Epigenetic Context Research Articles

Application of reversed-phase high-performance liquid chromatography with fluorimetric detection for simultaneous assessment of global DNA and total RNA methylation in Lepidium sativum: effect of plant exposure to Cd(II) and Se(IV)

In the present work, application of the previously established reversed-phase liquid chromatography procedure based on fluorescent labeling of cytosine and methylcytosine moieties with 2-bromoacetophenone (HPLC-FLD) is presented for simultaneous evaluation of global DNA and total RNA methylation at cytosine carbon 5. The need for such analysis was comprehended from the recent advances in the field of epigenetics that highlight the importance of non-coding RNAs in DNA methylation and suggest that RNA methylation might play a similar role in the modulation of genetic information, as previously demonstrated for DNA. In order to adopt HPLC-FLD procedure for DNA and RNA methylation analysis in a single biomass extract, two extraction procedures with different selectivity toward nucleic acids were examined, and a simplified calibration was designed allowing for evaluation of methylation percentage based on the ratio of chromatographic peak areas: cytidine/5-methylcytidine for RNA and 2'-deoxycytidine/5-methyl-2'-deoxycytidine for DNA. As a proof of concept, global DNA and total RNA methylation were determined in Lepidium sativum hydroponically grown in the presence of different Cd(II) or Se(IV) concentrations, expecting that plant exposure to abiotic stress might affect not only global DNA but also total RNA methylation. The results obtained showed the increase of DNA methylation in the treated plants up to concentration levels 2 mg L(-1) Cd and 1 mg L(-1) Se in the growth medium. For higher stressors' concentration, global DNA methylation tended to decrease. Most importantly, an inverse correlation was found between DNA and RNA methylation levels (r = -0.6788, p = 0.031), calling for further studies of this particular modification of nucleic acids in epigenetic context.

Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes

How the glucocorticoid receptor (GR) activates some genes while potently repressing others remains an open question. There are three current models for suppression: transrepression via GR tethering to AP-1/NF-κB sites, direct GR association with inhibitory elements (nGREs), and GR recruitment of the corepressor GRIP1. To gain insights into GR suppression, we used genomic analyses and genome-wide profiling of GR, p65, and c-Jun in LPS-stimulated macrophages. We show that GR mediates both activation and repression at tethered sites, GREs, and GRIP1-bound elements, indicating that motif classification is insufficient to predict regulatory polarity of GR binding. Interestingly, sites of GR repression utilize GRIP1's corepressor function and display reduced histone acetylation. Together, these findings suggest that while GR occupancy confers hormone responsiveness, the receptor itself may not participate in the regulatory effects. Furthermore, transcriptional outcome is not established bysequence but is influenced by epigenetic regulators, context, and other unrecognized regulatory determinants.

MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status

The methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene is an important predictive biomarker for benefit from alkylating agent therapy in glioblastoma. Recent studies in anaplastic glioma suggest a prognostic value for MGMT methylation. Investigation of pathogenetic and epigenetic features of this intriguingly distinct behavior requires accurate MGMT classification to assess high throughput molecular databases. Promoter methylation-mediated gene silencing is strongly dependent on the location of the methylated CpGs, complicating classification. Using the HumanMethylation450 (HM-450K) BeadChip interrogating 176 CpGs annotated for the MGMT gene, with 14 located in the promoter, two distinct regions in the CpG island of the promoter were identified with high importance for gene silencing and outcome prediction. A logistic regression model (MGMT-STP27) comprising probes cg1243587 and cg12981137 provided good classification properties and prognostic value (kappa = 0.85; log-rank p < 0.001) using a training-set of 63 glioblastomas from homogenously treated patients, for whom MGMT methylation was previously shown to be predictive for outcome based on classification by methylation-specific PCR. MGMT-STP27 was successfully validated in an independent cohort of chemo-radiotherapy-treated glioblastoma patients (n = 50; kappa = 0.88; outcome, log-rank p < 0.001). Lower prevalence of MGMT methylation among CpG island methylator phenotype (CIMP) positive tumors was found in glioblastomas from The Cancer Genome Atlas than in low grade and anaplastic glioma cohorts, while in CIMP-negative gliomas MGMT was classified as methylated in approximately 50 % regardless of tumor grade. The proposed MGMT-STP27 prediction model allows mining of datasets derived on the HM-450K or HM-27K BeadChip to explore effects of distinct epigenetic context of MGMT methylation suspected to modulate treatment resistance in different tumor types.Electronic supplementary materialThe online version of this article (doi:10.1007/s00401-012-1016-2) contains supplementary material, which is available to authorized users.

Estimated Comparative Integration Hotspots Identify Different Behaviors of Retroviral Gene Transfer Vectors

Integration of retroviral vectors in the human genome follows non random patterns that favor insertional deregulation of gene expression and may cause risks of insertional mutagenesis when used in clinical gene therapy. Understanding how viral vectors integrate into the human genome is a key issue in predicting these risks. We provide a new statistical method to compare retroviral integration patterns. We identified the positions where vectors derived from the Human Immunodeficiency Virus (HIV) and the Moloney Murine Leukemia Virus (MLV) show different integration behaviors in human hematopoietic progenitor cells. Non-parametric density estimation was used to identify candidate comparative hotspots, which were then tested and ranked. We found 100 significative comparative hotspots, distributed throughout the chromosomes. HIV hotspots were wider and contained more genes than MLV ones. A Gene Ontology analysis of HIV targets showed enrichment of genes involved in antigen processing and presentation, reflecting the high HIV integration frequency observed at the MHC locus on chromosome 6. Four histone modifications/variants had a different mean density in comparative hotspots (H2AZ, H3K4me1, H3K4me3, H3K9me1), while gene expression within the comparative hotspots did not differ from background. These findings suggest the existence of epigenetic or nuclear three-dimensional topology contexts guiding retroviral integration to specific chromosome areas.

X Inactivation and Progenitor Cancer Cells

In mammals, silencing of one of the two X chromosomes is necessary to achieve dosage compensation. The 17 kb non-coding RNA called Xist triggers X inactivation. Gene silencing by Xist can only be achieved in certain contexts such as in cells of the early embryo and in certain hematopoietic progenitors where silencing factors are present. Moreover, these epigenetic contexts are maintained in cancer progenitors in which SATB1 has been identified as a factor related to Xist-mediated chromosome silencing.

Fully-mature antral mouse oocytes are transcriptionally silent but their heterochromatin maintains a transcriptional permissive histone acetylation profile

The final stages of antral mouse oocytes maturation are characterised by the transition from transcriptionally active NSN to inactive SN oocytes. Here, we studied the profile of histone acetylation changes occurring during the NSN-to-SN transition. During the NSN-to-SN transition, oocytes were classified based on their chromatin organisation and the immunocytochemical profile of histones H2B, H3 and H4 acetylation was analysed. We described four patterns of immunostaining common to the three acetylated histones, corresponding to stages of progressive localisation: From a diffused distribution in NSN oocytes to the association with constitutive heterochromatin and then to the nucleolar surface region in SN oocytes. The maintenance of a favourable transcriptional epigenetic context, in the heterochromatin of transcriptionally silent SN oocytes, might be related to the early stages of development when transcripts from these heterochromatic regions are functional to preimplantation progression.

Acquired Traits Revisited

Most biology texts villify Lamarck's concept of “inheritance of acquired characters” and leave the impression that all acquired characters are never transmitted to offspring. However, recent research indicates that this is not true! Some “acquired” traits are inherited. I profile some of these striking cases and their importance for evolution and for understanding a broader epigenetic context for heredity and ontogeny (the emerging field of “evo-devo”). Further, I discuss how such cases, even considered as exceptions, contribute to understanding the nature of science, both the role of general rules in biology and the occurrence of conceptual change, or paradigm shifts.

Biomonitoring in Greenland: human biomarkers of exposure and effects - a short review

Since 1997 the Arctic Monitoring and Assessment Programme (AMAP) has produced integrated assessment reports on the status of and trends in environmental persistent organic pollutants (POPs) in the Arctic ecosystem. Three reports on biomonitoring POPs and their health risks for Arctic populations were published in 1998, 2002, and 2009. The present review summarizes data from Greenland on human monitoring of biomarkers of POP exposure and bioaccumulation and the determination of biomarkers for POP effects. The review focuses on hormone disruptive potentials and some genetic sensitivity biomarkers. The overview covers Greenlandic studies from 2000 to 2006. The Greenland biomonitoring studies showed general geographical and gender differences of bioaccumulated serum POP levels, which were primarily related to diet and lifestyle. A high intake of traditional Greenlandic diet (eg seal, whale, polar bear, and seabirds) together with smoking caused higher blood concentrations of POPs. The highest POP values were found on the east coast of Greenland. The receptor effect studies showed a general inverse relationship between high serum POP concentration and estrogen receptor (ER) and Ah-receptor (AhR) transactivity; in addition for men in the two West Greenlandic districts, Nuuk and Sisimiut, a trend towards increased induced AR activity was found. An observed trend to an opposite direction between the dioxin-like AhR and ER activity supports the perception of that dioxins exert an antiestrogen effect. In conclusion, the actual mixtures of serum POPs in Greenlandic Inuit have an endocrine disrupting potential. Comparisons between European and Greenlandic male serum POP levels showed significantly higher levels in Inuit; however, in the same study Inuit had significantly lower sperm DNA damage. Further studies are required to elucidate whether the serum POP related effects on hormone receptors and/or AhR are explanatory factors. 'The Arctic dilemma' is that along with the intake of the Greenlandic traditional diet that contains POPs, there are also a number of important nutrients, such as trace elements/antioxidants and marine unsaturated fatty acids which have favorable effects on health. However, a number of studies suggest that an increase in Western food items in the diet can lead to other health risks, such as the metabolic syndrome and its sequels increase in weight, hypertension, diabetes type 2, cardiovascular disease, and cancer, including breast cancer. To elucidate these aspects further studies are required, including those into biomarkers for exposure and effects, epigenetic contexts and the determination of relevant genetic polymorphisms, case-control as well as generation studies. Finally, there is a need for the development of new biomarkers to study the potential POP effects that inhibit the immune system and affect the development of the central nervous system.

Septomics: Application of Systems Approaches to Sepsis - Potential for Personalized Management of Septic Patients

Sepsis is one of the most complex human diseases that continue to be associated with high mortality rates and substantial medical costs. It is an infection-induced, complex traits systemic syndrome that engages most of the bodys systems and organs. Whereas several etiologic agents can elicit sepsis, disease susceptibility, severity and therapeutic outcomes are modulated by a complex interaction of numerous environmental and constitutive (e.g., genomic) factors. To effectively understand and treat different types of sepsis in susceptible individuals, we need to adopt holistic systems approaches that utilize network-based investigations to integrate disease related complex traits, themselves affected by variations in the host genomic and epigenetic contexts, physiogenomic, metabolomic status as well as by variations in the pathogen. Importantly, a systems approach to sepsis can provide a roadmap to help identify both the host and the pathogen pathways underlying sepsis or variable therapeutic responses to sepsis. This paper introduces the emerging field of “septomics” – i.e., the application of high-throughput omics technologies to sepsis related complex traits - in diagnosing and/or modulating susceptibility and outcomes of sepsis. Additionally, we discuss how unbiased, network-based systems approaches and biotools can help better understand novel gene-by-environment interactions in sepsis, and identify genetic, physiologic and soluble (e.g., proteomics) biomarkers that can precisely predict disease susceptibility, progression or response to therapeutic interventions. Finally, we note that septomics also signals a new application of genome-based medicine in the context of global public health against existing and emerging infectious diseases that are greatly affecting the world populations in both developed and developing countries.

The serotonin transporter gene and disease modification in psychosis: Evidence for systematic differences in allelic directionality at the 5-HTTLPR locus

A 44 base pair insertion (“l”)/deletion (“s”) polymorphism (called 5-HTTLPR) in the 5′ promoter region of the human serotonin transporter gene ( SLC6A4) modulates expression and has been associated to anxiety and depressive traits in otherwise healthy individuals. In individuals with psychiatric diagnoses, including schizophrenia, it seems to modulate symptom severity. Thus, it may be a disease modifying gene. In this study, 92 patients with psychosis (including schizophrenia, schizoaffective disorder, bipolar psychosis, and major depression) were assessed at their first hospital admission. Symptom ratings, including SANS negative symptoms, SAPS positive symptoms, and SCID depressive symptoms, were obtained. Stress was also assessed. Bi-allelic genotyping at the 5-HTTLPR locus was done. Using multiple regression models, we found that 5-HTTLPR genotype (especially in dominant models) accounted for a significant portion of the variance in SCID Depression and SANS (about 5%). In particular we found that the l allele was associated with greater psychopathology. This is consistent with our review of the literature and is at variance with findings in healthy controls that the s allele is associated with greater anxiety and depression levels. We believe that this set of findings argues for principled reversal of directionality in associations at the 5-HTTLPR locus and raises the possibility that allelic variation may have very different consequences for personality traits or psychiatric symptoms depending on epistasis or epigenetic context. Furthermore, these results also imply that categorical diagnostic distinctions may still be relevant in understanding some genetic effects.

Molecular Targets for Tumor Radiosensitization

Molecular Targets for Tumor Radiosensitization

Life-history traits of invasive bighead gobyNeogobius kessleri(Günther, 1861) from the middle Danube River, with a reflection on which goby species may win the competition

Summary Life history traits of an invasive population of bighead goby Neogobius kesslerei (Gunther, 1861) from the middle Danube, including absolute and relative fecundity, egg size, number of spawning batches and size at first maturation, were examined and evaluated within an epigenetic context. Ripe bighead goby females attained 42.8-142.5 mm LS, with absolute fecundities ranging from 669 to 5646 eggs (mean 2109 eggs), and relative fecundities of 61.6-174.0 eggs g )1 body weight (mean 119.6 eggs). Egg diameters varied between 0.04 mm and 1.70 mm (mean = 0.57 mm). In the pre-spawning period there was no clear size distinction in eggs (0.12-1.45 mm; mean = 0.52 mm) in 34.1% of females; whereas in 65.9% of females, two egg size groups were distinguished: group I diameters of 0.06-0.85 mm (mean = 0.43 mm), and group II diameters of 0.55-1.70 mm (mean = 1.17 mm). Females with size-group II eggs at the beginning of the reproductive season were assumed to be ready to spawn and the others to be subsequent spawners. Bighead goby appears to be altricial compared to the round goby, although in both species a shift from highly precocial towards a less precocial life history was observed. These differences, affected by epigenetic mecha- nisms and resulting in alternative ontogenies, may have important implications for a species potential success in novel environments, favouring the round goby over short time periods (several years) and bighead goby over longer periods of time (decades and longer).

The context and potential of epigenetics in oncology

Cancer has long been known to be a disease caused by alterations in the genetic blueprint of cells. In the past decade it has become evident that epigenetic processes have a function, at least equally important, in neoplasia. Epigenetics describes the mechanisms that result in heritable alterations in gene expression profiles without an accompanying change in DNA sequence. Genetics and epigenetics intricately interact in the pathogenesis of cancer (Esteller, 2007). In this review, we paint a broad picture of current understanding of epigenetic changes in cancer cells and reflect on the immense clinical potential of emerging knowledge of epigenetics in the diagnosis, prognostic assessment, treatment, and screening of cancer.

Discriminating nucleosomes containing histone H2A.Z or H2A based on genetic and epigenetic information

BackgroundNucleosomes are nucleoproteic complexes, formed of eight histone molecules and DNA, and they are responsible for the compaction of the eukaryotic genome. Their presence on DNA influences many cellular processes, such as transcription, DNA replication, and DNA repair. The evolutionarily conserved histone variant H2A.Z alters nucleosome stability and is highly enriched at gene promoters. Its localization to specific genomic loci in human cells is presumed to depend either on the underlying DNA sequence or on a certain epigenetic modification pattern.ResultsWe analyzed the differences in histone post-translational modifications and DNA sequences near nucleosomes that do or do not contain H2A.Z. We show that both the epigenetic context and underlying sequences can be used to classify nucleosomal regions, with highly significant accuracy, as likely to either contain H2A.Z or canonical histone H2A. Furthermore, our models accurately recapitulate the observed nucleosome occupancy near the transcriptional start sites of human promoters.ConclusionWe conclude that both genetic and epigenetic features are likely to participate in targeting H2A.Z to distinct chromatin loci.

An integrative approach for analyzing the interplay of genetic and epigenetic changes in tumors

Abstract The accumulation of chromosomal aberrations is a characteristic feature of tumor development. However, an understanding of tumorigenesis that assumes that changes in DNA copy number always cause equivalent changes in the corresponding RNA and protein levels is an oversimplification and completely ignores the individual genetic and epigenetic context in which an aberration has to be evaluated. We present a brief introduction to various techniques dedicated to the genome-wide analysis of genetic and epigenetic changes, and illustrate how complementary information derived from these various DNA array-based technologies can lead to a better understanding of the consequences of chromosomal aberrations.

An Integrative Approach for Analyzing the Interplay of Genetic and Epigenetic Changes in Tumors

The accumulation of chromosomal aberrations is a characteristic feature of tumor development. However, an understanding of tumorigenesis that assumes that changes in DNA copy number always cause equivalent changes in the corresponding RNA and protein levels is an oversimplification and completely ignores the individual genetic and epigenetic context in which an aberration has to be evaluated. We present a brief introduction to various techniques dedicated to the genome-wide analysis of genetic and epigenetic changes, and illustrate how complementary information derived from these various DNA array-based technologies can lead to a better understanding of the consequences of chromosomal aberrations.

Ontogenetic variability in the external morphology of monkey goby, Neogobius fluviatilis (Pallas, 1814) and its relevance to invasion potential

In the previous decade, four species of non-native gobies have invaded the middle section of the river Danube and its tributaries. An effective tool for understanding biological invasions is the evaluation of various biological traits (morphological, life history, ontogenetic) within an epigenetic context. The present study examines the external morphology of monkey goby Neogobius fluviatilis (Pallas, 1814) from the mouth of the River Hron, the morphological differences among three goby species (monkey, bighead and round) and the relevance of these differences for invasive potential. Monkey goby reach their definite phenotype very early in their ontogeny and thus represent a strongly precocial (specialized) species with direct development. The morphological differences between monkey and two other goby species also reflect its strong specialization for sandy substrata and smaller prey types. Thus, monkey goby are not expected to spread to new areas as fast as the round and bighead gobies, and their distribution is likely to be limited to sandy and/or sandy-gravel substrata. If this assumption is correct, then the potential adverse impact of monkey goby on native fauna or even ecosystem is likely to be less than that of the bighead and round gobies.

Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA

By using a microscopic approach, field inversion single-cell gel electrophoresis, we show that preformed single-strand discontinuities are present in the chromatin of resting and proliferating mammalian and yeast cells. These single-strand breaks are primarily nicks positioned at approximately 50-kbp intervals throughout the entire genome that could be efficiently labeled in situ by DNA polymerase I holoenzyme but not by Klenow fragment and terminal transferase unless after ribonucleolytic treatments. The RNA molecules involved appear to comprise R-loops, recognized by the S9.6 RNA/DNA hybrid-specific antibody. By using the breakpoint cluster region of the Mixed Lineage Leukemia (MLL) gene as a model, we have found that the number of manifest nicks detected by FISH performed after field inversion single-cell gel electrophoresis depends on epigenetic context, but the difference between germ-line and translocated MLL alleles is abolished by protease treatment. Our data imply that the double-stranded genomic DNA is composed of contiguous rather than continuous single strands and reveal an aspect of higher-order chromatin organization with ribonucleoprotein-associated persistent nicks defining approximately 50-kbp domains.

Genetic redundancy in human cervical carcinoma cells: Identification of cells with “normal” properties

Although it is generally assumed that cancer arises from a singular cell, a tumor must be considered as a dynamic and emergent biological structure, whose organizing principle is determined by genetic and epigenetic modifications, occurring variably in response to microenvironmental selection conditions. As previously shown, HPV-positive cervical carcinoma cells have lost their ability to induce IFN-beta upon TNF-alpha treatment. However, regarding cancer as a non-linear system, which may, even in the absence of an apparent selection pressure, fluctuate between different "metastable" phenotypes, we demonstrate that TNF-alpha mediated IFN-beta induction is not irreversibly disturbed in all cells. Using the IFN-beta sensitive Encephalomyocarditis virus (EMCV) as a tool to monitor antiviral activity in long-term established malignant HeLa cells, rare IFN-beta expressing clones were rescued from a population of non-responsive and EMCV-sensitive cells. Antiviral activity was mediated by the re-expression of IRF-1 and p48 (IRF-9), both key regulatory molecules normally found to be suppressed in cervical carcinoma cells. Upon inoculating of selected clones into immunocompromised animals, a reduced or even an absence of tumorigenicity of initially highly malignant cells could be discerned. These data indicate that both the absence of interferon signaling and the ability to form tumors were reversed in a minority of cells. We provide a paradigm for the existence of innate genetic redundancy mechanisms, where a particular phenotype persists and can be isolated without application of drugs generally changing the epigenetic context.

Brief inactivation of c-Myc is not sufficient for sustained regression of c-Myc-induced tumours of pancreatic islets and skin epidermis

BackgroundTumour regression observed in many conditional mouse models following oncogene inactivation provides the impetus to develop, and a platform to preclinically evaluate, novel therapeutics to inactivate specific oncogenes. Inactivating single oncogenes, such as c-Myc, can reverse even advanced tumours. Intriguingly, transient c-Myc inactivation proved sufficient for sustained osteosarcoma regression; the resulting osteocyte differentiation potentially explaining loss of c-Myc's oncogenic properties. But would this apply to other tumours?ResultsWe show that brief inactivation of c-Myc does not sustain tumour regression in two distinct tissue types; tumour cells in pancreatic islets and skin epidermis continue to avoid apoptosis after c-Myc reactivation, by virtue of Bcl-xL over-expression or a favourable microenvironment, respectively. Moreover, tumours progress despite reacquiring a differentiated phenotype and partial loss of vasculature during c-Myc inactivation. Interestingly, reactivating c-Myc in β-cell tumours appears to result not only in further growth of the tumour, but also re-expansion of the accompanying angiogenesis and more pronounced β-cell invasion (adenocarcinoma).ConclusionsGiven that transient c-Myc inactivation could under some circumstances produce sustained tumour regression, the possible application of this potentially less toxic strategy in treating other tumours has been suggested. We show that brief inactivation of c-Myc fails to sustain tumour regression in two distinct models of tumourigenesis: pancreatic islets and skin epidermis. These findings challenge the potential for cancer therapies aimed at transient oncogene inactivation, at least under those circumstances where tumour cell differentiation and alteration of epigenetic context fail to reinstate apoptosis. Together, these results suggest that treatment schedules will need to be informed by knowledge of the molecular basis and environmental context of any given cancer.