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Impaired memory CD8 T cell development in the absence of methyl-CpG-binding domain protein 2.

Intracellular differentiation events that determine which cells develop into memory CD8 T cells are currently incompletely understood. Methyl-CpG-binding domain protein 2 (MBD2) is a transcriptional repressor that binds to methylated DNA and mediates the biological consequences of epigenetic gene methylation. The role of MBD2 during the differentiation of naive CD8 T cells into effector and memory cells was determined following acute infection of MBD2-deficient mice with lymphocytic choriomeningitis virus. Despite rapid viral clearance and an efficient primary effector CD8 T cell response, reduced numbers of Ag-specific memory CD8 T cells were observed. Importantly, the appearance of precursor memory cells (IL-7Ralphahigh) was delayed. The remaining MBD2(-/-) memory cells were not fully protective during rechallenge, and memory cell characteristics were altered with regard to surface markers (IL-7Ralpha, KLRG-1, CD27, and others) and cytokine production. The defect was CD8 T cell intrinsic, because memory cell development was also delayed when MBD2(-/-) CD8 T cells were adoptively transferred into SCID mice. These data demonstrate that MBD2 is a previously unrecognized intracellular factor required for the efficient generation of protective memory CD8 T cells.

Animals↗

Expression of imprinted genes in cloned mice.

Genomic imprinting is a mammalian specific epigenetic modification of the genome. Assessment of the integrity of the imprinting memory in somatic cell cloned animals is important not only for understanding of the "reprogramming" process during cloning by nuclear transfer, but also for the applications of this technique for therapeutic cloning in the future. In this chapter, we summarize the analytical methods for assessment of monoallelic expression of imprinting genes and expression analysis. From a practical point of view, the authors suggest the use of intersubspecific F1 hybrids between the laboratory mouse (Mus musculus musculus) and the JF1 strain (Mus musculus molossinus). We also list the sequence for PCR primers to detect the polymorphism of imprinted genes between musculus and molossinus.

Animals↗

Identification and properties of imprinted genes and their control elements.

Imprinted genes have the unusual characteristic that the copy from one parent is destined to remain inactive. Though few in number they nonetheless constitute a functionally important part of the mammalian genome. With their memory of parental origin, imprinted genes represent an important model for the epigenetic regulation of gene function and will provide invaluable paradigms to test whether we can predict epigenetic state from DNA sequence. Since their first discovery, systematic screens and some good fortune have led to identification of over seventy imprinted genes in the mouse and human: recent microarray analysis may reveal many more. With a significant number of imprinted genes now identified and completion of key mammalian genome sequences, we are able systematically to examine the organization of imprinted loci, properties of their control elements and begin to recognize common themes in imprinted gene regulation.

Alleles↗

The prima donna of epigenetics: the regulation of gene expression by DNA methylation.

This review focuses on the mechanisms of DNA methylation, DNA methylation pattern formation and their involvement in gene regulation. Association of DNA methylation with imprinting, embryonic development and human diseases is discussed. Furthermore, besides considering changes in DNA methylation as mechanisms of disease, the role of epigenetics in general and DNA methylation in particular in transgenerational carcinogenesis, in memory formation and behavior establishment are brought about as mechanisms based on the cellular memory of gene expression patterns.

Animals↗

Epigenetic regulation of stem cell differentiation.

Stem cells undergo extensive self-renewal and have the capacity to differentiate along multiple cell lineages. Progression from stem cells into differentiated progeny requires long-lasting changes in gene expression. Epigenetic mechanisms, including DNA methylation, histone modifications, and non-coding RNA-mediated regulatory events, are essential to controlling the heritable cellular memory of gene expression during development. Recent studies on cell fate specification of embryonic and adult stem cells/progenitors have highlighted a general and critical role for dynamic epigenetic regulation in stem cell self-renewal and differentiation.

Adult↗

Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3.

In Saccharomyces cerevisiae, methylation of histone H3 at active genes is an epigenetic mark that distinguishes active from silent chromatin and functions as a short-term "memory" of recent transcription. Methylation of H3 at lysine residues K4 and K79 depends on ubiquitylation of histone H2B, but the mechanisms linking H2B ubiquitylation to H3 methylation are unknown. Here, we demonstrate that proteasomal ATPases Rpt4 and Rpt6 function to connect these two histone modifications. We show that recruitment of proteasome subunits to chromatin depends on H2B ubiquitylation and that mutations in Rpt4 and Rpt6 disrupt H3 methylation at K4 and K79 but leave H2B ubiquitylation intact. Consistent with their role in H3 methylation, we also find that mutations in Rpt4 and 6-but not components of the 20S proteasome-disrupt telomeric gene silencing. These data reveal that proteasome subunits function in epigenetic gene regulation by linking chromatin modifications that establish the histone code.

Adenosine Triphosphatases↗

Artificial and epigenetic regulation of the I factor, a nonviral retrotransposon of Drosophila melanogaster.

The I factor (IF) is a LINE-like transposable element from Drosophila melanogaster. IF is silenced in most strains, but under special circumstances its transposition can be induced and correlates with the appearance of a syndrome of female sterility called hybrid dysgenesis. To elucidate the relationship between IF expression and female sterility, different transgenic antisense and/or sense RNAs homologous to the IF ORF1 have been expressed. Increasing the transgene copy number decreases both the expression of an IF-lacZ fusion and the intensity of the female sterile phenotype, demonstrating that IF expression is correlated with sterility. Some transgenes, however, exert their repressive abilities not only through a copy number-dependent zygotic effect, but also through additional maternal and paternal effects that may be induced at the DNA and/or RNA level. Properties of the maternal effect have been detailed: (1) it represses hybrid dysgenesis more efficiently than does the paternal effect; (2) its efficacy increases with both the transgene copy number and the aging of sterile females; (3) it accumulates slowly over generations after the transgene has been established; and (4) it is maintained for at least two generations after transgene removal. Conversely, the paternal effect increases only with female aging. The last two properties of the maternal effect and the genuine existence of a paternal effect argue for the occurrence, in the IF regulation pathway, of a cellular memory transmitted through mitosis, as well as through male and female meiosis, and akin to epigenetic phenomena.

Aging↗

Cell history determines the maintenance of transcriptional differences between left and right ventricular cardiomyocytes in the developing mouse heart.

The molecular mechanisms that establish and maintain transcriptional differences between cardiomyocytes in the left and right ventricular chambers are unkown. We have previously analysed a myosin light chain 3f transgene containing an nlacZ reporter gene, which is transcribed in left but not right ventricular cardiomyocytes. In this report we examine the mechanisms involved in maintaining regionalised transgene expression. Primary cardiomyocytes prepared from left and right ventricular walls of transgenic mice were found to maintain transgene expression status in culture. However, similar cultures prepared from nontransgenic mice or rats show uniform expression after transient transfection of Mlc3f constructs, suggesting that the mechanism responsible for differential expression of the transgene between left and right ventricular cells does not operate on transiently introduced molecules. These data suggest that developmental cell history determines transgene expression status. Maintenance of transgene expression status is regulated by a cell-autonomous mechanism that is independent of DNA methylation, trichostatin A-sensitive histone deacetylation and miss-expression of transcription factors that are expressed in the left or right ventricles of the embryonic heart. Parallels between Mlc3f transgene repression in right ventricular cardiomyocytes and polycomb-mediated silencing in Drosophila suggest that Mlc3f regulatory sequences included on the transgene may contain a cellular memory module that is switched into an on or off state during early cardiogenesis. Epigenetic mechanisms may therefore be involved in maintaining patterning of the mammalian myocardium.

Animals↗

Genetic and epigenetic changes to the glucocorticoid receptor gene (NR3C1) and cognition in major depressive disorder.

INTRODUCTION: Many studies have found that hypothalamic-pituitary-adrenal (HPA) axis abnormalities are related to the pathophysiology of major depressive disorder (MDD) and cognitive functioning. Our aim was to assess the influence of genetic polymorphisms and methylation levels in three different promoter regions throughout the glucocorticoid receptor (GR) gene NR3C1 on cognitive performance in MDD. Plausible interactions with childhood adversity and mediation relationships between genetic and epigenetic variables were explored. MATERIALS AND METHODS: The sample included a total of 64 MDD patients and 82 healthy controls. Child maltreatment and neurocognitive performance were assessed in all participants. HPA negative feedback was analyzed using the dexamethasone suppression test after the administration of 0.25mg of dexamethasone. A total of 23 single-nucleotide polymorphisms were genotyped, and methylation levels at several CpGs in exons 1D, 1F and 1H of the GR gene were measured. RESULTS: Results show that, beyond the influence of other covariables, NR3C1 single-nucleotide polymorphisms and methylation levels predicted performance in executive functioning and working memory tasks. No significant interactions or mediation relationships were detected. CONCLUSIONS: Results suggest that genetic variations and epigenetic regulation of the GR gene are relevant factors influencing cognitive performance in MDD and could emerge as significant biomarkers and therapeutic targets in mood disorders and other stress-related disorders.

Humans↗

Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior.

A biological introduction serves to remind us that differentiation is an epigenetic process, that multistationarity can account for epigenetic differences, including those involved in cell differentiation, and that positive feedback circuits are a necessary condition for multistationarity and, by inference, for differentiation. The core of the paper is comprised of a formal description of feedback circuits and unions of disjoint circuits. We introduce the concepts of full-circuit (a circuit or union of disjoint circuits which involves all the variables of the system), and of ambiguous circuit (a circuit whose sign depends on the location in phase space). We describe the partition of phase space (a) according to the signs of the ambiguous circuits, and (b) according to the signs of the eigenvalues or their real part. We introduce a normalization of the system versus one of the circuits; in two variables, this permits an entirely general description in terms of a common diagram in the "circuit space." The paper ends with general statements concerning the requirements for multistationarity, stable periodicity, and deterministic chaos. (c) 2001 American Institute of Physics.

Journal Article↗

Multilevel Proteomics Reveals Epigenetic Signatures in BCG-Mediated Macrophage Activation.

The bacillus Calmette-Guérin BCG vaccine (Mycobacterium bovis) is primarily used to prevent tuberculosis (TB) infections but has wide-ranging immunogenic effects. One of its most notable properties is its ability to induce trained immunity, a memory-like response in innate immune cells such as macrophages. Through targeted analyses of well-established histone marks, prior research has shown that these changes are generated through epigenetic modification. Mass spectrometry-based proteomic approaches provide a way to globally profile various aspects of the proteome, providing data to further identify unexplored mechanisms of BCG-mediated immunomodulation. Here we use multi-level proteomics (total, histone, and phospho to identify networks and potential mechanisms that mediate BCG-induced immunomodulation in macrophages. Histone-focused proteomics and total proteomics were performed at the University of Cape Town (data available via ProteomeXchange with identifier PXD051187), while phosphoproteomics data was retrieved from the ProteomeXchange Repository (identifier PXD013171). We identify several epigenetic mechanisms that may drive BCG-induced training phenotypes. Evidence across the proteomics and histone-focused proteomics data set pair 6 epigenetic effectors (NuA4, NuRD, NSL, Sin3A, SIRT2, SIRT6) and their substrates.

Epigenesis, Genetic↗

Metabolic memory in diabetes--focus on insulin.

Large-scale clinical trials have demonstrated that metabolic control achieved early in the course of diabetes substantially reduces development and progression of diabetes and the associated microvascular complications. Additionally, prospective observational studies have demonstrated that atherogenic and inflammatory mediators are elevated even prior to the onset of diabetes and significantly contribute to subsequent development of macrovascular complications. Collectively, these data suggest that metabolic memories are stored early in the course of diabetes. We believe that insulin suppresses inflammation and also suppresses glucotoxicity and lipotoxicity (and the consequences thereof, such as the formation of advanced glycation end products and epigenetic phenomena), and thus has a pivotal and beneficial role. Comprehensive metabolic control, especially when instituted early, may alter the natural history of diabetic complications by affecting this metabolic memory. Thus, our overall goal is to understand in more detail the molecular mechanisms involved in these changes, thereby affording us opportunities to reduce the long-term effects of diabetes.

Diabetes Mellitus↗

Polycomb group genes as epigenetic regulators of normal and leukemic hemopoiesis.

Epigenetic modification of chromatin structure underlies the differentiation of pluripotent hemopoietic stem cells (HSCs) into their committed/differentiated progeny. Compelling evidence indicates that Polycomb group (PcG) genes play a key role in normal and leukemic hemopoiesis through epigenetic regulation of HSC self-renewal/proliferation and commitment. The PcG proteins are constituents of evolutionary highly conserved molecular pathways regulating cell fate in several other tissues through diverse mechanisms, including 1) regulation of self-renewal/proliferation, 2) regulation of senescence/immortalization, 3) interaction with the initiation transcription machinery, 4) interaction with chromatin-condensation proteins, 5) modification of histones, 6) inactivation of paternal X chromosome, and 7) regulation of cell death. It is therefore not surprising that PcG genes lead to pleiotropic phenotypes when mutated and have been associated with malignancies in several systems in both mice and humans. Although much remains to be learned regarding the PcG mechanism(s) of action, advances in identifying the functional domains and enzymatic activities of these multimeric protein complexes have provided insights into how PcG proteins accomplish such processes. Some of the new insights into a role for the PcG cellular memory system in regulating normal and leukemic hemopoiesis are reviewed here, with special emphasis on their potential involvement in epigenetic regulation of gene expression through modification of chromatin structure.

Animals↗

Monogenetic defects in common variable immunodeficiency: what can we learn about terminal B cell differentiation?

PURPOSE OF REVIEW: In human primary immunodeficiencies, more than 100 different genetic defects have been described. For the most prevalent primary immunodeficiency requiring medical attention, however, termed common variable immunodeficiency, no genetic cause had been defined until recently. In this review we will summarize the current progress in the molecular genetics of common variable immunodeficiency and put them in context with other important developments in the field. RECENT FINDINGS: In recent years the first three monogenetic defects in the inducible costimulator, transmembrane activator and CAML interactor (TACI), and CD19 were discovered in patients with common variable immunodeficiency revealing a multifaceted genetic background for this disease. As a concise phenotype cannot be assigned to each of these genetic defects, there is a need for further development of classification systems for common variable immunodeficiency and the search of epigenetic factors influencing the course of the disease. Subgroups of common variable immunodeficiency patients with low IgM memory B cells may suffer from an increased rate of infections. Human herpes virus type 8 infections were identified as a risk factor for the development of granulomatous disease complications. SUMMARY: The pathogenesis of common variable immunodeficiency shows a convergence on impaired terminal B cell differentiation. Recently discovered genetic defects support this view. A combined effort of genetic analysis and standardized assessment of immunological and clinical phenotypes will be necessary to further unravel the conundrum of common variable immunodeficiency.

Antigens, CD↗

[Epigenetics: gene and epigene networks in ontogeny and phylogeny].

An attempt was made to systematize theoretical and experimental epigenetic data in the framework of genetics as a science on laws of preservation, coding, transfer, and transformation of heritable information in the living systems. The structure of the total hereditary memory is discussed in context of the theory of epigenes, hereditary units of the next to genes level of complexity. In epigenes as cells of functional hereditary memory, part of the hereditary information is stored, coded, and transmitted to the progeny irrespective of the primary structure of the genomic DNA molecules. The principles of the structure and the general laws of functioning of cellular governing gene networks are presented. The ontogenetic and phylogenetic role of epigene networks as the second level of the hereditary system is considered. Arguments for inheritance of somatic epimutations are presented, as well as the results of in silico and in vivo experiments showing the possibility of an epigenetic mechanism of primary biochemical divergent determination (autodetermination). A network hypothesis on material carriers of the common heterotary memory is formulated.

Animals↗

Histone hypomethylation is an indicator of epigenetic plasticity in quiescent lymphocytes.

Post-translational modifications of histone amino termini are thought to convey epigenetic information that extends the coding potential of DNA. In particular, histone lysine methylation has been implicated in conveying transcriptional memory and maintaining lineage fidelity. Here an analysis of histone lysine methylation in quiescent (G(0)) and cycling lymphocytes showed that methylation of histone H3 at lysines 4 (H3K4), 9 (H3K9), 27 (H3K27) and histone H4 at lysine 20 is markedly reduced in resting B lymphocytes as compared with cycling cells. Quiescent B cells also lacked heterochromatin-associated HP1beta and Ikaros at pericentric chromatin and expressed low levels of Ezh2 and ESET histone methyl transferases (HMTases). Nuclei from resting B or T cells were approximately three times more efficiently reprogrammed in nuclear transfer assays than cells in which HMTase expression, histone methylation and HP1beta binding had been restored following mitotic stimulation. These results showing local and global changes in histone lysine methylation levels in vivo demonstrate that constitutive heterochromatin organization is modified in resting lymphocytes and suggest that histone hypomethylation is a useful indicator of epigenetic plasticity.

Animals↗

[Functions of paradoxical sleep and ontogenesis].

The hypotheses directly linked to cognitive and neurologic ontogenic processes ie consolidation of memory and learning, the maturation hypothesis of Roffwarg and the hypothesis of endogenous genetic programming of Jouvet, are analysed. The discussion of these theories are based on the analysis of: the neurophysiologic mechanism of REM sleep and its ontogenesis in human, the results of REM sleep deprivation in young animals and by a personal study of facial mimics during sleep in neonates. Active sleep could be assimilated, very early during ontogenesis, to REM sleep, it probably plays an important role in brain maturation during early development but the stimulation is probably, at this time, not very specific, later it could be a link between genetic programming and epigenetic processes.

Adolescent↗