Repressive Chromatin Marks Research Articles

Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells.

Background During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing persists to some extent in spermatids. Considering the many reports of XY-linked genes expressed and needed in the post-meiotic phase of mouse spermatogenesis, it is still unclear whether or not the mouse sex chromatin is a repressive or permissive environment, after meiosis.Results To determine the transcriptional and chromatin state of the sex chromosomes after meiosis, we re-analyzed ten ChIP-Seq datasets performed on mouse round spermatids and four RNA-seq datasets from male germ cells purified at different stages of spermatogenesis. For this, we used the last version of the genome (mm10/GRCm38) and included reads that map to several genomic locations in order to properly interpret the high proportion of sex chromosome-encoded multicopy genes. Our study shows that coverage of active epigenetic marks H3K4me3 and Kcr is similar on the sex chromosomes and on autosomes. The post-meiotic sex chromatin nevertheless differs from autosomal chromatin in its enrichment in H3K9me3 and its depletion in H3K27me3 and H4 acetylation. We also identified a posttranslational modification, H3K27ac, which specifically accumulates on the Y chromosome. In parallel, we found that the X and Y chromosomes are enriched in genes expressed post-meiotically and display a higher proportion of spermatid-specific genes compared to autosomes. Finally, we observed that portions of chromosome 14 and of the sex chromosomes share specific features, such as enrichment in H3K9me3 and the presence of multicopy genes that are specifically expressed in round spermatids, suggesting that parts of chromosome 14 are under the same evolutionary constraints than the sex chromosomes.ConclusionsBased on our expression and epigenomic studies, we conclude that, after meiosis, the mouse sex chromosomes are no longer silenced but are nevertheless regulated differently than autosomes and accumulate different chromatin marks. We propose that post-meiotic selective constraints are at the basis of the enrichment of spermatid-specific genes and of the peculiar chromatin composition of the sex chromosomes and of parts of chromosome 14.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0099-8) contains supplementary material, which is available to authorized users.

High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability

A translocation leading to the formation of an oncogenic EWS-ETS fusion protein defines Ewing sarcoma. The most frequent gene fusion, present in 85 percent of Ewing sarcomas, is EWS-FLI1. Here, a high-throughput RNA interference screen was performed to identify genes whose function is critical for EWS-FLI1 driven cell viability. In total, 6781 genes were targeted by siRNA molecules and the screen was performed both in presence and absence of doxycycline-inducible expression of the EWS-FLI1 shRNA in A673/TR/shEF Ewing sarcoma cells. The Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest hit reducing cell viability only in EWS-FLI1 expressing Ewing sarcoma cells. LRWD1 had been previously described as a testis specific gene with only limited information on its function. Analysis of LRWD1 mRNA levels in patient samples indicated that high expression associated with poor overall survival in Ewing sarcoma. Gene ontology analysis of LRWD1 co-expressed genes in Ewing tumors revealed association with DNA replication and analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells indicated a role in connective tissue development and cellular morphogenesis. Moreover, EWS-FLI1 repressed genes with repressive H3K27me3 chromatin marks were highly enriched among LRWD1 target genes in A673/TR/shEF Ewing sarcoma cells, suggesting that LRWD1 contributes to EWS-FLI1 driven transcriptional regulation. Taken together, we have identified LRWD1 as a novel regulator of EWS-FLI1 driven cell viability in A673/TR/shEF Ewing sarcoma cells, shown association between high LRWD1 mRNA expression and aggressive disease and identified processes by which LRWD1 may promote oncogenesis in Ewing sarcoma.

Proximal and distal regulation of the HYAL1 gene cluster by the estrogen receptor α in breast cancer cells.

Chromosomal and genome abnormalities at the 3p21.3 locus are frequent events linked to epithelial cancers, including ovarian and breast cancers. Genes encoded in the 3p21.3 cluster include HYAL1, HYAL2 and HYAL3 members of hyaluronidases involved in the breakdown of hyaluronan, an abundant component of the vertebrate extracellular matrix. However, the transcriptional regulation of HYAL genes is poorly defined. Here, we identified the estrogen receptor ERα as a negative regulator of HYAL1 expression in breast cancer cells. Integrative data mining using METABRIC dataset revealed a significant inverse correlation between ERα and HYAL1 gene expression in human breast tumors. ChIP-Seq analysis identified several ERα binding sites within the 3p21.3 locus, supporting the role of estrogen as an upstream signal that diversely regulates the expression of 3p21.3 genes at both proximal and distal locations. Of these, HYAL1 was repressed by estrogen through ERα binding to a consensus estrogen response element (ERE) located in the proximal promoter of HYAL1 and flanked by an Sp1 binding site, required to achieve optimal estrogen repression. The repressive chromatin mark H3K27me3 was increased at the proximal HYAL1 ERE but not at other EREs contained in the cluster, providing a mechanism to selectively downregulate HYAL1. The HYAL1 repression was also specific to ERα and not to ERβ, whose expression did not correlate with HYAL1 in human breast tumors. This study identifies HYAL1 as an ERα target gene and provides a functional framework for the direct effect of estrogen on 3p21.3 genes in breast cancer cells.

Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification

SummaryPrimordial germ cell (PGC) development is characterized by global epigenetic remodeling, which resets genomic potential and establishes an epigenetic ground state. Here we recapitulate PGC specification in vitro from naive embryonic stem cells and characterize the early events of epigenetic reprogramming during the formation of the human and mouse germline. Following rapid de novo DNA methylation during priming to epiblast-like cells, methylation is globally erased in PGC-like cells. Repressive chromatin marks (H3K9me2/3) and transposable elements are enriched at demethylation-resistant regions, while active chromatin marks (H3K4me3 or H3K27ac) are more prominent at regions that demethylate faster. The dynamics of specification and epigenetic reprogramming show species-specific differences, in particular markedly slower reprogramming kinetics in the human germline. Differences in developmental kinetics may be explained by differential regulation of epigenetic modifiers. Our work establishes a robust and faithful experimental system of the early events of epigenetic reprogramming and regulation in the germline.

H2AK119 monoubiquitination regulates Angiotensin II receptor mediated macrophage infiltration and renal fibrosis in type 2 diabetic rats.

Monocyte chemoattractant protein (MCP-1) and transforming growth factor-β (TGF-β1)-markers of inflammation and fibrosis, are central to type 2 diabetic nephropathy (T2DN) progression. The epigenetic basis of their expression has also been explored to certain extent. H2A lysine 119 monoubiquitination (H2AK119Ub), a repressive chromatin mark regulates progression of hyperglycaemia induced fibrosis in glomerular mesangial cells. However, how H2AK119Ub affects the expression of MCP-1 and TGF-β1 and their regulation by Angiotensin II receptor subtypes remains unknown. In the current study, we aimed to study the effect of Angiotensin II receptors' blockade on the macrophage infiltration and histone modifications occurring at the promoter region of Mcp1 and Tgfb1in high fat diet fed and low dose streptozotocin treated male Wistar rats. Hereby, we present the first report delineating a distinct link between H2AK119Ub and macrophage infiltration and fibrosis i.e. the enrichment of H2AUb at Mcp1 and Tgfb1 promoter region was found to reduce drastically in the T2DN which could be significantly reversed by Telmisartan and was further elevated by PD123319. We could conclude that the Angiotensin II mediated macrophage infiltration in T2DN is regulated at least partially by H2AK119Ub through both AT1 and AT2 receptors, which to the best of our knowledge, presents the first report for the regulation of Mcp1 by H2AK119Ub. Thus an approach targeting AT1R blockade and AT2R activation accompanied by an epigenetic modulator may be more suitable to ameliorate the macrophage infiltration and fibrosis associated with T2DN.

Cooperation between the H3K27me3 chromatin marker and non-CG methylation in epigenetic regulation

H3K27me3 is a repressive chromatin mark of genes and is catalyzed by homologs of Enhancer of zeste [E(z)], a component of Polycomb-repressive complex 2 (PRC2), while DNA methylation that occurs in CG and non-CG (CHG and CHH, where H is A, C, or T) contexts is a hallmark of transposon silencing in plants. However, the relationship between H3K27me3 and DNA methylation in gene repression remains unclear. In addition, the mechanism of PRC2 recruitment to specific genes is not known in plants. Here, we show that SDG711, a rice (Oryza sativa) E(z) homolog, is required to maintain H3K27me3 of many developmental genes after shoot meristem to leaf transition and that many H3K27me3-marked developmental genes are also methylated at non-CG sites in the body regions. SDG711-binding and SDG711-mediated ectopic H3K27me3 also target genes methylated at non-CG sites. Conversely, mutation of OsDRM2, a major rice CHH methyltransferase, resulted in loss of SDG711-binding and H3K27me3 from many genes and their de-repression. Furthermore, we show that SDG711 physically interacts with OsDRM2 and a putative CHG methylation-binding protein. These results together suggest that the repression of many developmental genes may involve both DRM2-mediated non-CG methylation and PRC2-mediated H3K27me3 and that the two marks are not generally mutually exclusive but may cooperate in repression of developmentally regulated genes in rice.

Repression of Astrocytic Connexins in Cortical and Subcortical Brain Regions and Prefrontal Enrichment of H3K9me3 in Depression and Suicide.

Background:Major depressive disorder has been associated with dysfunctional astrocytic networks. The underlying causes, extent, and consequences of such dysfunctions remain to be characterized. Astrocyte-astrocyte communication occurs principally through gap junction channels primarily formed by connexin 30 and 43 (CX30 and CX43). We previously reported decreased connexin expression in the prefrontal cortex of depressed suicides. In the present study, we investigated whether these changes are mediated by epigenetic regulation, and expanded gene expression quantifications to other cortical and subcortical regions to assess the regional distribution of connexion disruptions in depressed suicides.Methods:The expression of CX30 and CX43 was measured by real-time PCR in samples of neocortex (Brodmann areas 4 and 17), cerebellar cortex, mediodorsal thalamus, and caudate nucleus of 22 depressed suicides and 22 matched sudden-death controls. Chromatin immunoprecipitation was used to measure enrichment levels of the repressive chromatin mark H3K9me3 in the prefrontal cortex.Results:We found a consistent downregulation of connexin genes in all regions examined, except in the cerebellum where an increase in the expression of CX30 was measured and using chromatin immunoprecipitation we observed an enrichment of H3K9me3 for both Cx30 and Cx43 in the prefrontal cortex.Conclusions:Our study shows widespread astrocytic CX gene repression in depressed suicides that is mediated, at least in part, through epigenetic mechanisms. Taken together, these findings support the notion of widespread cerebral astrocytic dysfunction in major depressive disorder.

Abstract 950: Bistable switching of c-KIT by estrogen-mediated ceRNA and epigenetic silencing of miR-193a predicts survival in ovarian cancer

Abstract Ovarian cancer is one of the most lethal cancers in the female reproductive system. Our previous study has shown that ovarian cancer may be initiated by ovarian cancer initiating cells (OCIC) characterized by the surface antigen CD44 and c-KIT (CD117). Previous study also suggested that long term treatment of estrogen such as hormonal replacement therapy (HRT) may increase the risk of ovarian cancer, however the role of estrogen in ovarian carcinogenesis is still controversial. To unravel this complexity, we propose a mathematical model to explore how the ER signaling pathway contribute to c-KIT expression during ovarian carcinogenesis: one through a ceRNA competition of an ER target,E2F6 and c-KIT for their targeted miRNA, miR-193a; second by binding of E2F6 protein, in association with the polycomb complex, to the promoter of miR-193a to downregulate miR-193a transcription by epigenetic modifications. Our model found that epigenetic silencing of miR-193a generates a bistable switching of c-KIT during ovarian carcinogenesis based on the level of EZH2. To confirm our results, we performed ectopic expression of miR-193a and 3’UTR luciferase in ovarian cancer cell lines and confirmed that E2F6 and c-KIT are the targets of miR-193a. Importantly, treatment of E2 or bisphenol A (BPA) resulted in the up-regulation of E2F6 and c-kit mRNA in IOSE cells in which no or low methylation at the promoter CpG island of miR-193a was found. On the contrary, promoter hypermethylation of miR193a could be observed in miR-193a-underexpressed CP70 ovarian cancer cells but not in HeyC2 cells which showed similar expression level of miR-193a as in IOSE cells. Treatment of demethylating agent (5azaDC) or EZH2 inhibitor (GSK343) resulted in a reexpression of miR-193a in CP70 ovarian cancer cells. Overexpression of miR-193a inhibited tumor growth in vitro and in an animal model. Further ChIP-PCR assay also found that open chromatin mark H3K4me3 was enriched in the promoter region of miR-193a in HeyC2 but not in CP70 cells. On the contrary, repressive chromatin marks H3K9me3 and H3K27me3 were only enriched in CP70 cells. Clinically, ovarian cancer patients (n = 109) with higher promoter methylation of miR-193a were associated with poor survival (p>0.05). Additional analysis of the TCGA ovarian cancer dataset demonstrated that ovarian cancer patients with low expression of EZH2, a polycomb-group protein, showed positive correlation (p<0.05) between E2F6 and c-KIT which resembles the ceRNA phenomenon between these two mRNAs. Importantly, ovarian cancer patients with low expression of EZH2 tended to have lower expression of c-KIT. In conclusion, our mathematical model and experimental data suggests that miR-193a can be epigenetically regulated by both ceRNA and promoter methylation. Simultaneous EZH2 inhibition and anti-estrogen therapy can constitute an effective combined therapeutic strategy against ovarian cancer. Citation Format: Frank Hsueh-Che Cheng, Baltazar D. Aguda, Hon-Yi Lin, Je-Chiang Tsai, Marek Kochanczyk, Ru-Inn Lin, Jora M. J. Lin, Gary C. W. Chen, Cheng-Chang Chang, Hung-Cheng Lai, Kenneth P. Nephew, Tzy-Wei Hwang, Michael W. Y. Chan. Bistable switching of c-KIT by estrogen-mediated ceRNA and epigenetic silencing of miR-193a predicts survival in ovarian cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 950.

Cross-species analyses unravel the complexity of H3K27me3 and H4K20me3 in the context of neural stem progenitor cells

Neural stem progenitor cells (NSPCs) in the human subventricular zone (SVZ) potentially contribute to lifelong neurogenesis, yet subtypes of glioblastoma multiforme (GBM) contain NSPC signatures that highlight the importance of cell fate regulation. Among numerous regulatory mechanisms, the posttranslational methylations onto histone tails are crucial regulator of cell fate. The work presented here focuses on the role of 2 repressive chromatin marks trimethylations on histone H3 lysine 27 (H3K27me3) and histone H4 lysine 20 (H4K20me3) in the adult NSPC within the SVZ. To best model healthy human NSPCs as they exist in vivo for epigenetic profiling of H3K27me3 and H4K20me3, we used NSPCs isolated from the adult SVZ of baboon brain (Papio anubis) with brain structure and genomic level similar to human. The putative role of H3K27me3 in normal NSPCs predominantly falls into the regulation of gene expression, cell cycle, and differentiation, whereas H4K20me3 is involved in DNA replication/repair, metabolism, and cell cycle. Using conditional knockout mouse models to diminish Ezh2 and Suv4-20h responsible for H3K27me3 and H4K20me3, respectively, we found that both repressive marks have irrefutable function for cell cycle regulation in the NSPC population. Although both EZH2/H3K27me3 and Suv4-20h/H4K20me3 have implication in cancers, our comparative genomics approach between healthy NSPCs and human GBM specimens revealed that substantial sets of genes enriched with H3K27me3 and H4K20me3 in the NSPCs are altered in the human GBM. In sum, our integrated analyses across species highlight important roles of H3K27me3 and H4K20me3 in normal and disease conditions in the context of NSPC.

Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification

SummaryHuman male germ cell tumors (GCTs) are derived from primordial germ cells (PGCs). The master pluripotency regulator and neuroectodermal lineage effector transcription factor SOX2 is repressed in PGCs and the seminoma (SEM) subset of GCTs. The mechanism of SOX2 repression and its significance to GC and GCT development currently are not understood. Here, we show that SOX2 repression in SEM-derived TCam-2 cells is mediated by the Polycomb repressive complex (PcG) and the repressive H3K27me3 chromatin mark that are enriched at its promoter. Furthermore, SOX2 repression in TCam-2 cells can be abrogated by recruitment of the constitutively expressed H3K27 demethylase UTX to the SOX2 promoter through retinoid signaling, leading to expression of neuronal and other lineage genes. SOX17 has been shown to initiate human PGC specification, with its target PRDM1 suppressing mesendodermal genes. Our results are consistent with a role for SOX2 repression in normal germline development by suppressing neuroectodermal genes.

Abstract IA26: Selective activation of gene expression by targeting long noncoding RNA

Abstract Long noncoding RNA (lncRNA) can regulate transcription by recruiting epigenetic regulatory complexes to target genes. Polycomb repressive complex 2 (PRC2), an epigenetic transcriptional repressor, is recruited to its target genes via lncRNA. PRC2 represses transcription through the action of the histone methyltransferase EZH2, which methylates histone H3 at lysine 27 (applying the H3K27me3 repressive mark). Using RIP-Seq, we identified the genome-wide pool of RNA sequences that interact with PRC2. We design short single-strand oligonucleotides that hybridize to an individual lncRNA, and sterically block its binding to PRC2, without degrading the lncRNA. These oligonucleotides selectively block PRC2 binding to a specific lncRNA, thereby de-repressing the expression of an associated target mRNA, resulting in increased amounts of the therapeutic protein. This approach was used to increase SMN2 transcription as a potential treatment for Spinal Muscular Atrophy (SMA). Oligonucleotides that target an antisense lncRNA selectively increase SMN2 mRNA and protein levels in SMA patient cells in vitro and in a mouse SMA model that carries the human SMN2 locus. Data support a mechanism of action whereby the oligonucleotides block recruitment of PRC2 to SMN2 chromatin, decrease the H3K27me3 repressive chromatin mark, increase the presence of activating chromatin marks and increase RNA polymerase II association along the SMN2 gene. This therapeutic approach potentially can be used to elevate the expression of many genes whose gene products are limiting in various human diseases. Citation Format: Jim Barsoum. Selective activation of gene expression by targeting long noncoding RNA. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr IA26.

Epigenetic response to environmental stress: Assembly of BRG1–G9a/GLP–DNMT3 repressive chromatin complex on Myh6 promoter in pathologically stressed hearts

Chromatin structure is determined by nucleosome positioning, histone modifications, and DNA methylation. How chromatin modifications are coordinately altered under pathological conditions remains elusive. Here we describe a stress-activated mechanism of concerted chromatin modification in the heart. In mice, pathological stress activates cardiomyocytes to express Brg1 (nucleosome-remodeling factor), G9a/Glp (histone methyltransferase), and Dnmt3 (DNA methyltransferase). Once activated, Brg1 recruits G9a and then Dnmt3 to sequentially assemble repressive chromatin—marked by H3K9 and CpG methylation—on a key molecular motor gene (Myh6), thereby silencing Myh6 and impairing cardiac contraction. Disruption of Brg1, G9a or Dnmt3 erases repressive chromatin marks and de-represses Myh6, reducing stress-induced cardiac dysfunction. In human hypertrophic hearts, BRG1–G9a/GLP–DNMT3 complex is also activated; its level correlates with H3K9/CpG methylation, Myh6 repression, and cardiomyopathy. Our studies demonstrate a new mechanism of chromatin assembly in stressed hearts and novel therapeutic targets for restoring Myh6 and ventricular function. The stress-induced Brg1–G9a–Dnmt3 interactions and sequence of repressive chromatin assembly on Myh6 illustrates a molecular mechanism by which the heart epigenetically responds to environmental signals. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.

A phospho-dependent mechanism involving NCoR and KMT2D controls a permissive chromatin state at Notch target genes.

The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3 lysine-4 (H3K4) demethylases are key chromatin modifiers that establish the repressive chromatin state at Notch target genes. However, the counteracting histone methyltransferase required for the active chromatin state remained elusive. Here, we show that the RBP-J interacting factor SHARP is not only able to interact with the NCoR corepressor complex, but also with the H3K4 methyltransferase KMT2D coactivator complex. KMT2D and NCoR compete for the C-terminal SPOC-domain of SHARP. We reveal that the SPOC-domain exclusively binds to phosphorylated NCoR. The balance between NCoR and KMT2D binding is shifted upon mutating the phosphorylation sites of NCoR or upon inhibition of the NCoR kinase CK2β. Furthermore, we show that the homologs of SHARP and KMT2D in Drosophila also physically interact and control Notch-mediated functions in vivo. Together, our findings reveal how signaling can fine-tune a committed chromatin state by phosphorylation of a pivotal chromatin-modifier.

Abstract P5-08-21: Expression of EZH2 and its downstream effectors pEZH2 and H3K27 in pregnancy associated breast cancer (PABC)

Abstract Background: Pregnancy associated breast cancer (PABC) arises during or after pregnancy, is typically triple negative, and is associated with a poor prognosis. Enhancer of Zeste Homolog 2 (EZH2), a core protein of the polycomb-repressive complex, plays a vital role in the epigenetic maintenance of histone H3 lysine (H3K27) repressive chromatin mark and has been found to be aberrantly expressed in various cancers including the breast. EZH2 is involved in stem cell renewal and is involved the initiation, progression and maintenance of cancer cells. EZH2 has been reported to be highly expressed in triple negative breast cancers and to be associated with poor prognosis. In this study, we assessed expression of EZH2 and its downstream markers phosphorylated EZH2 (pEZH2) and H3K27 and correlated their expression with clinicopathologic characteristics in this aggressive type of breast carcinoma. Design: 23 patients diagnosed with PABC within 2 years of pregnancy (mean age=35.8, range=26-48) and control age-/stage-matched nulliparous women (mean age=37.5, range=29-51) were evaluated. Slides were reviewed and pathologic tumor characteristics were noted. Immunohistochemical stains for EZH2, pEZH2, H3K27 and the cancer stem cell marker ALDH1 were performed on 23 PABC and 15 control cases. Extent (1=1-25% positive tumor cells, 2=26-50%, 3=51-75% or 4=76-100%) and intensity (1=weak, 2=moderate or 3=strong) of staining were assessed. A composite score (CS) was calculated by multiplying the extent by intensity (range=0-9; weak=1-3; moderate=4-6 and strong=7-9). Results: PABCs were more likely than controls to have moderate to strong immunoreactivity for EZH2 (69.6% vs. 33.3%, p=0.04). All PABC and control cases expressed EZH2 and pEZH2, while 60.9% of PABC and 40% of control cases expressed H3K27. Within the PABC group, moderate to strong EZH2 expression was seen more frequently in grade 3 tumors (86.7% in grade 3 tumors vs. 37.5% in grades 1-2, p=0.03). Of interest, all triple negative (TN) PABC cases had moderate to strong EZH2 (100% vs. 43.8%, p=0.02). All five PABC cases with the strongest EZH2 (CS=9) were grade 3 tumors (3 TN, 1 HER2+ and 1 luminal B), 60% of which had positive lymph node metastasis. Although 83.3% of ALDH1+ cases also had moderate to strong EZH2, no significant correlation was observed. Conclusions: 1. PABCs express EZH2 and pEZH2 consistently. 2. PABCs are more likely than controls to have moderate to strong immunoreactivity for EZH2. 3. Within the PABC group, all triple negative tumors and the majority of grade 3 tumors have high EZH2 expression. 4. PABC cases with the strongest EZH2 are grade 3 tumors that have positive lymph nodes. Increased expression of EZH2 in PABC may contribute to the poor prognosis in these cases. Our findings add to the understanding of the molecular pathways that operate in different subtypes of breast carcinomas. Citation Format: Blanco Jr LZ, Parini V, Dhamne SA, Siziopikou KP. Expression of EZH2 and its downstream effectors pEZH2 and H3K27 in pregnancy associated breast cancer (PABC). [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-08-21.

The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin.

Differentiation of inflammatory macrophages from monocytes is characterized by an orderly integration of epigenetic and transcriptional regulatory mechanisms guided by lineage-determining transcription factors such as PU.1. Further activation of macrophages leads to a stimulus- or microenvironment-specific signal integration with subsequent transcriptional control established by the action of tissue- or signal-associated transcription factors. Here, we assess four histone modifications during human macrophage activation and integrate this information with the gene expression data from 28 different macrophage activation conditions in combination with GM-CSF. Bioinformatically, for inflammatory macrophages we define a unique network of transcriptional and epigenetic regulators (TRs), which was characterized by accessible promoters independent of the activation signal. In contrast to the general accessibility of promoters of TRs, mRNA expression of central TRs belonging to the TR network displayed stimulus-specific expression patterns, indicating a second level of transcriptional regulation beyond epigenetic chromatin changes. In contrast, stringent integration of epigenetic and transcriptional regulation was observed in networks of TRs established from somatic tissues and tissue macrophages. In these networks, clusters of TRs with permissive histone marks were associated with high gene expression whereas clusters with repressive chromatin marks were associated with absent gene expression. Collectively, these results support that macrophage activation during inflammation in contrast to lineage determination is mainly regulated transcriptionally by a pre-defined TR network.

P53 genes function to restrain mobile elements.

Throughout the animal kingdom, p53 genes govern stress response networks by specifying adaptive transcriptional responses. The human member of this gene family is mutated in most cancers, but precisely how p53 functions to mediate tumor suppression is not well understood. Using Drosophila and zebrafish models, we show that p53 restricts retrotransposon activity and genetically interacts with components of the piRNA (piwi-interacting RNA) pathway. Furthermore, transposon eruptions occurring in the p53(-) germline were incited by meiotic recombination, and transcripts produced from these mobile elements accumulated in the germ plasm. In gene complementation studies, normal human p53 alleles suppressed transposons, but mutant p53 alleles from cancer patients could not. Consistent with these observations, we also found patterns of unrestrained retrotransposons in p53-driven mouse and human cancers. Furthermore, p53 status correlated with repressive chromatin marks in the 5' sequence of a synthetic LINE-1 element. Together, these observations indicate that ancestral functions of p53 operate through conserved mechanisms to contain retrotransposons. Since human p53 mutants are disabled for this activity, our findings raise the possibility that p53 mitigates oncogenic disease in part by restricting transposon mobility.

Abstract 15235: Characterization of Hypoxia-induced Long Non-coding RNAs in Endothelial Cells

RNA deep sequencing revealed that the majority of the genome is transcribed, however, only 2% of all transcripts encode for proteins. The remaining transcripts are referred to as non-coding RNAs and can be divided into small non-coding RNAs (<200nt) and long non-coding RNAs (lncRNAs; >200nt). Recent studies suggest that lncRNAs can regulate gene expression at various stages, e.g. by acting as scaffolds, by modulating splicing, or by chromatin modification. Regarding endothelial cells (EC), the response to hypoxia and the regulation of angiogenic activity are key events in the context of several diseases, however, the involvement of regulatory lncRNAs and their molecular function is still elusive. To systematically determine the regulation of lncRNAs by hypoxia, we performed RNA-seq in HUVEC after exposure to hypoxia (24h; 0.2% O 2 ) and identified 71 lncRNAs to be significantly up- (p≤0.01) and 78 lncRNAs to be down-regulated in comparison to normoxic conditions. qRT-PCR was used to validate the hypoxia-dependent regulation of 5 selected lncRNAs (Hyp_up_1 to Hyp_up_5). Since hypoxia controls the angiogenic function of EC, we next investigated whether our candidate lncRNAs affect endothelial cell sprouting as an in vitro measurement for angiogenic response. Silencing was achieved by GapmeRs (Hyp_up_1, 3) or siRNAs (Hyp_up_2, 5). Strikingly, only silencing of Hyp_up_1 significantly reduced sprouting under basal conditions and VEGF stimulation. Therefore, we selected Hyp_up_1 for further functional characterization: First, nuclear cytoplasmic fractionation revealed its predominant nuclear localization. Second, RNA immunoprecipitation (RIP) showed that Hyp_up_1 is mainly associated with repressive chromatin marks (3meH3K27) indicating that it may be involved in epigenetic gene regulation. Third, GO term analysis based on exon array data revealed a reduced expression of angiogenesis related genes upon Hyp_up_1 silencing. Finally, using antisense affinity purification and mass spectrometry, we identified several Hyp_up_1 binding proteins and confirmed their interaction by RIP. Hyp_up_1 bound proteins included PTBP1/U2AF65, two splicing regulators, as well as LOXL2, a transcription factor known to mediate angiogenic functions in EC.

A gene expression signature identifying transient DNMT1 depletion as a causal factor of cancer-germline gene activation in melanoma

BackgroundMany human tumors show aberrant activation of a group of germline-specific genes, termed cancer-germline (CG) genes, several of which appear to exert oncogenic functions. Although activation of CG genes in tumors has been linked to promoter DNA demethylation, the mechanisms underlying this epigenetic alteration remain unclear. Two main processes have been proposed: awaking of a gametogenic program directing demethylation of target DNA sequences via specific regulators, or general deficiency of DNA methylation activities resulting from mis-targeting or down-regulation of the DNMT1 methyltransferase.ResultsBy the analysis of transcriptomic data, we searched to identify gene expression changes associated with CG gene activation in melanoma cells. We found no evidence linking CG gene activation with differential expression of gametogenic regulators. Instead, CG gene activation correlated with decreased expression of a set of mitosis/division-related genes (ICCG genes). Interestingly, a similar gene expression signature was previously associated with depletion of DNMT1. Consistently, analysis of a large set of melanoma tissues revealed that DNMT1 expression levels were often lower in samples showing activation of multiple CG genes. Moreover, by using immortalized melanocytes and fibroblasts carrying an inducible anti-DNMT1 small hairpin RNA (shRNA), we demonstrate that transient depletion of DNMT1 can lead to long-term activation of CG genes and repression of ICCG genes at the same time. For one of the ICCG genes (CDCA7L), we found that its down-regulation in melanoma cells was associated with deposition of repressive chromatin marks, including H3K27me3.ConclusionsTogether, our observations point towards transient DNMT1 depletion as a causal factor of CG gene activation in vivo in melanoma.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-015-0147-4) contains supplementary material, which is available to authorized users.

EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression

AbstractFetal hemoglobin (HbF, α2γ2) induction is a well-validated strategy for sickle cell disease (SCD) treatment. Using a small-molecule screen, we found that UNC0638, a selective inhibitor of EHMT1 and EHMT2 histone methyltransferases, induces γ-globin expression. EHMT1/2 catalyze mono- and dimethylation of lysine 9 on histone 3 (H3K9), raising the possibility that H3K9Me2, a repressive chromatin mark, plays a role in silencing γ-globin expression. In primary human adult erythroid cells, UNC0638 and EHMT1 or EHMT2 short hairpin RNA–mediated knockdown significantly increased γ-globin expression, HbF synthesis, and the percentage of cells expressing HbF. At effective concentrations, UNC0638 did not alter cell morphology, proliferation, or erythroid differentiation of primary human CD34+ hematopoietic stem and progenitor cells in culture ex vivo. In murine erythroleukemia cells, UNC0638 and Ehmt2 CRISPR/Cas9-mediated knockout both led to a marked increase in expression of embryonic β-globin genes Hbb-εy and Hbb-βh1. In primary human adult erythroblasts, chromatin immunoprecipitation followed by sequencing analysis revealed that UNC0638 treatment leads to genome-wide depletion in H3K9Me2 and a concomitant increase in the activating mark H3K9Ac, which was especially pronounced at the γ-globin gene region. In RNA-sequencing analysis of erythroblasts, γ-globin genes were among the most significantly upregulated genes by UNC0638. Further increase in γ-globin expression in primary human adult erythroid cells was achieved by combining EHMT1/2 inhibition with the histone deacetylase inhibitor entinostat or hypomethylating agent decitabine. Our data provide genetic and pharmacologic evidence that EHMT1 and EHMT2 are epigenetic regulators involved in γ-globin repression and represent a novel therapeutic target for SCD.

Shockingly Early: Chromatin-Mediated Loss of the Heat Shock Response

In this issue of Molecular Cell, Labbadia and Morimoto (2015) show that there is a precipitous decline in stress resistance at the onset of reproduction in C.elegans and that this transition is regulated by changes in repressive chromatin marks.