Lys27 Trimethylation Research Articles

Amphetamine exposure during development causes epigenetic trans‐generational changes in drug sensitivity in Caenorhabditis elegans (803.8)

It’s well known that psychostimulants like amphetamine (AMPH) increase the amount of dopamine in the synaptic cleft. In C. elegans, it has been shown that a dopamine increase in the synapses causes a unique behavior named swimming induced paralysis (SWIP). Previous studies demonstrated that SWIP is a valid tool to investigate the effect of addictive drugs. Here, we explored the response to AMPH in C. elegans adult animals following previous exposure to the drug during development, as well as the second generation to see if a change in response was passed to progeny. Our results show that adult animals (F0) exposed to AMPH during development had a higher AMPH‐induced SWIP with respect to control‐exposed animals. Further, we found an elevated SWIP response in the second generation (F1) of animals originated from maternal lines that were exposed to AMPH during development. Epigenetic mechanisms were investigated to explain the inherited change in response to AMPH. Histone3 Lys4 trimethylation (H3K4me3) and histone3 Lys27 (H3K27me3) are promoter‐specific histone modifications associated with active transcription and gene repression, respectively. To test if H3K4 or H3K27 methylation were a contributing factor in the increased SWIP response seen after AMPH exposure, we performed western blot assays against H3K4me3 and H3K27me3 in protein samples collected from F0 and F1 animals. Our data shows that AMPH exposure during development decreases H3K4me3 expression in the F1 generation, while no change is seen in H3K27. These results suggest that epigenetic mechanisms underlie the trans‐generational effects induced by AMPH. Other epigenetic markers are currently under investigation.Grant Funding Source: Supported by P20 GM104360‐1 NIH Grant

3-Deazaneplanocin A (DZNep), an Inhibitor of S-Adenosylmethionine-dependent Methyltransferase, Promotes Erythroid Differentiation

EZH2, a core component of polycomb repressive complex 2 (PRC2), plays a role in transcriptional repression through histone H3 Lys-27 trimethylation and is involved in various biological processes, including hematopoiesis. It is well known that 3-deazaneplanocin A (DZNep), an inhibitor of S-adenosylmethionine-dependent methyltransferase that targets the degradation of EZH2, preferentially induces apoptosis in various hematological malignancies, suggesting that EZH2 may be a new target for epigenetic treatment. Because PRC2 participates in epigenetic silencing of a subset of GATA-1 target genes during erythroid differentiation, inhibition of EZH2 may influence erythropoiesis. To explore this possibility, we evaluated the impact of DZNep on erythropoiesis. DZNep treatment significantly induced erythroid differentiation of K562 cells, as assessed by benzidine staining and quantitative RT-PCR analysis for representative erythroid-related genes, including globins. When we evaluated the effects of DZNep in human primary erythroblasts derived from cord blood CD34-positive cells, the treatment significantly induced erythroid-related genes, as observed in K562 cells, suggesting that DZNep induces erythroid differentiation. Unexpectedly, siRNA-mediated EZH2 knockdown had no significant effect on the expression of erythroid-related genes. Transcriptional profiling of DZNep-treated K562 cells revealed marked up-regulation of SLC4A1 and EPB42, previously reported as representative targets of the transcriptional corepressor ETO2. In addition, DZNep treatment reduced the protein level of ETO2. These data suggest that erythroid differentiation by DZNep may not be directly related to EZH2 inhibition but may be partly associated with reduced protein level of hematopoietic corepressor ETO2. These data provide a better understanding of the mechanism of action of DZNep, which may be exploited for therapeutic applications for hematological diseases, including anemia.

Inhibitors of suppressive histone modification promote direct reprogramming of fibroblasts to cardiomyocyte-like cells

We recently reported that the combination of Gata4, Hand2, Tbx5, and the fusion gene MM3 between Mef2c and the transactivation domain of MyoD (MM3-GHT) produces 18 times as many clusters of beating cells (induced cardiomyocyte-like cells or iCMs) as the wild-type combination (M-GHT).1 In the current study, we added the chemicals GSK126 and UNC0638 to MM3-GHT to examine whether depletion of suppressive histone markers further increases the efficiency of making iCMs. GSK126 inhibits Enhancer of Zeste Homolog 2 (Ezh2), which induces di- and trimethylation of Lys27 on histone H3 (H3K27me2 and H3K27me3, respectively) as a catalytic subunit of the Polycomb Repressive Complex 2 (PRC2).2 UNC0638 inhibits two closely related enzymes, G9a and GLP, which form a heterodimer in vivo and mediate mono- and dimethylation of Lys9 on histone H3 (H3K9me and H3K9me2) and methylation of non-histone substrates such as p53.3 H3K27me3 and H3K9me2 are typically associated with suppressed genes although the underlying mechanisms have not been fully characterized. We prepared fibroblasts from the heads of Day 13.5 mouse embryos and incubated them with 1 μM GSK126 for 2 days to verify a decrease of H3K27me3 (see Supplementary material online, Figure S1 A ). To test the effect of GSK126 on reprogramming, fibroblasts were transduced with MM3-GHT on Day −1 and 0, and GSK126 was added to the culture medium at different time points ( Figure 1 A ). The most effective schedule was to add GSK126 from Day 1 to 4, resulting in 2.1 times as many iCM clusters as negative control without GSK126 ( Figure 1A , encircled and Supplementary material online, Figure S1 B ). Ca2+ oscillations in the cells were monitored using a transgene encoding the Ca2+ indicator protein GCaMP5, which emits stronger green fluorescence in the presence of …

Heat Shock Improves Sca-1+ Stem Cell Survival and Directs Ischemic Cardiomyocytes Toward a Prosurvival Phenotype Via Exosomal Transfer: A Critical Role for HSF1/miR-34a/HSP70 Pathway

Stem cell-based therapy is a promising intervention for ischemic heart diseases. However, the functional integrity of stem cells is impaired in an ischemic environment. Here, we report a novel finding that heat shock significantly improves Sca-1(+) stem cell survival in an ischemic environment by the regulation of the triangle: heat shock factor 1 (HSF1), HSF1/miR-34a, and heat shock protein 70 (HSP70). Initially we prove that HSP70 is the key chaperone-mediating cytoprotective effect of heat shock in Sca-1(+) cells and then we establish miR-34a as a direct repressor of HSP70. We found that miR-34a was downregulated in heat shocked Sca-11 stem cells (HSSca-11 cells) [corrected]. Intriguingly, we demonstrate that the downregulation of miR-34a is attributed to HSF1-mediated epigenetic repression through histone H3 Lys27 trimethylation (H3K27me3) on miR-34a promoter. Moreover, we show that heat shock induces exosomal transfer of HSF1 from Sca-1(+) cells, which directs ischemic cardiomyocytes toward a prosurvival phenotype by epigenetic repression of miR-34a. In addition, our in vivo study demonstrates that transplantation of (HS) Sca-1(+) cells significantly reduces apoptosis, attenuates fibrosis, and improves global heart functions in ischemic myocardium. Hence, our study provides not only novel insights into the effects of heat shock on stem cell survival and paracrine behavior but also may have therapeutic values for stem cell therapy in ischemic heart diseases.

Context dependency of Set1/COMPASS-mediated histone H3 Lys4 trimethylation

The stimulation of trimethylation of histone H3 Lys4 (H3K4) by H2B monoubiquitination (H2Bub) has been widely studied, with multiple mechanisms having been proposed for this form of histone cross-talk. Cps35/Swd2 within COMPASS (complex of proteins associated with Set1) is considered to bridge these different processes. However, a truncated form of Set1 (762-Set1) is reported to function in H3K4 trimethylation (H3K4me3) without interacting with Cps35/Swd2, and such cross-talk is attributed to the n-SET domain of Set1 and its interaction with the Cps40/Spp1 subunit of COMPASS. Here, we used biochemical, structural, in vivo, and chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) approaches to demonstrate that Cps40/Spp1 and the n-SET domain of Set1 are required for the stability of Set1 and not the cross-talk. Furthermore, the apparent wild-type levels of H3K4me3 in the 762-Set1 strain are due to the rogue methylase activity of this mutant, resulting in the mislocalization of H3K4me3 from the promoter-proximal regions to the gene bodies and intergenic regions. We also performed detailed screens and identified yeast strains lacking H2Bub but containing intact H2Bub enzymes that have normal levels of H3K4me3, suggesting that monoubiquitination may not directly stimulate COMPASS but rather works in the context of the PAF and Rad6/Bre1 complexes. Our study demonstrates that the monoubiquitination machinery and Cps35/Swd2 function to focus COMPASS's H3K4me3 activity at promoter-proximal regions in a context-dependent manner.

Abstract P5-08-10: Upregulation of microRNA-181a promotes metastasis of breast cancer cells following chemotherapy

Abstract Recent studies indicated that genotoxic treatment may promote cancer cell invasion. Moreover, resistance to chemotherapy highly correlates with high metastatic potential in breast cancer patients. Nevertheless, the molecular mechanisms linking chemotherapeutic resistance to metastasis remain poorly understood. Here, we show that microRNA-181a (miR-181a) plays an important role in promoting chemodrug-induced breast cancer metastasis. Treatment with genotoxic drugs increases miR-181a expression in triple-negative breast cancer cells, which is dependent on NF-kB activation by DNA damaging agents. Genotoxic NF-κB activation upregulates IL-6 expression and secretion in breast cancer cells, which leads to STAT3 (signal transducer and activator of transcription 3) phosphorylation and activation. Activated STAT3 translocates onto miR-181a gene promoter region and enhances its transcription in response to genotoxic treatments. Interestingly, chemodrug treatment also induces epigenetic modifications, such as increased histone H3 Ser28 phosphorylation and decreased H3 Lys27 trimethylation, at miR-181a promoter region, which are also required for miR-181a up-regulation. In addition, we found overexpression of miR-181a in breast cancer cells significantly enhanced cell invasion and metastasis, while inhibiting miR-181a reduced cell aggressiveness upon genotoxic exposure. We further show that miR-181a directly suppresses the expression of ataxia telangiectasia mutated (ATM) in breast cancer cells, which plays a pivotal role in DNA damage response and cancer progression. Therefore, our findings support a critical role of DNA damage-induced miR-181a in promoting breast cancer metastasis following chemotherapeutic treatment. Further exploration of molecular mechanisms regulating miR-181a induction and miR-181a-driven aggressive behaviors of breast cancer cells in response to chemotherapy may reveal novel approaches to reduce metastasis and improve therapeutic response in breast cancers by targeting miRNAs. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-08-10.

SCF-β-TrCP E3 Ubiquitin Ligase-Mediated Proteolysis Of EZH2 Regulates H3K27 Trimethylation Activity In Germinal Center-Derived B-Cell Lymphomas

EZH2 is a critical enzymatic subunit of the PRC2 which trimethylates histone H3 (H3K27) to mediate gene repression. While overexpression of EZH2 and its increased H3K27 methylation have generally been associated with hematologic malignancies and solid tumors, recurrent gain of function somatic mutations in EZH2 have been recently reported in germinal center B-cell (GCB) derived lymphomas. These mutations, which replace a single tyrosine in the SET domain of the EZH2 protein (Y641), occur in 7.2% of FLs (follicular lymphoma) and 21.7% of GCB DLBCL (diffuse large B-cell lymphoma) and are absent from ABC DLBCLs. Consequently, B-cell lymphoma cell lines and lymphoma primary samples harboring heterozygous EZH2Y641mutations exhibit increased levels of histone H3 Lys27 trimethylation (H3K27me3) and promote a lymphoproliferative phenotype with expansion of the GC B cell compartment.Although extensive studies have been conducted to understand the role of polycomb group of proteins in cancer pathogenesis, few studies have been aimed at understanding the post-translational regulation of these proteins. Skp1/Cullin1/F- box protein (SCF) ubiquitin ligase complexes are the largest family of multicomponent ring E3 ubiquitin ligases that control the degradation of many important regulatory proteins and have been implicated in the regulation of epigenetic regulators. However, the mechanism of EZH2 degradation and its implication in PRC2 mediated methyl transferase activity in a cancer-specific context is not fully understood.Cullin-ring ubiquitin ligases (CRLs) form the largest known class of multicomponent E3 ubiqutin ligase family in eukaryotes and target a wide array of substrates involved in several biological processes. To investigate a CRL-mediated basis for post-translational EZH2 regulation, we screened a panel of cullin family E3 ligases for interaction with EZH2 and discovered that EZH2 was immunoprecipitated by cullin1 exclusively among all other cullins (cul2,3,4a,4b,5 and 7). We engineered and expressed a cullin1 dominant negative protein which resulted in EZH2 accumulation in a dose dependent manner. Using co-immunoprecipitation approach, we screened 8 different F box proteins and observed that SCF E3 ubiquitin ligase β-TrCP (FBXW1) uniquely and specifically interacted with EZH2. Further, RNAi-mediated silencing of β-TrCP resulted in EZH2 stabilization with attendant increase in H3K27 trimethylation activity. Importantly, the Y641 mutants recurrently identified and relevant in lymphoma pathogenesis were unable to bind β-TrCP. Further, cycloheximide chase experiments showed that Y641 mutants endogenously expressed in lymphoma-derived cells exhibit increased EZH2 stability as well as enhanced H3K27 trimethylation activity.Our studies demonstrate that β-TrCP plays an important role in controlling H3K27 trimethylation activity via an unusual recognition mechanism targeting EZH2 for proteasomal degradation. Our findings delineate a novel β-TrCP/EZH2 axis requiring an intact Y641 residue for EZH2 regulation by β-TrCP. Oncogenic mutations in Y641 in GCB-cell derived lymphomas confer increased stability to EZH2 and render it resistant to β-TrCP-mediated degradation. This newly identified mechanism might help in design potential novel therapeutic approaches for clinical management of cancer potentially driven by aberrant accumulation/function of EZH2. Disclosures:No relevant conflicts of interest to declare.

Abstract B254: Targeted disruption of the EZH2-EED complex inhibits EZH2-dependent cancer.

Abstract Enhancer of zeste homolog 2 (EZH2) is the histone lysine N-methyltransferase component of the Polycomb repressive complex 2 (PRC2), which, in conjunction with embryonic ectoderm development (EED) and suppressor of zeste 12 homolog(SUZ12), regulates cell lineage determination and homeostasis. Enzymatic hyperactivity of EZH2 has been linked to aberrant repression of tumor suppressor genes in diverse cancers. Here, we report the development of stabilized a-helix of EZH2 (SAH-EZH2) peptides that selectively inhibit H3 Lys27 trimethylation by dose-responsively disrupting the EZH2-EED complex and reducing EZH2 protein levels, a mechanism distinct from that reported for small-molecule EZH2 inhibitors targeting the enzyme catalytic domain. The essential α-helical domain of EZH2 (residues 40-68) that engages EED established the basis for designing hydrocarbon-stapled derivatives to disrupt the specific protein interaction. Non-natural amino acids with olefinic side chains were substituted at (i, i + 4) positions within the EZH2 α-helical sequence, followed by ruthenium-catalyzed olefin metathesis, to yield SAH-EZH2 peptides. Our lead, cell-permeable analog effectively targeted EED in situ, dissociated the EZH2-EED complex and impaired the function of PRC2, as reflected by reduction of the H3K27me3 and EZH2 protein levels, and increased expression of PRC2-regulated cell differentiation marker genes. In response to SAH-EZH2 treatment, murine MLL-AF9 leukemia cells, which are PRC2-dependent, manifested growth arrest and monocyte-macrophage differentiation, in accordance with the phenotypic consequences of shRNA-mediated reduction of EZH2 (or EED) or genetic ablation of Ezh2 (or Eed). In evaluating SAH-EZH2 activity alongside the small-molecule EZH2 inhibitor GSK126 in a series of B-cell lymphoma lines, we observed sequence-specific antiproliferative responses, transcriptional modulation, cellular specificity and a distinct mechanism of action for SAH-EZH2. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B254. Citation Format: Woojin Kim, Gregory H. Bird, Tobias Neff, Guoji Guo, Marc A. Kerenyi, Loren D. Walensky, Stuart H. Orkin. Targeted disruption of the EZH2-EED complex inhibits EZH2-dependent cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B254.

Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters

PRDM9 directs human meiotic crossover hotspots to intergenic sequence motifs, whereas budding yeast hotspots overlap low nucleosome density regions in gene promoters. To investigate hotspots in plants, which lack PRDM9, we used coalescent analysis of Arabidopsis genetic variation. Crossovers increase towards gene promoters and terminators, and hotspots are associated with active chromatin modifications, including H2A.Z, histone H3K4me3, low nucleosome density and low DNA methylation. Hotspot-enriched A-rich and CTT-repeat DNA motifs occur upstream and downstream of transcriptional start respectively. Crossovers are asymmetric around promoters and highest over CTT-motifs and H2A.Z-nucleosomes. Pollen-typing, segregation and cytogenetic analysis show decreased crossovers in the arp6 H2A.Z deposition mutant, at multiple scales. During meiosis H2A.Z and DMC1/RAD51 recombinases form overlapping chromosomal foci. As arp6 reduces DMC1/RAD51 foci, H2A.Z may promote formation or processing of meiotic DNA double-strand breaks. We propose that gene chromatin ancestrally designates hotspots within eukaryotes and PRDM9 is a derived state within vertebrates.

Development of Multiple Cell-Based Assays for the Detection of Histone H3 Lys27 Trimethylation (H3K27me3)

Posttranslational modification of histone proteins in eukaryotes plays an important role in gene transcription and chromatin structure. Dysregulation of the enzymes involved in histone modification has been linked to many cancer forms, making this target class a potential new area for therapeutics. A reliable assay to monitor small-molecule inhibition of various epigenetic enzymes should play a critical role in drug discovery to fight cancer. However, it has been challenging to develop cell-based assays for high-throughput screening (HTS) and compound profiling. Recently, two homogeneous cell-based assay kits using the AlphaLISA(®) and LanthaScreen(®) technologies to detect trimethyl histone H3 Lysine 27 have become commercially available, and a heterogeneous cell assay with modified dissociation-enhanced lanthanide fluorescence immunoassay (DELFIA(®)) format has been reported. To compare their pros and cons, we evaluated, optimized, and validated these three assay formats in three different cell lines and compared their activities with traditional Western blot detection of histone methylation inhibition by using commercial and in-house small-molecule inhibitors. Our data indicate that, although all four formats produced acceptable results, the homogeneous AlphaLISA assay was best suited for HTS and compound profiling due to its wider window and ease of automation. The DELFIA and Western blot assays were useful as validation tools to confirm the cell activities and eliminate potential false-positive compounds.

Targeted disruption of the EZH2–EED complex inhibits EZH2-dependent cancer

Enhancer of zeste homolog2 (EZH2) is the histone lysine N-methyltransferase component of the Polycomb repressive complex 2 (PRC2), which in conjunction with embryonic ectoderm development (EED) and suppressor of zeste 12 homolog (SUZ12), regulates cell lineage determination and homeostasis. Enzymatic hyperactivity has been linked to aberrant repression of tumor suppressor genes in diverse cancers. Here, we report the development of stabilized alpha-helix of EZH2 (SAH-EZH2) peptides that selectively inhibit H3 Lys27 trimethylation by dose-responsively disrupting the EZH2/EED complex and reducing EZH2 protein levels, a mechanism distinct from that reported for small molecule EZH2 inhibitors targeting the enzyme catalytic domain. MLL-AF9 leukemia cells, which are dependent on PRC2, undergo growth arrest and monocyte/macrophage differentiation upon treatment with SAH-EZH2, consistent with observed changes in expression of PRC2-regulated, lineage-specific marker genes. Thus, by dissociating the EZH2/EED complex, we pharmacologically modulate an epigenetic “writer” and suppress PRC2-dependent cancer cell growth.

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

Hox genes controlling motor neuron subtype identity are expressed in rostro-caudal patterns that are spatially and temporally collinear with their chromosomal organization. Here we demonstrate that Hox chromatin is subdivided into discrete domains, controlled by rostro-caudal patterning signals that trigger rapid, domain-wide clearance of repressive H3K27me3 Polycomb modifications. Treatment of differentiating mouse neural progenitors with retinoic acid (RA) leads to activation and binding of RA receptors (RARs) to Hox1-5 chromatin domains, followed by a rapid domain-wide removal of H3K27me3 and acquisition of cervical spinal identity. Wnt and FGF signals induce expression of Cdx2 transcription factor that binds and clears H3K27me3 from Hox1-9 chromatin domains, leading to specification of brachial/thoracic spinal identity. We propose that rapid clearance of repressive modifications in response to transient patterning signals encodes global rostro-caudal neural identity and that maintenance of these chromatin domains ensures transmission of the positional identity to postmitotic motor neurons later in development.

Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence

Senescence is a stress-responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lamina lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence. Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for Lys9 trimethylation on histone H3 (H3K9me3). LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3-positive heterochromatin, thus promoting SAHF formation, which could be inhibited by ectopic LMNB1 expression. Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed. These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genome-wide redistribution: first, through the spatial reorganization of chromatin and, second, through gene repression.

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

Senescence is a stable proliferation arrest, associated with an altered secretory pathway, thought to promote tumor suppression and tissue aging. While chromatin regulation and lamin B1 down-regulation have been implicated as senescence effectors, functional interactions between them are poorly understood. We compared genome-wide Lys4 trimethylation on histone H3 (H3K4me3) and H3K27me3 distributions between proliferating and senescent human cells and found dramatic differences in senescence, including large-scale domains of H3K4me3- and H3K27me3-enriched "mesas" and H3K27me3-depleted "canyons." Mesas form at lamin B1-associated domains (LADs) in replicative senescence and oncogene-induced senescence and overlap DNA hypomethylation regions in cancer, suggesting that pre-malignant senescent chromatin changes foreshadow epigenetic cancer changes. Hutchinson-Gilford progeria syndrome fibroblasts (mutant lamin A) also show evidence of H3K4me3 mesas, suggesting a link between premature chromatin changes and accelerated cell senescence. Canyons mostly form between LADs and are enriched in genes and enhancers. H3K27me3 loss is correlated with up-regulation of key senescence genes, indicating a link between global chromatin changes and local gene expression regulation. Lamin B1 reduction in proliferating cells triggers senescence and formation of mesas and canyons. Our data illustrate profound chromatin reorganization during senescence and suggest that lamin B1 down-regulation in senescence is a key trigger of global and local chromatin changes that impact gene expression, aging, and cancer.

Epigenetic Repression of Male Gametophyte-Specific Genes in the Arabidopsis Sporophyte

Tissue formation, the identity of cells, and the functions they fulfill, are results of gene regulation. The male gametophyte of plants, pollen, is outstanding in this respect as several hundred genes expressed in pollen are not expressed in the sporophyte. How pollen-specific genes are down-regulated in the sporophyte has yet to be established. In this study, we have performed a bioinformatics analysis of publicly available genome-wide epigenetics data of several sporophytic tissues. By combining this analysis with DNase I footprinting data, we assessed means by which the repression of pollen-specific genes in the Arabidopsis sporophyte is conferred. Our findings show that, in seedlings, the majority of pollen-specific genes are associated with histone-3 marked by mono- or trimethylation of Lys-27 (H3K27me1/H3K27me3), both of which are repressive markers for gene expression in the sporophyte. Analysis of DNase footprint profiles of pollen-specific genes in the sporophyte displayed closed chromatin proximal to the start codon. We describe a model of two-staged gene regulation in which a lack of nucleosome-free regions in promoters and histone modifications in open reading frames repress pollen-specific genes in the sporophyte.

The involvement of epigenetic silencing of Foxa2 in cellular replicative and premature senescence induced by hydrogen peroxide

Foxa2 is one member of the Foxa subfamily of winged helix/forkhead box (Fox) transcription factors which has been found to play important roles in multiple stages of mammalian life, beginning with early development, continuing during organogenesis, and finally in metabolism and homeostasis in the adult. To explore the involvement of Foxa2 and its epigenetic regulations in cellular senescence, we established the premature senescence model induced by hydrogen peroxide in comparison with replicative senescence. The mRNA level of Foxa2 was downregulated in both replicative and premature senescent cells. We further found the increased DNA methylation level and new methylation at CpG sites in the promoter with 43.6% of methylated CpG islands in premature senescence, while only 5.7% and 17.1% in young cells and replicative senescence separately. Moreover, we noted the alterations of histone modifications including decreased histone H3 acetylation, increased H4 (Lys-20) trimethylation at the Foxa2 CpG islands in the promoter in replicative or premature senescence, while decreased histone H3 (Lys-4) trimethylation across the transcription start regions in cellular senescence. Taken together, epigenetic silencing of Foxa2 is associated with an increased DNA methylation level and histone H4 (Lys-20) trimethylation, decreased histone H3 acetylation and histone H3 (Lys-4) trimethylation, involved in cellular replicative or premature senescence.

Epigenetic transcriptional activation of monocyte chemotactic protein 3 contributes to long-lasting neuropathic pain

A multiplex analysis for profiling the expression of candidate genes along with epigenetic modification may lead to a better understanding of the complex machinery of neuropathic pain. In the present study, we found that partial sciatic nerve ligation most remarkably increased the expression of monocyte chemotactic protein 3 (MCP-3, known as CCL7) a total of 33 541 genes in the spinal cord, which lasted for 4 weeks. This increase in MCP-3 gene transcription was accompanied by the decreased trimethylation of histone H3 at Lys27 at the MCP-3 promoter. The increased MCP-3 expression associated with its epigenetic modification observed in the spinal cord was almost abolished in interleukin 6 knockout mice with partial sciatic nerve ligation. Consistent with these findings, a single intrathecal injection of recombinant proteins of interleukin 6 significantly increased MCP-3 messenger RNA with a decrease in the level of Lys27 trimethylation of histone H3 at the MCP-3 promoter in the spinal cord of mice. Furthermore, deletion of the C-C chemokine receptor type 2 (CCR2) gene, which encodes a receptor for MCP-3, failed to affect the acceleration of MCP-3 expression in the spinal cord after partial sciatic nerve ligation. A robust increase in MCP-3 protein, which lasted for up to 2 weeks after surgery, in the dorsal horn of the spinal cord of mice with partial sciatic nerve ligation was seen mostly in astrocytes, but not microglia or neurons. On the other hand, the increases in both microglia and astrocytes in the spinal cord by partial sciatic nerve ligation were mostly abolished in interleukin 6 knockout mice. Moreover, this increase in microglia was almost abolished by CCR2 gene deletion, whereas the increase in astrocytes was not affected in nerve-ligated mice that lacked the CCR2 gene. We also found that either in vivo or in vitro treatment with MCP-3 caused robust microglia activation. Under these conditions, intrathecal administration of MCP-3 antibody suppressed the increase in microglia within the mouse spinal cord and neuropathic pain-like behaviours after nerve injury. With the use of a functional magnetic resonance imaging analysis, we demonstrated that a single intrathecal injection of MCP-3 induced dramatic increases in signal intensity in pain-related brain regions. These findings suggest that increased MCP-3 expression associated with interleukin 6 dependent epigenetic modification at the MCP-3 promoter after nerve injury, mostly in spinal astrocytes, may serve to facilitate astrocyte-microglia interaction in the spinal cord and could play a critical role in the neuropathic pain-like state.

Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer

Inactivation of the von Hippel-Lindau tumor suppressor (VHL) is an archetypical tumor-initiating event in clear cell renal carcinoma (ccRCC), leading to the activation of hypoxia-inducible transcription factors (HIFs). However, VHL mutation status in ccRCC is not correlated with clinical outcome. Here we show that during ccRCC progression, cancer cells exploit diverse epigenetic alterations to empower a branch of the VHL-HIF pathway for metastasis, and the strength of this activation is associated with poor clinical outcome. By analyzing metastatic subpopulations of VHL-deficient ccRCC cells, we discovered an epigenetically altered VHL-HIF response specific to metastatic ccRCC. Focusing on the two most prominent pro-metastatic VHL-HIF target genes, we show that liberation from PRC2-dependent repressive histone methylation (H3K27me3) activates HIF-driven CXCR4 expression in support of chemotactic cell invasion, whereas loss of DNA methylation enables HIF-driven CYTIP expression to protect cancer cells from death cytokine signals. Thus, metastasis in ccRCC is based on an epigenetically expanded output of the tumor-initiating pathway.

Tandem PHD Fingers of MORF/MOZ Acetyltransferases Display Selectivity for Acetylated Histone H3 and Are Required for the Association with Chromatin

MORF [MOZ (monocytic leukemia zinc-finger protein)-related factor] and MOZ are catalytic subunits of histone acetyltransferase (HAT) complexes essential in hematopoiesis, neurogenesis, skeletogenesis and other developmental programs and implicated in human leukemias. The canonical HAT domain of MORF/MOZ is preceded by a tandem of plant homeodomain (PHD) fingers whose biological roles and requirements for MORF/MOZ activity are unknown. Here, we demonstrate that the tandem PHD1/2 fingers of MORF recognize the N-terminal tail of histone H3. Acetylation of Lys9 (H3K9ac) or Lys14 (H3K14ac) enhances binding of MORF PHD1/2 to unmodified H3 peptides twofold to threefold. The selectivity for acetylated H3 tail is conserved in the double PHD1/2 fingers of MOZ. This interaction requires the intact N-terminus of histone H3 and is inhibited by trimethylation of Lys4. Biochemical analysis using NMR, fluorescence spectroscopy and mutagenesis identified key amino acids of MORF PHD1/2 necessary for the interaction with histones. Fluorescence microscopy and immunoprecipitation experiments reveal that both PHD fingers are required for binding to H3K14ac in vivo and localization to chromatin. The HAT assays indicate that the interaction with H3K14ac may promote enzymatic activity in trans. Together, our data suggest that the PHD1/2 fingers play a role in MOZ/MORF HATs association with the chromatic regions enriched in acetylated marks.

P53-mediated heterochromatin reorganization regulates its cell fate decisions

p53 is a major sensor of cellular stresses, and its activation influences cell fate decisions. We identified SUV39H1, a histone code 'writer' responsible for the histone H3 Lys9 trimethylation (H3K9me3) mark for 'closed' chromatin conformation, as a target of p53 repression. SUV39H1 downregulation was mediated transcriptionally by p21 and post-translationally by MDM2. The H3K9me3 repression mark was found to be associated with promoters of representative p53 target genes and was decreased upon p53 activation. Overexpression of SUV39H1 maintained higher levels of the H3K9me3 mark on these promoters and was associated with decreased p53 promoter occupancy and decreased transcriptional induction in response to p53. Conversely, SUV39H1 pre-silencing decreased H3K9me3 levels on these promoters and enhanced the p53 apoptotic response. These findings uncover a new layer of p53-mediated chromatin regulation through modulation of histone methylation at p53 target promoters.