However, other retinal subtypes were unaffected by this knockdown. Using a retina‐specific knockout of Utx in mice, the in vivo effects of UTX down‐regulation were examined. Again, the number of PKCα‐positive rod ON‐bipolar cells was reduced, and no other apparent phenotypes, including retinal progenitor proliferation, apoptosis or differentiation, were observed. Finally, we examined retina‐specific Utx and Jmjd3 double‐knockout mice and found that although the number of rod ON‐bipolar cells was reduced, no additional effects from the loss of Utx and Jmjd3 were observed. Taken together, our data show that UTX contributes to retinal differentiation in a lineage‐specific manner.     

H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours

Diagnosing MPNST can be challenging, but genetic alterations recently identified in polycomb repressive complex 2 (PRC2) core component genes, EED and SUZ12, resulting in global loss of the histone 3 lysine 27 trimethylation (H3K27me3) epigenetic mark, represent drivers of malignancy and a valuable diagnostic tool. However, the reported loss of H3K27me3 expression ranges from 35% to 84%. We show that advances in molecular pathology now allow many MPNST mimics to be classified confidently. We confirm that MPNSTs harbouring mutations in PRC2 core components are associated with loss of H3K27me3 expression; whole-genome doubling was detected in 68%, and SSTR2 was amplified in 32% of MPNSTs. We demonstrate that loss of H3K27me3 expression occurs overall in 38% of MPNSTs, but is lost in 76% of histologically classical cases, whereas loss was detected in only 23% cases with heterologous elements and 14% where the diagnosis could not be provided on morphology alone. H3K27me3 loss is rarely seen in other high-grade sarcomas and was not found to be associated with an inferior outcome in MPNST. We show that DNA methylation profiling distinguishes MPNST from its histological mimics, was unrelated to anatomical site, and formed two main clusters, MeGroups 4 and 5. MeGroup 4 represents classical MPNSTs lacking H3K27me3 expression in the majority of cases, whereas MeGroup 5 comprises MPNSTs exhibiting non-classical histology and expressing H3K27me3 and cluster with undifferentiated sarcomas. The two MeGroups are distinguished by differentially methylated PRC2-associated genes, the majority of which are hypermethylated in the promoter regions in MeGroup 4, indicating that the PRC2 target genes are not expressed in these tumours. The methylation profiles of MPNSTs with retention of H3K27me3 in MeGroups 4 and 5 are independent of mutations in PRC2 core components and the driver(s) in these groups remain to be identified. Our results open new avenues of investigation. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.