Role Of Histone Modifications Research Articles

Epigenetic Mechanisms in Psychiatry

Epigenetic Mechanisms in Psychiatry

Impaired secretion of interferons by dendritic cells from aged subjects to influenza : role of histone modifications.

Increased susceptibility to respiratory infections such as influenza is the hallmark of advancing age. The mechanisms underlying the impaired immune response to influenza are not well understood. In the present study, we have investigated the effect of advancing age on dendritic cell (DC) function because they are critical in generating robust antiviral responses. Our results indicate that monocyte derived DCs from the aged are impaired in their capacity to secrete interferon (IFN)-I in response to influenza virus. Additionally, we observed a severe reduction in the production of IFN-III, which plays an important role in defense against viral infections at respiratory mucosal surfaces. This reduction in IFN-I and IFN-III were a result of age-associated modifications in the chromatin structure. Investigations using chromatin immunoprecipitation with H3K4me3 and H3K9me3 antibodies revealed that there is increased association of IFN-I and IFN-III promoters with the repressor histone, H3K9me3 in non-stimulated aged DCs compared to young DCs. This was accompanied by decreased association of these promoters with activator histone, H3K4me3 in aged DCs after activation with influenza. In contrast to interferons, the association of TNF-alpha promoter with both these histones was comparable between aged and young subjects. Investigations at 48 h suggested that these changes are not stable and change with time. In summary, our study demonstrates that myeloid DCs from aged subjects are impaired in their capacity to produce IFNs in response to influenza virus and that age-associated altered histone expression patterns are responsible for the decrease in IFN production.

The role of histone modifications and DNA methylation in renal cell carcinoma development

Epigenetic mechanisms of gene regulation play a key role in carcinogenesis. This review will focus on the recent advances of epigenetic investigations in the development of human cancer. The role of histone modifications, genomic imprinting and DNA methylation in renal cell carcinoma development and progression will be considered.

Comment on: Winkler et al. Histone Deacetylase 6 (HDAC6) Is an Essential Modifier of Glucocorticoid-Induced Hepatic Gluconeogenesis. Diabetes 2012;61:513–523

Histone deacetylase 6 (HDAC 6) is known to play a critical role in histone modification and transcription regulation of a wide variety of genes involved in cell cycle regulation and cell proliferation, migration, and development. Recently, Winkler et al. (1) analyzed the role of HDAC6 in regulation of metabolism-mediating transcription of gluconeogenic genes G6P , FBP , PEPCK , and PCX …

Abstract 145: Epigenetic Modifications of Bone-Marrow Progenitor Cells Promote an M1 Phenotype in Peripheral Macrophages in Diabetes

Introduction: Diabetic wounds are characterized by a chronic inflammatory state that is maintained by overexpression of pro-inflammatory cytokines generated by immune cells, namely macrophages. To understand this imbalance, it is critical of understand how changes in immune cells at the systemic level influence the peripheral immune cells. Work from our lab has shown that cytokines induce a histone post-translational “epigenetic signature” at promoter sites of specific genes. However, the role of histone modification of DNA on diabetic progenitor and differentiated immune cells and their impact on chronic inflammation in the periphery has not been studied. We hypothesized that epigenetic changes to bone marrow cells influences peripheral macrophage phenotypes. Methods: Bone marrow was harvested from 7 diet-induced obese mice (DIO) (mean glucose= 290) and 7 wildtype (WT) controls. In some of the mice, lin -/ckit+ population was isolated and flow cytometry (FACS) analysis was performed to isolate hematopoietic stem cells (HSC) and myeloid progenitor cells (MYP). HSC were defined as cells expressing sca1+/CD150+/flt3+ and MYP co-expression of sca1+/CD150+/FcgR-/CD105low. HSC and MYP were analyzed via FACS for the presence of chromatin marks. In other mice, BMD macrophages were isolated and propagated in cell culture. Macrophages were either untreated or skewed towards an M1 or M2 phenotype with IF-gamma or IL-4, respectively. Levels of protein and mRNA of M1/M2 products were analyzed. Additionally, at 6, 24 and 72 hours the macrophages were assessed for expression of chromatin remodeling marks via FACS analysis. Results: HSC had a 2 fold decrease in the expression of H3K9 histone methylation marks in the DIO mice as compared to WT. (Figure 1A) This pattern was also observed in the more differentiated MYP cells. (Fig 1B) Macrophages isolated from diabetic mice also reflected these histone changes, supporting the role of histone methylation on fully-differentiated macrophage gene expression. (Fig 1C) DIO macrophages demonstrated increased levels of TNF-alpha and CCL3, classic M1 phenotype markers. (Fig 1D) Conclusions: Epigenetic changes initiated in the bone marrow progenitor cells effect immune cells in the periphery, and may contribute to the chronic inflammation seen in diabetics. Manipulation of these histone modifications at the bone marrow level could allow for the development of therapies to prevent chronic inflammation in the periphery of diabetics.

Vezf1 protein binding sites genome-wide are associated with pausing of elongating RNA polymerase II

The protein Vezf1 plays multiple roles important for embryonic development. In Vezf1(-/-) mouse embryonic stem (mES) cells, our earlier data showed widespread changes in gene-expression profiles, including decreased expression of the full-length active isoform of Dnmt3b methyltransferase and concomitant genome-wide reduction in DNA methylation. Here we show that in HeLaS3 cells there is a strong genome-wide correlation between Vezf1 binding and peaks of elongating Ser2-P RNA polymerase (Pol) ll, reflecting Vezf1-dependent slowing of elongation. In WT mES cells, the elongating form of RNA pol II accumulates near Vezf1 binding sites within the dnmt3b gene and at several other Vezf1 sites, and this accumulation is significantly reduced at these sites in Vezf1(-/-) mES cells. Depending upon genomic location, Vezf1-mediated Pol II pausing can have different regulatory roles in transcription and splicing. We find examples of genes in which Vezf1 binding sites are located near cassette exons, and in which loss of Vezf1 leads to a change in the relative abundance of alternatively spliced messages. We further show that Vezf1 interacts with Mrg15/Mrgbp, a protein that recognizes H3K36 trimethylation, consistent with the role of histone modifications at alternatively spliced sites.

Compensatory functions of histone deacetylase 1 (HDAC1) and HDAC2 regulate transcription and apoptosis during mouse oocyte development

Dramatic changes in chromatin structure and histone modification occur during oocyte growth, as well as a global cessation of transcription. The role of histone modifications in these processes is poorly understood. We report the effect of conditionally deleting Hdac1 and Hdac2 on oocyte development. Deleting either gene has little or no effect on oocyte development, whereas deleting both genes results in follicle development arrest at the secondary follicle stage. This developmental arrest is accompanied by substantial perturbation of the transcriptome and a global reduction in transcription even though histone acetylation is markedly increased. There is no apparent change in histone repressive marks, but there is a pronounced decrease in histone H3K4 methylation, an activating mark. The decrease in H3K4 methylation is likely a result of increased expression of Kdm5b because RNAi-mediated targeting of Kdm5b in double-mutant oocytes results in an increase in H3K4 methylation. An increase in TRP53 acetylation also occurs in mutant oocytes and may contribute to the observed increased incidence of apoptosis. Taken together, these results suggest seminal roles of acetylation of histone and nonhistone proteins in oocyte development.

Thyroid hormone receptor actions on transcription in amphibia: The roles of histone modification and chromatin disruption

Thyroid hormone (T3) plays diverse roles in adult organ function and during vertebrate development. The most important stage of mammalian development affected by T3 is the perinatal period when plasma T3 level peaks. Amphibian metamorphosis resembles this mammalian postembryonic period and is absolutely dependent on T3. The ability to easily manipulate this process makes it an ideal model to study the molecular mechanisms governing T3 action during vertebrate development. T3 functions mostly by regulating gene expression through T3 receptors (TRs). Studies in vitro, in cell cultures and reconstituted frog oocyte transcription system have revealed that TRs can both activate and repress gene transcription in a T3-dependent manner and involve chromatin disruption and histone modifications. These changes are accompanied by the recruitment of diverse cofactor complexes. More recently, genetic studies in mouse and frog have provided strong evidence for a role of cofactor complexes in T3 signaling in vivo. Molecular studies on amphibian metamorphosis have also revealed that developmental gene regulation by T3 involves histone modifications and the disruption of chromatin structure at the target genes as evidenced by the loss of core histones, arguing that chromatin remodeling is an important mechanism for gene activation by liganded TR during vertebrate development.

High-Throughput Computational Approaches to Analyzing Histone Modification Next-Generation Sequencing Data

Chromatin immunoprecipitation followed by sequencing (ChIP–seq) facilitates systematic analysis of chemical modifications of histone tails. As the cost of next-generation sequencing continues to drop, genome-wide histone modification sequencing becomes a common approach in a variety of researches in the epigenetic area. However, challenges of efficient ChIP–seq data analysis are now the main hurdle to interpret the histone modification ChIP-seq data, calling for continued enhancements of computational approaches. Here we provide a pragmatic overview of available computational approaches for the study of histone modification ChIP-seq data. We present the latest advances of computational methods for systematically detecting and functionally characterizing various types of histone modification ChIP-seq data, discuss the software packages currently available for performing tasks from short read mapping, peak calling to downstream genomic characterization and genome-wide visualization. We also present that the regulatory roles of histone modifications upon gene expression can be inferred by developing algorithms and methods specifically for histone modification ChIP-seq data. Such approaches will facilitate the epigenetic regulatory network construction and provide explicit biological hypothesis for further experiment testing. We also describe some challenges and important directions for histone modification analysis based on ChIP-seq data in future. We envision that the advances of computational approaches will bring more about a bright future for large-scale histone modification studies.

ChemInform Abstract: Histone Tails: Ideal Motifs for Probing Epigenetics Through Chemical Biology Approaches

AbstractReview: 150 refs.

The role of histone modifications in differentiation and effector function of CD8 T cells: Update review including genome-wide analysis

Evidence including genome-wide analyses have uncovered that epigenetic mechanisms regulate differentiation and effector functions in CD8 T cells. Gene expression profiles change when CD8 T cells differentiate from naïve T cells to memory T cells. It has been shown that this programmed differentiation is regulated by epigenetic mechanisms. Upon antigen stimulation, CD8 T cells activate and acquire effector functions to target cells. Effector molecule gene expressions are upregulated by epigenetic mechanisms in CD8 T cells. It is suggested that memory T cells respond more rapidly to antigens because chromatin structures of effector molecule genes are open and their gene transcriptions are poised for activation.

Role of histone modification on transcriptional regulation and HIV-1 gene expression: possible mechanisms of periodontal diseases in AIDS progression

Although approximately 200 distinct cell types - including fibroblasts, neurons, and hematopoietic cells - possess the same DNA sequence, they have diverse functions in humans and exhibit considerably different gene expression patterns. It has become increasingly clear that epigenetic regulation plays an important role in gene expression. There are two major forms of epigenetic regulation: posttranslational modification of DNA-associated histone proteins in chromatin and methylation of DNA. These forms are regulated by distinct but coupled pathways. Notably, histone Lys acetylation by histone acetyltransferase and deacetylation by histone deacetylases play a crucial role in on-off regulation of gene expression. It is now understood that epigenetics plays an important role not only in the regulation of gene expression but also in the pathogenesis of a broad range of diseases such as cancer and microbial infections. We have determined that epigenetic regulation is involved in the establishment and maintenance of HIV-1 latency and in the reactivation of HIV-1 by periodontopathic bacteria. In this review, we focus on the effect of histone modification on transcriptional regulation and the contribution thereof to the regulation of HIV-1 gene expression during the lytic and latent stages of HIV-1 infection. Likewise, we discuss the mechanisms by which periodontal diseases may accelerate AIDS progression in infected individuals as a new systemic disease caused by periodontitis and describe potential therapeutic interventions based on epigenetic mechanisms.

Pygo2 Associates with MLL2 Histone Methyltransferase and GCN5 Histone Acetyltransferase Complexes To Augment Wnt Target Gene Expression and Breast Cancer Stem-Like Cell Expansion

Resent studies have identified Pygopus as a core component of the β-catenin/T-cell factor (TCF)/lymphoid-enhancing factor 1 (LEF) transcriptional activation complex required for the expression of canonical Wg/Wnt target genes in Drosophila. However, the biochemical involvement of mammalian Pygopus proteins in β-catenin/TCF/LEF gene activation remains controversial. In this study, we perform a series of molecular/biochemical experiments to demonstrate that Pygo2 associates with histone-modifying enzymatic complexes, specifically the MLL2 histone methyltransferase (HMT) and STAGA histone acetyltransferase (HAT) complexes, to facilitate their interaction with β-catenin and to augment Wnt1-induced, TCF/LEF-dependent transcriptional activation in breast cancer cells. We identify a critical domain in Pygo2 encompassing the first 47 amino acids that mediates its HMT/HAT interaction. We further demonstrate the importance of this domain in Pygo2's ability to transcriptionally activate both artificial and endogenous Wnt target genes and to expand breast cancer stem-like cells in culture. This work now links mechanistically Pygo2's role in histone modification to its enhancement of the Wnt-dependent transcriptional program and cancer stem-like cell expansion.

Computational Micromodel for Epigenetic Mechanisms

Characterization of the epigenetic profile of humans since the initial breakthrough on the human genome project has strongly established the key role of histone modifications and DNA methylation. These dynamic elements interact to determine the normal level of expression or methylation status of the constituent genes in the genome. Recently, considerable evidence has been put forward to demonstrate that environmental stress implicitly alters epigenetic patterns causing imbalance that can lead to cancer initiation. This chain of consequences has motivated attempts to computationally model the influence of histone modification and DNA methylation in gene expression and investigate their intrinsic interdependency. In this paper, we explore the relation between DNA methylation and transcription and characterize in detail the histone modifications for specific DNA methylation levels using a stochastic approach.

Variable histone modifications at the Avy metastable epiallele

The ability of environmental factors to shape health and disease involves epigenetic mechanisms that mediate gene-environment interactions. Metastable epiallele genes are variably expressed in genetically identical individuals due to epigenetic modifications established during early development. DNA methylation within metastable epialleles is stochastic due to probabilistic reprogramming of epigenetic marks during embryogenesis. Maternal nutrition and environment have been shown to affect metastable epiallele methylation patterns and subsequent adult phenotype. Little is known, however, about the role of histone modifications in influencing metastable epiallele expression and phenotypic variation. Utilizing chromatin immunoprecipitation followed by qPCR, we observe variable histone patterns in the 5’ long terminal repeat (LTR) of the murine viable yellow agouti (Avy) metastable epiallele. This region contains 6 CpG sites, which are variably methylated in isogenic Avy/a offspring. Yellow mice, which are hypomethylated at the Avy LTR and exhibit constitutive ectopic expression of agouti (a), also display enrichment of H3 and H4 di-acetylation (p=0.08 and 0.09, respectively). Pseudoagouti mice, in which Avy hypermethylation is thought to silence ectopic expression, exhibit enrichment of H4K20 tri-methylation (p=0.01). No differences are observed for H3K4 tri-methylation (p=0.7), a modification often enriched in the promoter of active genes. These results show for the first time the presence of variable histone modifications at a metastable epiallele, indicating that DNA methylation acts in concert with histone modifications to affect inter-individual variation of metastable epiallele expression. Therefore, the potential for environmental factors to influence histone modifications, in addition to DNA methylation, should be addressed in environmental epigenomic studies.

Menin and RNF20 recruitment is associated with dynamic histone modifications that regulate signal transducer and activator of transcription 1 (STAT1)-activated transcription of the interferon regulatory factor 1 gene (IRF1)

BackgroundSignal transducer and activator of transcription (STAT) activation of gene expression is both rapid and transient, and when properly executed it affects growth, differentiation, homeostasis and the immune response, but when dysregulated it contributes to human disease. Transcriptional activation is regulated by alterations to the chromatin template. However, the role of histone modification at gene loci that are activated for transcription in response to STAT signaling is poorly defined.ResultsUsing chromatin immunoprecipitation, we profiled several histone modifications during STAT1 activation of the interferon regulatory factor 1 gene (IRF1). Methylated lysine histone proteins H3K4me2, H3K4me3, H3K79me3, H3K36me3 and monoubiquitinated histone ubH2B are dynamic and correlate with interferon (IFN)γ induction of STAT1 activity. Chemical inhibition of H3K4 methylation downregulates IRF1 transcription and decreases RNA polymerase II (Pol II) occupancy at the IRF1 promoter. MEN1, a component of a complex proteins associated with Set1 (COMPASS)-like complex and the hBRE1 component, RNF20, are localized to IRF1 in the uninduced state and are further recruited when IRF1 is activated. RNAi-mediated depletion of RNF20 lowers both ubH2B and H3K4me3, but surprisingly, upregulates IFNγ induced IRF1 transcription. The dynamics of phosphorylation in the C-terminal domain (CTD) of Pol II are disrupted during gene activation as well.ConclusionsH2B monoubiquitination promotes H3K4 methylation, but the E3 ubiquitin ligase, RNF20, is repressive of inducible transcription at the IRF1 gene locus, suggesting that ubH2B can, directly or indirectly, affect Pol II CTD phosphorylation cycling to exert control on ongoing transcription.

The Epigenetics of Germ‐line Immortality: Lessons from an Elegant Model System

Epigenetic mechanisms are thought to help regulate the unique transcription program that is established in germ cell development. During the germline cycle of many organisms, the epigenome undergoes waves of extensive resetting events, while a part of epigenetic modification remains faithful to specific loci. Little is known about the mechanisms underlying these events, how loci are selected for, or avoid, reprogramming, or even why these events are required. In particular, although the significance of genomic imprinting phenomena involving DNA methylation in mammals is now well accepted, the role of histone modification as a transgenerational epigenetic mechanism has been the subject of debate. Such epigenetic mechanisms may help regulate transcription programs and/or the pluripotent status conferred on germ cells, and contribute to germ line continuity across generations. Recent studies provide new evidence for heritability of histone modifications through germ line cells and its potential effects on transcription regulation both in the soma and germ line of subsequent generations. Unraveling transgenerational epigenetic mechanisms involving highly conserved histone modifications in elegant model systems will accelerate the generation of new paradigms and inspire research in a wide variety of fields, including basic developmental studies and clinical stem cell research.

Role of Histone Modifications and DNA Methylation in the Regulation of O6-Methylguanine-DNA Methyltransferase Gene Expression in Human Stomach Cancer Cells

To determine a possible function of histone modifications in stomach carcinogenesis, we analyzed global and MGMT-promoter levels of di-methyl-H3-K9, di-methyl-H3-K4 and acetyl-H3-K9, as well as MGMT DNA methylation and mRNA expression following treatment with 5-aza-2' -deoxycytidine and/or Trichostatin A. We found that histone H3-K9 di-methylation, H3-K4 di-methylation, H3-K9 acetylation and DNA methylation work in combination to silence MGMT. The results indicate that histone modifications as well as DNA methylation may be involved in stomach carcinogenesis. In addition to its effect on DNA methylation, 5-aza-2' -deoxycytidine can act at histone modification level to reactivate MGMT expression in a region-specific and DNA methylation-dependent manner.

Abstract 4868: Interaction between DNMT3B and polycomb repression complexes and their role in histone modification

Abstract Epigenetic modifications, such as DNA methylation and the histone code, play crucial roles in regulating gene expression during development. Aberrant DNA methylation patterns, characterized by global genomic hypomethylation and gene specific hypermethylation at CpG islands, are found in all cancer cells and contribute directly to tumor development. DNA methyltransferases are responsible for the de novo or heritable maintenance of DNA methylation. DNMT3A and DNMT3B de novo methyltransferases contribute largely to the methylation of retrotransposon sequences and satellite repeats in pericentromeric regions. It is still unclear how gene-specific epigenetic modification patterns are established and maintained in cancer cells. Recently, high-throughput studies reported an overlapping distribution of polycomb repression complexes regulating histone modifications and DNA methyltransferase mediated DNA methylation, suggesting that there are interactions among these epigenetic regulators. Our previous data from DNA methyltransferase knock out cell lines revealed that epigenetic modifiers and the histone code influence the propensity of a gene to become hypermethylated in cancer and that DNMT3B plays an important role in regulating PRC1 function. To gain insight into the mechanisms of how DNMT3B/DNA methylation effects the histone code, and vice versa, we studied the protein-protein interactions between PRC1 components and DNA methyltransferase 3B and their functional consequences. We expressed DNMT3B and each PRC component in both baculovirus and E. coli expression systems. Pull down assays showed that there were multiple interactions between PRC1 components (eg. CBX4 /hPc2) and DNMT3B. Protein-protein interaction domains were further mapped. We then used an in vitro ubiquitination system to study the role of DNMT3B in histone H2A ubiquitination and also studied the effects of these interactions on gene expression in human tumor cell lines. Our results suggest that the interplay between DNMT3B/DNA methylation and PRC1 is important for the function of each protein/complex and that aberrations in these interactions contribute to epigenetic dysregulation in cancer cells. (Supported by NCI grant R01CA114229) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4868.

Role of Histone Modifications and DNA Methylation in the Regulation of O6-Methylguanine-DNA Methyltransferase Gene Expression in Human Stomach Cancer Cells

ABSTRACTTo determine a possible function of histone modifications in stomach carcinogenesis, we analyzed global and MGMT-promoter levels of di-methyl-H3-K9, di-methyl-H3-K4 and acetyl-H3-K9, as well as MGMT DNA methylation and mRNA expression following treatment with 5-aza-2′ -deoxycytidine and/or Trichostatin A. We found that histone H3-K9 di-methylation, H3-K4 di-methylation, H3-K9 acetylation and DNA methylation work in combination to silence MGMT. The results indicate that histone modifications as well as DNA methylation may be involved in stomach carcinogenesis. In addition to its effect on DNA methylation, 5-aza-2′ -deoxycytidine can act at histone modification level to reactivate MGMT expression in a region-specific and DNA methylation-dependent manner.