H3K4 Mono Research Articles

Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module

The SET1/MLL family of histone methyltransferases is conserved in eukaryotes and regulates transcription by catalyzing histone H3K4 mono-, di-, and tri-methylation. These enzymes form a common five-subunit catalytic core whose assembly is critical for their basal and regulated enzymatic activities through unknown mechanisms. Here, wepresent the crystal structure of the intact yeastCOMPASS histone methyltransferase catalytic module consisting of Swd1, Swd3, Bre2, Sdc1, and Set1. The complex is organized by Swd1, whose conserved C-terminal tail not only nucleates Swd3 and a Bre2-Sdc1 subcomplex, but also joins Set1 to construct a regulatory pocket next to the catalytic site. This inter-subunit pocket is targeted by a previously unrecognized enzyme-modulating motif in Swd3 and features a doorstop-style mechanism dictating substrate selectivity among SET1/MLL family members. By spatially mapping the functional components of COMPASS, our results provide a structural framework for understanding the multifaceted functions and regulation of the H3K4 methyltransferase family.

Effect of BIX-01294 on proliferation, apoptosis and histone methylation of acute T lymphoblastic leukemia cells

ObjectiveTo determine effect of G9a inhibitor BIX-01294 on proliferation, apoptosis and histone methylation of acute T lymphoblastic leukemia cells (MOLT-4 and Jurkat) and to explore the underlying mechanism. MethodsCell proliferation was detected by MTT assay and apoptosis and cell cycle were measured by flow cytometry. Western blot was performed to determine expression of caspase-3, Bcl-2, Bax, P21, P15 and DNMT1 as well as levels of histone H3 acetylation, histone H3K9 mono- di- and tri-methylation. ResultsBIX-01294 inhibits expression of Bcl-2, upregulates expression of Bax and caspase-3 and induces cell apoptosis. BIX-01294 upregulates cell cycle inhibitor P21 expression and induces cell cycle arrest in the phase G0/G1. Furthermore, BIX-01294 suppresses expression of DNA demethylase DNMT1 and promotes expression of tumor suppressor protein P15, thereby inhibiting proliferation of MOLT-4 and Jurkat cells. BIX-01294 downregulates histone H3K9 mono- and di-methylation levels and has no effect on H3K9 trimethylation and histone H3 acetylation. ConclusionTaken together, our results indicate that by regulating H3K9 methylation and cell cycle, BIX-01294 inhibits the proliferation and induces apoptosis of acute T lymphoblastic leukemia cells.

MAP Kinase-Dependent RUNX2 Phosphorylation Is Necessary for Epigenetic Modification of Chromatin During Osteoblast Differentiation.

RUNX2, an essential transcription factor for osteoblast differentiation and bone formation is activated by ERK/MAP kinase-dependent phosphorylation. However, relationship between these early events and specific epigenetic modifications of chromatin during osteoblast differentiation have not been previously examined. Here, we explore these relationships using chromatin immunoprecipitation (ChIP) to detect chromatin modifications in RUNX2-binding regions of Bglap2 and Ibsp. Growth of MC3T3-E1c4 preosteoblast cells in differentiation conditions rapidly induced Bglap2 and lbsp mRNAs. For both genes, osteogenic stimulation increased chromatin-bound P-ERK, P-RUNX2, p300, and RNA polymerase II as well as histone H3K9 and H4K5 acetylation. The level of H3K4 di-methylation, another gene activation-associated histone mark, also increased. In contrast, levels of the gene repressive marks, H3K9 mono-, di-, and tri-methylation in the same regions were reduced. Inhibition of MAP kinase signaling blocked differentiation-dependent chromatin modifications and Bglap2 and Ibsp expression. To evaluate the role of RUNX2 phosphorylation in these responses, RUNX2-deficient C3H10T1/2 cells were transduced with adenovirus encoding wild type or phosphorylation site mutant RUNX2 (RUNX2 S301A/S319A). Wild type RUNX2, but not the non-phosphorylated mutant, increased H3K9 and H4K5 acetylation as well as chromatin-associated P-ERK, p300, and polymerase II. Thus, RUNX2 phosphorylation is necessary for subsequent epigenetic changes required for osteoblast gene expression. Taken together, this study reveals a molecular mechanism through which osteogenic genes are controlled by a MAPK and P-RUNX2-dependent process involving epigenetic modifications of specific promoter regions. J. Cell. Physiol. 232: 2427-2435, 2017. © 2016 Wiley Periodicals, Inc.

H3K4 Methyltransferase Activity Is Required for MLL4 Protein Stability

Transcriptional enhancers play a key role in cell type-specific gene expression and cell fate transition. Enhancers are marked by histone H3K4 mono- and di-methylation (H3K4me1/2). The tumor suppressor MLL4 (KMT2D) is a major enhancer H3K4 mono- and di-methyltransferase with a partial functional redundancy with MLL3 (KMT2C). However, the functional role of MLL4 enzymatic activity remains elusive. To address this issue, we have generated MLL4 enzyme-dead knock-in (KI) embryonic stem (ES) cells and mice, which carry Y5477A/Y5523A/Y5563A mutations in the enzymatic SET domain of the MLL4 protein. Homozygous MLL4 enzyme-dead KI (Mll4KI/KI) mice are embryonic lethal and die around E10.5, which phenocopies Mll4 knockout mice. Interestingly, enzyme-dead MLL4 protein in ES cells is highly unstable. Like Mll4 knockout ES cells, Mll4KI/KI ES cells show reduced levels of H3K4me1/2. Furthermore, we show that ectopic expression of histone H3.3 lysine 4-to-methionine (K4M) mutant, which reduces endogenous H3K4 methylation levels in ES cells, decreases the protein stability of MLL3 and MLL4 but not that of H3K4 methyltransferases SET1A (KMT2F) and SET1B (KMT2G). Taken together, our findings indicate that MLL4 protein stability is tightly regulated by its H3K4 methyltransferase activity.

Altered expression of BRG1 and histone demethylases, and aberrant H3K4 methylation in less developmentally competent embryos at the time of embryonic genome activation.

Epigenetics is a fundamental regulator underlying many biological functions, such as development and cell differentiation. Epigenetic modifications affect key chromatin regulation, including transcription and DNA repair, which are critical for normal embryo development. In this study, we profiled the expression of epigenetic modifiers and patterns of epigenetic changes in porcine embryos around the period of embryonic genome activation (EGA). We observed that Brahma-related gene 1 (BRG1) and Lysine demethylase 1A (KDM1A), which can alter the methylation status of lysine 4 in histone 3 (H3K4), localize to the nucleus at Day 3-4 of development. We then compared the abundance of epigenetic modifiers between early- and late-cleaving embryos, which were classified based on the time to the first cell cleavage, to investigate if their nuclear localization contributes to developmental competence. The mRNA abundance of BRG1, KDM1A, as well as other lysine demethylases (KDM1B, KDM5A, KDM5B, and KDM5C), were significantly higher in late- compared to early-cleaving embryos near the EGA period, although these difference disappeared at the blastocyst stage. The abundance of H3K4 mono- (H3K4me) and di-methylation (H3K4me2) during the EGA period was reduced in late-cleaving and less developmentally competent embryos. By contrast, BRG1, KDM1A, and H3K4me2 abundance was greater in embryos with more than eight cells at Day 3-4 of development compared to those with fewer than four cells. These findings suggest that altered epigenetic modifications of H3K4 around the EGA period may affect the developmental capacity of porcine embryos to reach the blastocyst stage. Mol. Reprod. Dev. 84: 19-29, 2017. © 2016 Wiley Periodicals, Inc.

FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3

SummaryFOXA1 is a pioneer factor that binds to enhancer regions that are enriched in H3K4 mono- and dimethylation (H3K4me1 and H3K4me2). We performed a FOXA1 rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) screen in ERα-positive MCF-7 breast cancer cells and found histone-lysine N-methyltransferase (MLL3) as the top FOXA1-interacting protein. MLL3 is typically thought to induce H3K4me3 at promoter regions, but recent findings suggest it may contribute to H3K4me1 deposition. We performed MLL3 chromatin immunoprecipitation sequencing (ChIP-seq) in breast cancer cells, and MLL3 was shown to occupy regions marked by FOXA1 occupancy and H3K4me1 and H3K4me2. MLL3 binding was dependent on FOXA1, indicating that FOXA1 recruits MLL3 to chromatin. MLL3 silencing decreased H3K4me1 at enhancer elements but had no appreciable impact on H3K4me3 at enhancer elements. We propose a mechanism whereby the pioneer factor FOXA1 recruits the chromatin modifier MLL3 to facilitate the deposition of H3K4me1 histone marks, subsequently demarcating active enhancer elements.

Targeted Disruption of the Interaction between WD-40 Repeat Protein 5 (WDR5) and Mixed Lineage Leukemia (MLL)/SET1 Family Proteins Specifically Inhibits MLL1 and SETd1A Methyltransferase Complexes

MLL1 belongs to the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, composed of MLL1–4 and SETd1A/B. MLL1 translocations are present in acute leukemias, and mutations in several family members are associated with cancer and developmental disorders. MLL1 associates with a subcomplex containing WDR5, RbBP5, ASH2L, and DPY-30 (WRAD), forming the MLL1 core complex required for H3K4 mono- and dimethylation and transcriptional activation. Core complex assembly requires interaction of WDR5 with the MLL1 Win (WDR5 interaction) motif, which is conserved across the SET1 family. Agents that mimic the SET1 family Win motif inhibit the MLL1 core complex and have become an attractive approach for targeting MLL1 in cancers. Like MLL1, other SET1 family members interact with WRAD, but the roles of the Win motif in complex assembly and enzymatic activity remain unexplored. Here, we show that the Win motif is necessary for interaction of WDR5 with all members of the human SET1 family. Mutation of the Win motif-WDR5 interface severely disrupts assembly and activity of MLL1 and SETd1A complexes but only modestly disrupts MLL2/4 and SETd1B complexes without significantly altering enzymatic activity in vitro. Notably, in the absence of WDR5, MLL3 interacts with RAD and shows enhanced activity. To further probe the role of the Win motif-WDR5 interaction, we designed a peptidomimetic that binds WDR5 (Kd ∼3 nm) and selectively inhibits activity of MLL1 and SETd1A core complexes within the SET1 family. Our results reveal that SET1 family complexes with the weakest Win motif-WDR5 interaction are more susceptible to Win motif-based inhibitors.

CHD7, Oct3/4, Sox2, and Nanog control FoxD3 expression during mouse neural crest-derived stem cell formation.

Neural crest-derived stem cells (NCSCs) are tissue-specific stem cells derived from multipotent neural crest cells. NCSCs are present in some adult tissues such as dorsal root ganglia, sciatic nerve, and bone marrow. However, little is known about the formation mechanisms of these cells. We have shown that BMP2/Wnt3a signaling and a chromatin remodeler, CHD7, in mice help to maintain the multipotency of neural crest cells and lead to the formation of NCSCs. In the present study, we analyzed a regulatory gene cascade in the formation of mouse NCSCs. The inhibition of FoxD3 expression significantly suppressed the expression of Sox10, which is an indispensable transcription factor for mouse NCSC formation, in the presence of BMP2/Wnt3a. CHD7, Oct3/4, Sox2, and Nanog occupied multiple conserved regions of mouse FoxD3, mE1, mE2, and mE3, in a BMP2/Wnt3a-dependent manner. Furthermore, siRNA of CHD7, Oct3/4, Sox2, and Nanog significantly suppressed FoxD3 expression. The inhibition of histone H3K4 mono- or trimethylation also repressed FoxD3 expression. The present data suggest that CHD7, Oct3/4, Sox2, and Nanog directly induce FoxD3 expression when stimulated by BMP2/Wnt3a signaling, that FoxD3 promotes Sox10 expression, and that histone H3K4 methylation plays important roles in this process of mouse NCSC formation.

Abstract B25: Disruption of KMT2D-dependent histone methylation perturbs GC B cell development and cooperates with BCL2 deregulation in lymphomagenesis

Abstract Modulation of chromatin accessibility through histone modification is a key step in the regulation of gene transcription and its disruption by genetic lesions has been implicated in malignant transformation. Indeed, a consistent theme in recent cancer genome studies has been the discovery of recurrent mutations in multiple histone/chromatin modifier genes, including methyltransferases, acetyltransferases and histone themselves. Among these, KMT2D (MLL2 or MLL4), encoding for a histone H3K4 methyltransferase, emerged as one of the most common targets of genetic lesion in B cell non-Hodgkin lymphoma, being found in ~30% of diffuse large B cell lymphoma (DLBCL) and ~90% of follicular lymphoma (FL), which together account for over 70% of all lymphoma diagnoses (Pasqualucci et al, Nat Genetics 2011; Morin et al, Nature 2011). KMT2D mutations are mostly represented by truncating events that are predicted to remove the protein C-terminal enzymatic domains, thus inactivating its function; however, missense mutations were also found in a subset of cases, suggesting selection for a functional role. These events are biallelically distributed in one third of mutated cases, while the remaining >60% harbor monoallelic mutations, consistent with a role as a tumor suppressor. Interestingly, analysis of the history of clonal evolution during FL transformation to DLBCL suggests that KMT2D mutations may be already present in a common precursor clone before divergent evolution to FL or DLBCL, suggesting an early role during B cell clonal expansion (Pasqualucci et al, Cell Rep, 2014; Green et al, Blood, 2013). To elucidate the functional consequences of KMT2D mutations, we first examined the effects of 16 DLBCL/FL-derived KMT2D missense mutant alleles on its enzymatic activity in vitro. The results showed that all 8 mutants located in the C-terminal portion of the protein were associated with significantly diminished H3K4 mono-, di- and tri-methylation activity. Consistently, a significant reduction in global methylation was observed in Kmt2d deficient murine B-cells, as well as in 4 biallelically truncated cell lines, indicating that this methyltransferase can influence all three H3K4 modifications. To gain further insights into the program regulated by KMT2D in germinal center (GC) B cells (i.e. the normal counterpart of FL/DLBCL) and the mechanism by which its loss contributes to lymphomagenesis, we crossed mice carrying a conditional Kmt2d knockout allele (Lee J et al, Elife, 2013) with either CD19Cre or Cγ1Cre deletor mice, leading to gene inactivation early during B-cell development (Kmt2dCD19KO), thus mimicking the postulated “common precursor model,” or specifically in mature, GC B-cells (Kmt2dCγ1KO). Notably, deletion of Kmt2d before, but not after initiation of the GC reaction led to a significant increase in GC B-cells and enhanced B cell proliferation. These changes were accompanied by the acquisition of distinct transcriptional signatures enriched in cell cycle regulation and apoptosis genes. A cross-species strategy combining gene expression profile analysis of murine GC B-cells and Kmt2d chromatin immunoprecipitation and sequencing of purified human GC B cells identified a core of KMT2D direct targets genes involved in biological programs with critical functions in B cells physiology, including B cell receptor signaling, lymphocyte migration, and chemokine signaling components. Finally, while loss of Kmt2d alone in Kmt2dCγ1KO was not sufficient to induce tumor development, its combination with VavP-BCL2 transgenic mice increased the incidence of GC-derived lymphomas resembling the features of the human tumors. These data support a role for KMT2D as a tumor suppressor gene whose early loss during B cell development facilitates lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cell. Citation Format: Jiyuan Zhang, David Dominguez-Sola, Shafinaz Hussein, Ji-Eun Lee, Antony B. Holmes, Mukesh Bansal, Sofija Vlasevska, Tongwei Mo, Hongyan Tang, Katia Basso, Kai Ge, Riccardo Dalla-Favera, Laura Pasqualucci. Disruption of KMT2D-dependent histone methylation perturbs GC B cell development and cooperates with BCL2 deregulation in lymphomagenesis. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B25.

The KDM3A-KLF2-IRF4 Axis Maintains Myeloma Cell Survival

Histone methylations are tightly regulated by a balance between methyltransferases and demethylases that mediate the addition and removal of these modifications. Importantly, dysregulation of histone methylation is implicated in pathogenesis of cancers, including multiple myeloma (MM). For example, the t(4;14) (p16;q32) is present in 15 - 20% of MM patients and results in overexpression of WHSC1, a histone H3 lysine 36 (H3K36) methyltransferase. On the other hand, approximately 10% of MM patients without the t(4;14) have inactivating mutations in KDM6A, a H3K27 demethylase.KDM3A is a Jumonji C-domain-containing histone demethylase which catalyzes removal of H3K9 mono- and dimethylation (H3K9me1 and H3K9me2). KDM3A is implicated in pathogenesis of different types of cancers. Here we investigated the biological impact of KDM3A in MM.KDM3A expression was significantly elevated in MM patient samples compared to normal plasma cells in publicly available dataset (GSE5900, GSE6691). To evaluate the functional role of KDM3A, shRNAs targeting KDM3A were transduced into MM cell lines: knockdown of KDM3A significantly inhibited MM cell growth (RPMI8226, MM.1S, U266, H929) in vitro and in xenograft model (MM.1S). Apo2.7 staining showed that apoptotic cells were significantly increased after knockdown of KDM3A.We next examined gene expression profiles after knockdown of KDM3A in RPMI8226 cells. With a cutoff of > 1.5-fold downregulation, a total of 305 probe sets were downregulated in KDM3A-knockdown cells relative to control cells. Among putative KDM3A targets, a gene of particular interest is KLF2 which plays a key role in maintenance of B cell and plasma cell phenotype, and function. Another intriguing gene is IRF4, given its known crucial role in MM cell survival. We confirmed that expression of KLF2 and IRF4 was downregulated after knockdown of KDM3A by quantitative realtime PCR and immunoblots in RPMI82226, MM.1S, and U266 cells. KDM3A binding to KLF2 and IRF4 core promoters was demonstrated by chromatin immunoprecipitation (ChIP) assay in RPMI8226 cells. Moreover, knockdown of KDM3A increased H3K9me1 and me2 levels at both promoter regions, indicating that KDM3A directly regulates KLF2 and IRF4 expression by removing H3K9 methylation marks at their promoters in MM cells.shRNAs targeting KLF2 were next transduced into MM cell lines: silencing of KLF2 significantly reduced cell growth of MM cell lines, associated with decreased IRF4. Promoter reporter assays using human IRF4 promoter showed that KLF2 significantly increased luciferase expression in a dose-dependent manner. Moreover, ChIP assay showed that KLF2 bound to IRF4 promoter in RPMI8226 cells. Since transcription factors could form an autoregulatory feedback loop, we hypothesized that IRF4 might regulate KLF2 expression. As expected, knockdown of IRF4 downregulated KLF2 expression at both the mRNA and protein levels in 3 MM cell lines. In addition, ChIP assays demonstrated that IRF4 bound to KLF2 second intron that contains tandem IRF4 motifs in RPMI8226 cells. Collectively, these results suggest that KLF2 activates IRF4 expression and vice versa, forming an autoregulatory loop in MM cells.KLF2 has been reported to control homing of plasma cells to the bone marrow; we therefore hypothesized that KDM3A-KLF2-IRF4 axis might regulate adhesion and homing of MM cells to the bone marrow. Importantly, knockdown of KDM3A, KLF2, or IRF4 decreased adhesion of 3 MM cell lines to bone marrow stromal cells. Furthermore, bone marrow homing of MM.1S cells was significantly reduced after knockdown of KDM3A, KLF2, or IRF4 in a murine xenograft MM model, indicating that KDM3A-KLF2-IRF4 axis regulates, at least in part, MM cell adhesion and homing to the bone marrow.In conclusion, our study demonstrated that KDM3A is a crucial epigenetic regulator of MM cell survival, and that inhibition of KDM3A represents a novel therapeutic strategy in MM. [Display omitted] DisclosuresRaje:Amgen: Consultancy; Takeda: Consultancy; Novartis: Consultancy; Celgene Corporation: Consultancy; BMS: Consultancy; Acetylon: Research Funding; Eli Lilly: Research Funding; Onyx: Consultancy; AstraZeneca: Research Funding; Millenium: Consultancy. Richardson:Gentium S.p.A.: Membership on an entity's Board of Directors or advisory committees, Research Funding; Millennium Takeda: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Membership on an entity's Board of Directors or advisory committees; Celgene Corporation: Membership on an entity's Board of Directors or advisory committees. Harigae:Chugai Pharmaceutical Co., Ltd.: Research Funding. Anderson:Oncopep: Equity Ownership; Gilead: Consultancy; BMS: Consultancy; Millennium: Consultancy; Celgene: Consultancy; Acetylon: Equity Ownership.

Methylation of histone H3 lysine 9 occurs during translation

Histone post-translational modifications are key contributors to chromatin structure and function, and participate in the maintenance of genome stability. Understanding the establishment and maintenance of these marks, along with their misregulation in pathologies is thus a major focus in the field. While we have learned a great deal about the enzymes regulating histone modifications on nucleosomal histones, much less is known about the mechanisms establishing modifications on soluble newly synthesized histones. This includes methylation of lysine 9 on histone H3 (H3K9), a mark that primes the formation of heterochromatin, a critical chromatin landmark for genome stability. Here, we report that H3K9 mono- and dimethylation is imposed during translation by the methyltransferase SetDB1. We discuss the importance of these results in the context of heterochromatin establishment and maintenance and new therapeutic opportunities in pathologies where heterochromatin is perturbed.

SET7/9 Enzyme Regulates Cytokine-induced Expression of Inducible Nitric-oxide Synthase through Methylation of Lysine 4 at Histone 3 in the Islet β Cell

SET7/9 is an enzyme that methylates histone 3 at lysine 4 (H3K4) to maintain euchromatin architecture. Although SET7/9 is enriched in islets and contributes to the transactivation of β cell-specific genes, including Ins1 and Slc2a, SET7/9 has also been reported to bind the p65 subunit of nuclear factor κB in non-β cells and modify its transcriptional activity. Given that inflammation is a central component of β cell dysfunction in Type 1 and Type 2 diabetes, the aim of this study was to elucidate the role of SET7/9 in proinflammatory cytokine signaling in β cells. To induce inflammation, βTC3 insulinoma cells were treated with IL-1β, TNF-α, and IFN-γ. Cytokine treatment led to increased expression of inducible nitric-oxide synthase, which was attenuated by the diminution of SET7/9 using RNA interference. Consistent with previous reports, SET7/9 was co-immunoprecipitated with p65 and underwent cytosolic to nuclear translocation in response to cytokines. ChIP analysis demonstrated augmented H3K4 mono- and dimethylation of the proximal Nos2 promoter with cytokine exposure. SET7/9 was found to occupy this same region, whereas SET7/9 knockdown attenuated cytokine-induced histone methylation of the Nos2 gene. To test this relationship further, islets were isolated from SET7/9-deficient and wild-type mice and treated with IL-1β, TNF-α, and IFN-γ. Cytokine-induced Nos2 expression was reduced in the islets from SET7/9 knock-out mice. Together, our findings suggest that SET7/9 contributes to Nos2 transcription and proinflammatory cytokine signaling in the pancreatic β cell through activating histone modifications.

Dynamic and distinct histone modifications of osteogenic genes during osteogenic differentiation.

Many skeletal diseases have common pathological phenotype of defective osteogenesis of bone marrow stromal cells (BMSCs), in which histone modifications play an important role. However, few studies have examined the dynamics of distinct histone modifications during osteogenesis. In this study, we examined the dynamics of H3K9/K14 and H4K12 acetylation; H3K4 mono-, di- and tri-methylation; H3K9 di-methylation and H3K27 tri-methylation in osteogenic genes, runt-related transcription factor 2 (Runx2), osterix (Osx), alkaline phosphatase, bone sialoprotein and osteocalcin, during C3H10T1/2 osteogenesis. H3 and H4 acetylation and H3K4 di-methylation were elevated, and H3K9 di-methylation and H3K27 tri-methylation were reduced in osteogenic genes during C3H10T1/2 osteogenesis. C3H10T1/2 osteogenesis could be modulated by altering the patterns of H3 and H4 acetylation and H3K27 tri-methylation. In a glucocorticoid-induced osteoporosis mouse model, we observed the attenuation of osteogenic potential of osteoporotic BMSCs in parallel with H3 and H4 hypo-acetylation and H3K27 hyper-tri-methylation in Runx2 and Osx genes. When H3 and H4 acetylation was elevated, and H3K27 tri-methylation was reduced, the attenuated osteogenic potential of osteoporotic BMSCs was rescued effectively. These observations provide a deeper insight into the mechanisms of osteogenic differentiation and the pathophysiology of osteoporosis and can be used to design new drugs and develop new therapeutic methods to treat skeletal diseases.

Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure.

Genome-wide chromatin immunoprecipitation (ChIP) studies have brought significant insight into the genomic localization of chromatin-associated proteins and histone modifications. The large amount of data generated by these analyses, however, require approaches that enable rapid validation and analysis of biological relevance. Furthermore, there are still protein and modification targets that are difficult to detect using standard ChIP methods. To address these issues, we developed an immediate chromatin immunoprecipitation procedure which we call ZipChip. ZipChip significantly reduces the time and increases sensitivity allowing for rapid screening of multiple loci. Here we describe how ZipChIP enables detection of histone modifications (H3K4 mono- and trimethylation) and two yeast histone demethylases, Jhd2 and Rph1, which were previously difficult to detect using standard methods. Furthermore, we demonstrate the versatility of ZipChIP by analyzing the enrichment of the histone deacetylase Sir2 at heterochromatin in yeast and enrichment of the chromatin remodeler, PICKLE, at euchromatin in Arabidopsis thaliana.

Abstract 5158: The H3K9 demethyltransferase gene JMJD1C has tumor suppressor functions in multiple myeloma

Abstract Increasing evidence points towards the importance of epigenetic changes in the pathogenesis of multiple myeloma (MM). The biochemical modifications that govern epigenetics are DNA methylation, and post-translational modifications of histone proteins. Histone methylation is catalyzed by histone methyltransferases (HMT) and histone demethylases (HDMT). The purpose of our study was to interrogate genomics data to identify HMT or HDMT genes that are altered in MM. We mined copy number, gene expression and whole genome sequencing data generated as part of the Multiple Myeloma Research Consortium Genomics Initiative. Collectively, the datasets converged on numerous alterations involving histone methylation of lysine 9 (H3K9). One of these genes, the HDMT JMJD1C, was downregulated in approximately 25% of MM samples examined and was associated with worst clinical outcome. We validated these data by quantitative RT-PCR and by immunohistochemistry (IHC) on a tissue microarray (TMA) consisting of over 60 MM samples. Next we demonstrated a negative correlation between JMJD1C expression and H3K9 methylation by IHC and western blot in 6/10 HMCL and in over 60% of clinical samples examined on the TMA. To study the direct effects of JMJD1C on H3K9 methylation and determine the functional significance, we generated a knockout isogenic cell line pair in KMS11 MM cells using zinc finger nuclease technology. JMJD1C depletion resulted in an increase in H3K9 mono- and dimethylation as demonstrated by western blot and immunofluorescence, confirming its association to H3K9 methylation. H3K9 trimethylation was unaffected by JMJD1C depletion. Differential gene expression analysis demonstrated defects in cell cycle and G2/M transition. Most notably, NEK2, Cyclin B, CDC20, PLK1 and TTK were among genes upregulated in response to JMJD1C depletion. Accordingly, we assessed cell growth using CellTiter-Glo® and demonstrated increased cell growth in JMJD1C-depleted cells. We also demonstrated a more pronounced G2/M peak by FACS. DNA methylation analysis using the HumanMethylation 450K BeadChip showed global hypomethylation in response to JMJD1C loss, a phenotype indicative of myeloma progression. Results to date validate the H3K9 demethylase activity of JMJD1C, and suggest a tumor suppressive function, which may be lost in MM. Data demonstrate a novel biological and molecular understanding of JMJD1C, pointing us to therapeutic vulnerabilities in MM. Studies are ongoing to further characterize the genomic, epigenomic and functional significance of JMJD1C in MM. Citation Format: Danielle DiPerna, Gerald C. Gooden, Brooke Hjelm, Sara Nasser, Janine LoBello, Aprill Watanabe, Bodour Salhia. The H3K9 demethyltransferase gene JMJD1C has tumor suppressor functions in multiple myeloma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5158. doi:10.1158/1538-7445.AM2014-5158

Alterations of Global Histone H3K9 and H3K27 Methylation Levels in Bladder Cancer

Background: Epigenetic alterations, including histone modifications, play an important role during carcinogenesis. This study was designed to systematically investigate histone H3K9 and H3K27 methylation levels in bladder cancer (BCa) tissue. Methods: A tissue microarray with urothelial BCa (150 non-muscle-invasive BCa, NMIBC; 121 muscle-invasive BCa, MIBC; 31 metastatic BCa, MET) and normal urothelium (29, CTRL) specimen was used to determine the global levels of H3K9 and H3K27 mono-, di- and tri-methylation. Results: Global levels of H3K9 and H3K27 methylation were significantly higher in CTRL than in BCa, and levels in NMIBC were higher compared to MIBC. Histone methylation levels of MET resembled MIBC. We observed furthermore a correlation of histone methylation levels with pT stage (H3K9me1, H3K9me2, H3K9me3, H3K27me1, H3K27me3) and grade (H3K9me2, H3K9me3, H3K27me1) in NMIBC. H3K9me1, H3K9me3, H3K27me1 and H3K27me3 levels were also correlated with pT stage in MIBC. Histone modifications were not associated with recurrence-free or cancer-specific survival. Conclusions: Global histone H3K9 and H3K27 methylation levels are altered in BCa.

H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation.

Enhancers play a central role in cell-type-specific gene expression and are marked by H3K4me1/2. Active enhancers are further marked by H3K27ac. However, the methyltransferases responsible for H3K4me1/2 on enhancers remain elusive. Furthermore, how these enzymes function on enhancers to regulate cell-type-specific gene expression is unclear. In this study, we identify MLL4 (KMT2D) as a major mammalian H3K4 mono- and di-methyltransferase with partial functional redundancy with MLL3 (KMT2C). Using adipogenesis and myogenesis as model systems, we show that MLL4 exhibits cell-type- and differentiation-stage-specific genomic binding and is predominantly localized on enhancers. MLL4 co-localizes with lineage-determining transcription factors (TFs) on active enhancers during differentiation. Deletion of Mll4 markedly decreases H3K4me1/2, H3K27ac, Mediator and Polymerase II levels on enhancers and leads to severe defects in cell-type-specific gene expression and cell differentiation. Together, these findings identify MLL4 as a major mammalian H3K4 mono- and di-methyltransferase essential for enhancer activation during cell differentiation. DOI: http://dx.doi.org/10.7554/eLife.01503.001.

Abstract A028: Progression of structural change in the breast cancer genome

Abstract Purpose: Through the utilization of large-insert mate-pair sequencing, we strive to uncover structural variations (SVs) driving metastasis in breast cancer. Background: Recent sequencing studies have shown that any given breast tumor harbors an immense number of point mutations. However, few are recurrent making identification of mutated ‘driver genes’ extremely difficult. Further, although the traditional paired-end sequencing methodology is extremely powerful at detecting point mutations, it is severely limited in detecting large structural changes (insertions, deletions) that occur near repetitive regions or ‘balanced’ events such as translocations or inversions. Current sequencing studies rely almost exclusively on tissues from primary disease rather than recurrent or metastatic disease. Together this suggests that current studies are likely missing (1) a large fraction of a major class of genetic events (i.e. SVs) and (2) the mutation events most likely to impact long term survivability (i.e. metastatic enriched). Methods: Through the University of Pittsburgh Rapid Autopsy Program and the Health Sciences Tissue Bank, we obtained 26 fresh-frozen tissue specimens from 4 individuals originating from a combination of matched normal, primary tumor, recurrent tumor, lymph node metastases, and distant metastases. To overcome the limitations of traditional paired-end sequencing in detecting SVs, multiple large-insert (3-5, 5-8, & 8-12 kb) mate-pair sequencing was performed. Mate-pair sequencing is currently underway, however, one ‘patient set’ (adjacent normal, primary tumor, lymph node metastasis) has been fully completed. Alignment was conducted via NovoAlign while breakpoints were determined via Breakdancer and the recently published paired-end/split-read, integrative breakpoint caller, Lumpy-sv. Additionally, to supplement the mate-pair sequencing findings and allow for detailed integrative analysis, genome-wide copy number profiling, RNA-seq, exome-seq, and targeted methyl-seq have either been completed or are in process. Results: Analysis of the completed single ‘patient set’ has revealed SVs acquired by the primary tumor, shared between the primary and metastatic tumors, and specific to the metastasis. The most striking finding was a cluster of metastatic specific SVs involving chromosome 14, potentially the result of chromothripsis. These included intra-chromosomal SVs (including large inversions) and inter-chromosomal translocations (with chromosomes 8 & 19). Interestingly, the t(8;14) SV involves ASH2L, a member of the Set1 histone methyltransferase complex that is responsible for H3K4 mono- and di-methylation. Conclusions: Extensive SV occurs during breast cancer tumorigenesis and metastasis, potentially the result of chromothripsis. As more samples and distant metastases are sequenced, orthologous datasets (RNA-seq) will be used to help prioritize specific metastatic specific SVs for functional studies. Citation Format: Ryan J. Hartmaier, Adrian V. Lee. Progression of structural change in the breast cancer genome. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A028.

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

BackgroundMammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers.ResultsWe integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. These two classes of 5′ capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. Nevertheless, elncRNAs are more tissue-restricted, less highly expressed and less well conserved during evolution. Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis.ConclusionsWe have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci.

A T-Cell Specific Element Activates the TAL1 Oncogene Via an Interchromosomal Interaction During Leukemogenesis

AbstractAbstract 3507T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignant disease of thymocytes that mainly affects children and has very poor prognosis with high rates of relapse. A prominent feature observed in 60% of T-ALL childhood patients is the ectopic expression of a key hematopoietic transcription factor TAL1/SCL. Although several enhancers has been identified to play an important role in normal hematopoietic differentiation, the histone modification patterns and chromatin organization over the whole TAL1 locus reveled that none of them is active in T-ALL cell lines such as Jurkat and Rex cells. It remains currently unknown how TAL1 is activated in the majority of T-ALL patients lacking the TAL1 locus rearrangements. To understand the molecular mechanism underlying regulation of the TAL1 oncogene in leukemic T-cells, we employed circularized chromosome conformation capture (4C) methodology to identify new regulatory elements that activate TAL1 specifically in T-ALL leukemia. Using the TAL1 promoter 1a as the bait, we discovered that the TAL1 promoter 1a interacts with the TIL16 element (TAL1 interacting locus in chromosome 16) that is located at ∼15 Kb downstream of T-cell specific CD2BP2 gene in T-ALL cell line Jurkat, but not in erythroid progenitor K562 cells. The CD2BP2 protein is a cellular adapter protein that was originally identified as a binding partner of the T cell adhesion protein CD2 in the context of T cell signaling. The TIL16 element contains the bind sites for several transcription factors that are important for hematopoiesis such as C-Maf, Pax5, HoxA7 and USF2. The inter-chromosomal interaction between the TIL16 and the TAL1 promoter 1a was further confirmed by chromosome conformation capture (3C) assay in three TAL1 over-expressing T-ALL cell lines, Jurkat, REX and Molt4, but not in K562 cells. Recent genome wide study has correlates H3K4 mono- or dimethyl marks with distal enhancers while trimethyl H3K4 is enriched in promoters of active genes. To further test if the TIL16 acts as T-cell specific enhancer for TAL1 activation in T-ALL cells, we carried out ChIP-seq and ChIP analysis in CD4 T cells, Jurkat, and K562 cells. We found that the TIL16 element is specifically marked by H3K4me1 in Jurkat and CD4+ T-cells but not in K562 cells. The enrichment of H3K4me1 is correlated with the binding of c-Maf, a T-cell specific transcription factor. To further test whether the TIL16 element contributes to transcription activity, a DNA fragments containing the TIL16 element were cloneed into SV40 minimal promoter driven luciferase reporter and introduced into K562 and several T-ALL cell lines. Compared to the pGL3-SV40 vector that showed only minimal luciferase activity, the 1 Kb TIL element specifically activated transcription of the luciferase reporter in T-ALL cells, but not in erythroid progenitor K562 cells suggesting that the TIL16 element functions as a T-cell specific TAL1 enhancer. Thus, our data revealed a novel epigenetic mechanism by which the TAL1 oncogene is ectopically activated in T-cell leukemia. Disclosures:No relevant conflicts of interest to declare.