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Results for “Epigenetic memory”

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At least 217 records · Page 12Linked to original sources

PubMed2005

DNA deamination in immunity.

A functional immune system is one of the prerequisites for the survival of a species. Humans have one of the most complicated immune systems, with the ability to learn from and adapt to pathogens. At first, a primary repertoire of antibodies is generated, which, upon antigen encounter, will diversify and adapt to produce a highly specific and potent secondary response, part of which is kept in memory to fight off future infections. In this review, the mechanism as well as the specificities of the key protein in the secondary immune response, activation-induced cytidine deaminase (AID), are highlighted, as well as its role in the DNA deamination model of immunoglobulin diversification. The review also highlights aspects of AID's regulation on both the transcriptional as well as post-translational level and its potential molecular mechanism and specificity. Furthermore, it expands outside the involvement of AID in somatic hypermutation, class switching, and gene conversion to discuss the implications of DNA deamination in epigenetic modifications of DNA (as a potential demethylase), the induction of mutations during oncogenesis, and includes an evolutionary comparison to the DNA deaminase family member APOBEC3G, a key protein in human immunodeficiency virus pathogenesis.

B-Lymphocytes↗

PubMed1991

Effects of a novel differentiation factor on the development of catecholamine traits in noncatecholamine neurons from various regions of the rat brain: studies in tissue culture.

The muscle-derived differentiation factor called MDF initiated expression of the catecholamine (CA) enzyme tyrosine hydroxylase (TH) in non-CA neurons isolated from a variety of regions in the rat brain. Specifically, subpopulations of neurons from the striatum, collicular plate, and cerebellum were TH-immunoreactive after an overnight exposure to MDF in culture. The number of immunopositive cells was greatest in the striatum, where more than half of all plated neurons expressed the enzyme. In contrast, MDF had no effect on the central neurons of the hippocampus or on peripheral sensory neurons. In 3H-thymidine studies, only brain neurons that had already withdrawn from mitosis expressed TH. These cells remained open to the epigenetic influence of MDF only during a brief and defined critical period that appears to be timed intrinsically. Without daily replenishment of MDF, expression of the enzyme disappeared after several days in culture, suggesting that MDF was rapidly depleted or degraded in vitro. However, in the continued presence of MDF, TH expression was maintained indefinitely, thus producing a permanent alteration in phenotype. Moreover, a single exposure to MDF during the critical period was sufficient to render neurons permanently receptive to the molecule so that TH expression could be reinitiated many days later. It is postulated that a memory of this biochemical interaction was established in these neurons, making transmitter phenotypic plasticity possible at later stages.

Animals↗

PubMed1989

Neuronal models of cognitive functions.

Understanding the neural bases of cognition has become a scientifically tractable problem, and neurally plausible models are proposed to establish a causal link between biological structure and cognitive function. To this end, levels of organization have to be defined within the functional architecture of neuronal systems. Transitions from any one of these interacting levels to the next are viewed in an evolutionary perspective. They are assumed to involve: (1) the production of multiple transient variations and (2) the selection of some of them by higher levels via the interaction with the outside world. The time-scale of these "evolutions" is expected to differ from one level to the other. In the course of development and in the adult this internal evolution is epigenetic and does not require alteration of the structure of the genome. A selective stabilization (and elimination) of synaptic connections by spontaneous and/or evoked activity in developing neuronal networks is postulated to contribute to the shaping of the adult connectivity within an envelope of genetically encoded forms. At a higher level, models of mental representations, as states of activity of defined populations of neurons, are discussed in terms of statistical physics, and their storage is viewed as a process of selection among variable and transient pre-representations. Theoretical models illustrate that cognitive functions such as short-term memory and handling of temporal sequences may be constrained by "microscopic" physical parameters. Finally, speculations are offered about plausible neuronal models and selectionist implementations of intentions.

Animals↗

PubMed2006

Transgeneration memory of stress in plants.

Owing to their sessile nature, plants are constantly exposed to a multitude of environmental stresses to which they react with a battery of responses. The result is plant tolerance to conditions such as excessive or inadequate light, water, salt and temperature, and resistance to pathogens. Not only is plant physiology known to change under abiotic or biotic stress, but changes in the genome have also been identified. However, it was not determined whether plants from successive generations of the original, stressed plants inherited the capacity for genomic change. Here we show that in Arabidopsis thaliana plants treated with short-wavelength radiation (ultraviolet-C) or flagellin (an elicitor of plant defences), somatic homologous recombination of a transgenic reporter is increased in the treated population and these increased levels of homologous recombination persist in the subsequent, untreated generations. The epigenetic trait of enhanced homologous recombination could be transmitted through both the maternal and the paternal crossing partner, and proved to be dominant. The increase of the hyper-recombination state in generations subsequent to the treated generation was independent of the presence of the transgenic allele (the recombination substrate under consideration) in the treated plant. We conclude that environmental factors lead to increased genomic flexibility even in successive, untreated generations, and may increase the potential for adaptation.

Acclimatization↗

PubMed2004

Silence of the fathers: early X inactivation.

X chromosome inactivation is the mammalian answer to the dilemma of dosage compensation between males and females. The study of this fascinating form of chromosome-wide gene regulation has yielded surprising insights into early development and cellular memory. In the past few months, three papers reported unexpected findings about the paternal X chromosome (X(p)). All three studies agree that the X(p) is imprinted to become inactive earlier than ever suspected during embryonic development. Although apparently incomplete, this early form of inactivation insures dosage compensation throughout development. Silencing of the X(p) persists in cells of extraembryonic tissues, but it is erased and followed by random X inactivation in cells of the embryo proper. These findings challenge several aspects of the current view of X inactivation during early development and may have profound impact on studies of pluripotency and epigenetics.

Animals↗

PubMed2004

Chromatin inheritance upon Zeste-mediated Brahma recruitment at a minimal cellular memory module.

Polycomb group and trithorax group proteins maintain the memory of repressed and active chromatin states by regulating chromatin of their target genes via DNA sequences termed Polycomb- and trithorax response elements. Since these elements often overlap and are able to convey the memory of both silent and active chromatin through cell division, they were also defined as cellular memory modules (CMMs). We identify here a minimal CMM of 219 bp from the Drosophila Fab-7 region that regulates the homeotic gene Abdominal-B. This CMM conveys the inheritance of active chromatin states induced by an embryonic pulse of transcriptional activation via recruitment of the trithorax group proteins Trithorax (TRX) and Brahma (BRM), the Drosophila homologue of the SWI2/SNF2 ATPase involved in chromatin remodelling. Within this CMM, DNA-binding sites for the Zeste protein are necessary for the inheritance of active chromatin through Zeste-dependent recruitment of BRM, while TRX can bind the CMM even in their absence. Thus, epigenetic inheritance of active chromatin states involves the recruitment of multiple cooperative chromatin-modifying complexes at closely spaced but distinct sites within a CMM.

Animals↗

PubMed1996

The inner world in the outer world: the phenomenology of posttraumatic stress disorder from a psychoanalytic perspective.

The intrapsychic processes underlying the phenomenology of PTSD symptoms appear to derive their fate from the states of consciousness at the time of traumatic experiences. The operative mechanisms of consciousness-condensation, avoidance of censorship, representability, and secondary revision-are the elements of trauma work as they are of dream work. These mechanisms establish an ever-present dynamic mental state of space consciousness, which is defined as an essential component of mental activities. This state of space consciousness exists beyond any experience of the self and beyond any processes regulated by the pleasure principle. When the sensory impressions derive from perceptions of and interactions with the mother, the matrix consists of the relationship between infant and mother. When the sensory impressions relate to traumatic circumstances the matrix reverts from the epigenetic context to the genetic one. The genetic matrix is manifest through disturbances in the activities of the higher mental functions. Under the impact of trauma, the epigenetic experiences are akin to a population floating without direction on a boat at the mercy of the elements-the raging higher mental functions. The factors operating on the higher mental functions create an inner world under traumatic circumstances, leading to an interpretation of the outer space according to the mental activities of the inner space. The concept of a dynamic process producing numerous modifications in mental scenes, thought, feelings, and reactions provides no surprise to psychoanalysts. The higher mental functions are seen as operating at the juncture of the physical and the mental. This juncture is the place where spatial consciousness and memories begin their common journey. Goodman wrote, "The conventional dichotomy between physical (organic) and mental (functional) is linguistic/conceptual rather than inherent in nature, and all events and processes involved in the etiology, pathogenesis, symptomatic manifestation, and treatment of psychiatric disorders are simultaneously biological and psychological" (Goodman, 1991, p. 553). The subjective experience of the dynamic unconscious activities of the higher mental functions form the inner nucleus selecting the relevant sensory impressions from the outer world. The juncture between the physical and the mental could be a crossroad for the psychic events occupying space and the psychic events determined by time factors. The psychic events that begin at this juncture find their composition evolving in time, in sequence, and in simultaneity. They follow a course determined by the four mechanisms responsible for the creation of dreams, of memories, of behaviors, and of narratives. The descriptive criteria of PTSD have in common the quality of persistence. The associated features show more variability and their appearance coincide with the appropriate circumstances that stimulate their arousal. Internal genetic factors remain persistent factors in the arousal of the reexperiencing phenomenon, of the avoidant behaviors and of the physiological reactivity. They furnish the impetus for the construction of the inner world, which is an indispensable tool in the management of ourselves, our bodies, and our environment. To paraphrase Freud's quotation used at the beginning of this article, there is a process in the inner world, stimulated by unconscious factors, that give rise to our view of the world and of our soul. The contents of this article-the ideas, the concepts, and the discourse itself-are a product of a continuing, evolving psychoanalytic way of thinking. The total of the analytic considerations gathered under the theory of trauma psychology could not be presented without the contributions of Freud, Hartmann, Rapaport, Erikson, Holt, Klein, Schafer, and others. We believe trauma psychology to be in its infancy, at a stage comparable to the stage of the libido theory at the time of the writing of The Interpretation

Adaptation, Psychological↗

PubMed2005

Intergenic transcription through a polycomb group response element counteracts silencing.

Polycomb group response elements (PREs) mediate the mitotic inheritance of gene expression programs and thus maintain determined cell fates. By default, PREs silence associated genes via the targeting of Polycomb group (PcG) complexes. Upon an activating signal, however, PREs recruit counteracting trithorax group (trxG) proteins, which in turn maintain target genes in a transcriptionally active state. Using a transgenic reporter system, we show that the switch from the silenced to the activated state of a PRE requires noncoding transcription. Continuous transcription through the PRE induced by an actin promoter prevents the establishment of PcG-mediated silencing. The maintenance of epigenetic activation requires transcription through the PRE to proceed at least until embryogenesis is completed. At the homeotic bithorax complex of Drosophila, intergenic PRE transcripts can be detected not only during embryogenesis, but also at late larval stages, suggesting that transcription through endogenous PREs is required continuously as an anti-silencing mechanism to prevent the access of repressive PcG complexes to the chromatin. Furthermore, all other PREs outside the homeotic complex we tested were found to be transcribed in the same tissue as the mRNA of the corresponding target gene, suggesting that anti-silencing by transcription is a fundamental aspect of the cellular memory system.

Animals↗

PubMedDate not supplied

Role of neurotrophic factors in adaptational processes of the nervous system.

Neurotrophic factors (NTF) are low-molecular-weight proteins which epigenetically determine neuron survival during embryogenesis and the maintenance of their morphofunctional properties in the adult organism. NTF are located in mesenchymal tissues and reach neuron bodies by means of retrograde axoplasmic transport in nerve fibers; in cell bodies, NTF increase anabolic activity, neurotransmitter synthesis, and structural protein production. Neuron cell bodies have two types of specialized receptors for binding the most common NTF, nerve growth factor (NGF). In the brain, NGF does not affect adrenergic neurons, as it does in the periphery, but acts on cholinergic neurons in the basal part of the forebrain. The forebrain plays the major role in the processes of learning, memory, and plasticity, i.e., in the entire complex of adaptational responses of the nervous system, and these may thus depend on the biological activities of substances, including NTF, in forebrain tissues. An experimental model was developed consisting of organotypic co-cultivation of rat hippocampus fragments with chick embryo dorsal root ganglia. This model was used to demonstrate that epileptiform activity in the hippocampus is associated with increases in NTF release, which can be regarded as an adaptive compensatory response to nerve cell damage occurring during convulsive activity.

Adaptation, Physiological↗

PubMed1998

Helper T cell differentiation is controlled by the cell cycle.

Helper T (Th) cell differentiation is highly regulated by cytokines but initiated by mitogens. By examining gene expression in discrete generations of dividing cells, we have delineated the relationship between proliferation and differentiation. Initial expression of IL-2 is cell cycle-independent, whereas effector cytokine expression is cell cycle-dependent. IFNgamma expression increases in frequency with successive cell cycles, while IL-4 expression requires three cell divisions. Cell cycle progression and cytokine signaling act in concert to relieve epigenetic repression and can be supplanted by agents that hyperacetylate histones and demethylate DNA. Terminally differentiated cells exhibit stable epigenetic modification and cell cycle-independent gene expression. These data reveal a novel mechanism governing Th cell fate that initially integrates proliferative and differentiative signals and subsequently maintains stability of the differentiated state.

Animals↗

PubMed1999

Neurocognitive impairments in schizophrenia: a piece of the epigenetic puzzle.

This paper is a review of studies examining the neurobehavioral antecedents of schizophrenia which flesh out neurodevelopmental models of schizophrenia by detailing the time course of the ontogeney of neurobehavioral impairments in schizophrenia. A follow back design was used to identify precursors of psychotic symptoms in children with a schizophrenic disorder. The vast majority of children with a schizophrenic disorder had significant developmental delays beginning early in life. For example, gross deficits in early language development were found in almost 80% of the schizophrenic children. Somewhat later in development impairments in fine motor and bi-manual coordination are noted. Some of these early developmental delays are transitory. For example, basic language skills are among the best preserved neurocognitive functions in children and adults with schizophrenia. The results of our cross-sectional neurocognitive studies suggest that children with schizophrenia suffer from limitations in the ability to engage in effortful cognitive processing or impairments in working memory. The links between these elementary neurocognitive impairments and the development of formal thought disorder as well as discourse deficits in children with a schizophrenic disorder will be discussed.

Adult↗

PubMed2000

Familial Creutzfeldt-Jakob disease: a neuropsychological case study.

The spectrum of neuropsychological features of familial Creutzfeldt-Jakob disease (CJD) have seldom been reported, possibly because of (a) the rarity of this hereditary form of prion disease; (b) frequent delays in diagnosis, and; (c) the typically rapid demise of the patient, which affords little opportunity for comprehensive testing or serial analysis. Here we describe the neurobehavioral characteristics of a 48-year-old right-handed male (JD) who presented with complaints of poor depth perception, unsteady gait, and unusual sensory experiences in his face and neck. JD was followed serially over the final 4 months of his 5-month illness. Immediately following hospital admission, he underwent a neuropsychological evaluation that revealed moderate to severe impairment of delayed (30-minute) verbal memory, tactual performance in his right hand, and word-finding ability. In contrast, other abilities that are commonly classified within the verbal, visuospatial, and memory domains showed minimal or no compromise. Parallel studies of electroencephalographic activity revealed diffuse slowing and, later, 1-Hz rhythmical discharges over the left hemisphere, and mild prominence of the lateral ventricles and cerebral sulci on magnetic resonance imaging. Autopsy revealed spongiform changes and reactive astrocytosis, and genetic testing demonstrated a codon 200 mutation in the prion protein gene. These findings indicate that CJD can result in clinical manifestations compatible with multifocal asymmetric cerebral involvement before more diffuse neurodegeneration ensues, providing a strong impetus for the study of additional cases. This long-term understanding can help to determine whether the multiple loci of clinical involvement are specified by genetic or epigenetic factors, or both.

Clinical Conference↗

PubMed2005

Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis.

Plant shoots are characterized by indeterminate growth resulting from the action of a population of stem cells in the shoot apical meristem (SAM). Indeterminacy within the SAM is specified in part by the class I knox homeobox genes. The myb domain proteins rough sheath2 (RS2) and ASYMMETRIC LEAVES1 (AS1) from maize (Zea mays) and Arabidopsis thaliana, respectively, are required to establish determinacy during leaf development. These proteins are part of a cellular memory system that in response to a stem cell-derived signal keeps knox genes in an off state during organogenesis. Here, we show that RS2/AS1 can form conserved protein complexes through interaction with the DNA binding factor ASYMMETRIC LEAVES2, a predicted RNA binding protein (RIK, for RS2-Interacting KH protein), and a homologue of the chromatin-remodeling protein HIRA. Partial loss of HIRA function in Arabidopsis results in developmental defects comparable to those of as1 and causes reactivation of knox genes in developing leaves, demonstrating a direct role for HIRA in knox gene repression and the establishment of determinacy during leaf formation. Our data suggest that RS2/AS1 and HIRA mediate the epigenetic silencing of knox genes, possibly by modulating chromatin structure. Components of this process are conserved in animals, suggesting the possibility that a similar epigenetic mechanism maintains determinacy during both plant and animal development.

Arabidopsis↗

PubMed2024

Increasing histone acetylation improves sociability and restores learning and memory in KAT6B-haploinsufficient mice.

Mutations in genes encoding chromatin modifiers are enriched among mutations causing intellectual disability. The continuing development of the brain postnatally, coupled with the inherent reversibility of chromatin modifications, may afford an opportunity for therapeutic intervention following a genetic diagnosis. Development of treatments requires an understanding of protein function and models of the disease. Here, we provide a mouse model of Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS) (OMIM 603736) and demonstrate proof-of-principle efficacy of postnatal treatment. SBBYSS results from heterozygous mutations in the KAT6B (MYST4/MORF/QFK) gene and is characterized by intellectual disability and autism-like behaviors. Using human cells carrying SBBYSS-specific KAT6B mutations and Kat6b heterozygous mice (Kat6b+/-), we showed that KAT6B deficiency caused a reduction in histone H3 lysine 9 acetylation. Kat6b+/- mice displayed learning, memory, and social deficits, mirroring SBBYSS individuals. Treatment with a histone deacetylase inhibitor, valproic acid, or an acetyl donor, acetyl-carnitine (ALCAR), elevated histone acetylation levels in the human cells with SBBYSS mutations and in brain and blood cells of Kat6b+/- mice and partially reversed gene expression changes in Kat6b+/- cortical neurons. Both compounds improved sociability in Kat6b+/- mice, and ALCAR treatment restored learning and memory. These data suggest that a subset of SBBYSS individuals may benefit from postnatal therapeutic interventions.

Animals↗

PubMedDate not supplied

Making scents of olfactory neurogenesis.

Olfaction was long considered to belong more to the realm of art than to that of science. As a result, how the brain perceives, discriminates, and recognizes odorant molecules is still a mystery. Recent progress has nonetheless been made at early stages of the olfactory pathway when olfactory studies entered into the molecular era to elucidate the first contact of an odor molecule with a receptor. Our group focuses on the analysis of odor information in the olfactory bulb, the first processing relay in the mammalian brain. Using this model, we are attempting to decipher the code for odorant information. Furthermore, the olfactory bulb also provides an attractive model to investigate neuronal proliferation, differentiation, migration, and neuronal death, processes involving an interplay between genetic and epigenetic influences. Finally, our goal is to explore the possible consequences of the olfactory bulb plasticity, in olfactory performance. For these purposes, we aim to combine morphological, electrophysiological and behavioral approaches to investigate: (1) how the olfactory bulb processes odor molecule information, (2) how neural precursors differentiate into olfactory bulb interneurons, (3) how these newly-generated neurons integrate into an operational neural network, (4) what role they play in the adult olfactory bulb, and (5) how are basic olfactory functions maintained in such a sensory system subjected to continuous renewal of a large percentage of its neuronal population. These questions should provide new fuel for the molecular and cellular bases of sensory perception and shed light onto cellular bases of learning and memory.

Animals↗

PubMed2026

Dysregulated adult hippocampal neurogenesis in major depressive disorder.

Major depressive disorder (MDD) is associated with reduced hippocampal volume, altered connectivity and negative memory bias, suggesting disrupted hippocampal plasticity. Dysregulated adult hippocampal neurogenesis is a potential contributor, but its relevance in humans and role in MDD remain unclear. Here we investigated the molecular basis of hippocampal dysfunction in nonmedicated individuals with MDD by integrating analyses of neurogenic trajectories, cell-type- and subfield-specific gene expression, chromatin accessibility and protein expression. We identify a neurogenic lineage in the adult human hippocampal subgranular zone and provide evidence for a stalled neurogenic process in MDD, associated with transcriptional regulation, stress-related reprogramming and interferon signaling across developmental stages. Excitatory and inhibitory neurons show dysregulation of transcription factor networks affecting cell states. Cellular stress, excitatory-inhibitory imbalance, impaired synaptic plasticity, reduced metabolic capacity and immune activation, underlie impaired neurogenesis and reduced hippocampus circuit plasticity. Findings indicate genetic and epigenetic regulation of gene expression in MDD, and overlapping pathogenetic mechanisms with autoimmune, neurodevelopmental and neurodegenerative diseases. This work provides a new understanding of the pathogenesis of hippocampus-dependent cognitive symptoms in MDD and suggests potential therapeutic targets.

Journal Article↗

PubMed2006

A short history of diagnostic tests for von Willebrand disease: in memory of Barry Firkin (1930 to 2001) and Ted Zimmerman (1937 to 1988).

By the end of the 1960s, von Willebrand disease (vWD) was accepted as a combined deficiency of factor (F) VIII coagulation and a plasma factor responsible for normal platelet adhesion. Just how these two functions related to each other was unclear, and the diagnostic tests available at the time were poorly reproducible, cumbersome, and unreliable. As a consequence, the condition was poorly delineated from other coagulation and platelet disorders. In the early 1970s, ristocetin-induced platelet aggregation was described and formed the basis of the first consistent and reliable test that quantified the platelet adhesive function missing in vWD. Immunoprecipitating techniques specific for the molecule missing in vWD were defined. The application of these technologies allowed a clearer understanding of the heterogeneity of vWD and continues to form a basis for the diagnosis of this condition. Concurrently, exploration of the structure and function of von Willebrand factor (vWF) has contributed greatly to the understanding of platelet physiology, ligand receptor interaction, and pathways of cellular interaction and activation. Despite all of the progress during the last 35 years, including extensive developments in the field of molecular biology and genetics of vWD, the diagnosis of this condition in many, if not most cases, remains controversial. The final plasma level of vWF is influenced substantially by epigenetic and environmental factors. This natural heterogeneity is further compounded by significant imprecision of existing tests. As a consequence, defining vWD on the basis of a variation from the normal range alone is more than likely to be incorrect. The high frequency of a positive bleeding disorder in the normal population does not assist discrimination. It has been suggested that the diagnosis of mild type 1 vWD be discarded because it does not exhibit consistent linkage to the VWF gene and does not predict bleeding.

Clinical Laboratory Techniques↗

PubMed2021

Evolution of DNA methylation in the human brain.

DNA methylation is a critical regulatory mechanism implicated in development, learning, memory, and disease in the human brain. Here we have elucidated DNA methylation changes during recent human brain evolution. We demonstrate dynamic evolutionary trajectories of DNA methylation in cell-type and cytosine-context specific manner. Specifically, DNA methylation in non-CG context, namely CH methylation, has increased (hypermethylation) in neuronal gene bodies during human brain evolution, contributing to human-specific down-regulation of genes and co-expression modules. The effects of CH hypermethylation is particularly pronounced in early development and neuronal subtypes. In contrast, DNA methylation in CG context shows pronounced reduction (hypomethylation) in human brains, notably in cis-regulatory regions, leading to upregulation of downstream genes. We show that the majority of differential CG methylation between neurons and oligodendrocytes originated before the divergence of hominoids and catarrhine monkeys, and harbors strong signal for genetic risk for schizophrenia. Remarkably, a substantial portion of differential CG methylation between neurons and oligodendrocytes emerged in the human lineage since the divergence from the chimpanzee lineage and carries significant genetic risk for schizophrenia. Therefore, recent epigenetic evolution of human cortex has shaped the cellular regulatory landscape and contributed to the increased vulnerability to neuropsychiatric diseases.

Animals↗