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Chromatin memory

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https://www.readbyqxmd.com/read/28916764/rapid-and-reversible-epigenome-editing-by-endogenous-chromatin-regulators
#1
Simon M G Braun, Jacob G Kirkland, Emma J Chory, Dylan Husmann, Joseph P Calarco, Gerald R Crabtree
Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells...
September 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28910569/hierarchical-recruitment-of-polycomb-complexes-revisited
#2
Eshagh Dorafshan, Tatyana G Kahn, Yuri B Schwartz
Polycomb Group (PcG) proteins epigenetically repress key developmental genes and thereby control alternative cell fates. PcG proteins act as complexes that can modify histones and these histone modifications play a role in transmitting the "memory" of the repressed state as cells divide. Here we consider mainstream models that link histone modifications to hierarchical recruitment of PcG complexes and compare them to results of a direct test of interdependence between PcG complexes for recruitment to Drosophila genes...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28904110/the-chromatin-accessibility-signature-of-human-immune-aging-stems-from-cd8-t-cells
#3
Duygu Ucar, Eladio J Márquez, Cheng-Han Chung, Radu Marches, Robert J Rossi, Asli Uyar, Te-Chia Wu, Joshy George, Michael L Stitzel, A Karolina Palucka, George A Kuchel, Jacques Banchereau
Aging is linked to deficiencies in immune responses and increased systemic inflammation. To unravel the regulatory programs behind these changes, we applied systems immunology approaches and profiled chromatin accessibility and the transcriptome in PBMCs and purified monocytes, B cells, and T cells. Analysis of samples from 77 young and elderly donors revealed a novel and robust aging signature in PBMCs, with simultaneous systematic chromatin closing at promoters and enhancers associated with T cell signaling and a potentially stochastic chromatin opening mostly found at quiescent and repressed sites...
September 13, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28890149/distinct-roles-for-the-deacetylase-domain-of-hdac3-in-the-hippocampus-and-medial-prefrontal-cortex-in-the-formation-and-extinction-of-memory
#4
Yasaman Alaghband, Janine L Kwapis, Alberto J López, André O White, Osasumwen V Aimiuwu, Amni Al-Kachak, Kasuni K Bodinayake, Nicole C Oparaugo, Richard Dang, Mariam Astarabadi, Dina P Matheos, Marcelo A Wood
Histone deacetylases (HDACs) are chromatin modifying enzymes that have been implicated as powerful negative regulators of memory processes. HDAC3 has been shown to play a pivotal role in long-term memory for object location as well as the extinction of cocaine-associated memory, but it is unclear whether this function depends on the deacetylase domain of HDAC3. Here, we tested whether the deacetylase domain of HDAC3 has a role in object location memory formation as well as the formation and extinction of cocaine-associated memories...
September 7, 2017: Neurobiology of Learning and Memory
https://www.readbyqxmd.com/read/28881969/chromatin-accessibility-prediction-via-convolutional-long-short-term-memory-networks-with-k-mer-embedding
#5
Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang
Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28863321/the-role-of-necroptosis-in-status-epilepticus-induced-brain-injury-in-juvenile-rats
#6
Qianyun Cai, Jing Gan, Rong Luo, Yi Qu, Shiping Li, Chaomin Wan, Dezhi Mu
PURPOSE: To study the role of necroptosis in status epilepticus (SE)-induced injury in the developing brain and the possible associations of necroptosis with epileptogenesis and cognitive dysfunction. METHODS: The lithium-pilocarpine epilepsy model was reproduced in male rats at postnatal day 25. Propidium iodide (PI) staining was used to detect cell death after SE. Transmission electron microscopy (TEM) was performed to observe morphological changes in injured neurons...
August 29, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/28851627/charting-the-dynamic-epigenome-during-b-cell-development
#7
REVIEW
Jose I Martin-Subero, Christopher C Oakes
The epigenetic landscape undergoes a widespread modulation during embryonic development and cell differentiation. Within the hematopoietic system, B cells are perhaps the cell lineage with a more dynamic DNA methylome during their maturation process, which involves approximately one third of all the CpG sites of the genome. Although each B-cell maturation step displays its own DNA methylation fingerprint, the DNA methylome is more extensively modified in particular maturation transitions. These changes are gradually accumulated in specific chromatin environments as cell differentiation progresses and reflect different features and functional states of B cells...
August 26, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28851397/nf-%C3%AE%C2%BAb-regulated-microrna-574-5p-underlies-synaptic-and-cognitive-impairment-in-response-to-atmospheric-pm2-5-aspiration
#8
Tingting Ku, Ben Li, Rui Gao, Yingying Zhang, Wei Yan, Xiaotong Ji, Guangke Li, Nan Sang
BACKGROUND: PM2.5 (particulate matter ≤ 2.5 μm) is one of the leading environmental risk factors for the global burden of disease. Whereas increasing evidence has linked the adverse roles of PM2.5 with cardiovascular and respiratory diseases, limited but growing emerging evidence suggests that PM2.5 exposure can affect the nervous system, causing neuroinflammation, synaptic dysfunction and cognitive deterioration. However, the molecular mechanisms underlying the synaptic and cognitive deficits elicited by PM2...
August 29, 2017: Particle and Fibre Toxicology
https://www.readbyqxmd.com/read/28835928/impaired-dna-replication-derepresses-chromatin-and-generates-a-transgenerationally-inherited-epigenetic-memory
#9
Adam Klosin, Kadri Reis, Cristina Hidalgo-Carcedo, Eduard Casas, Tanya Vavouri, Ben Lehner
Impaired DNA replication is a hallmark of cancer and a cause of genomic instability. We report that, in addition to causing genetic change, impaired DNA replication during embryonic development can have major epigenetic consequences for a genome. In a genome-wide screen, we identified impaired DNA replication as a cause of increased expression from a repressed transgene in Caenorhabditis elegans. The acquired expression state behaved as an "epiallele," being inherited for multiple generations before fully resetting...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28818969/distinct-phases-of-polycomb-silencing-to-hold-epigenetic-memory-of-cold-in-arabidopsis
#10
Hongchun Yang, Scott Berry, Tjelvar S G Olsson, Matthew Hartley, Martin Howard, Caroline Dean
Gene silencing by Polycomb complexes is central to eukaryotic development. Cold-induced epigenetic repression of FLOWERING LOCUS C (FLC) in the plant Arabidopsis provides an opportunity to study initiation and maintenance of Polycomb silencing. Here, we show that a subset of Polycomb Repressive Complex 2 factors nucleate silencing in a small region within FLC, locally increasing H3K27me3 levels. This nucleation confers a silenced state that is metastably inherited, with memory held in the local chromatin. Metastable memory is then converted to stable epigenetic silencing through separate Polycomb factors, which spread across the locus after cold to enlarge the domain containing H3K27me3...
August 17, 2017: Science
https://www.readbyqxmd.com/read/28804462/heat-acclimation-mediated-cross-tolerance-origins-in-within-life-epigenetics
#11
REVIEW
Michal Horowitz
The primary outcome of heat acclimation is increased thermotolerance, which stems from enhancement of innate cytoprotective pathways. These pathways produce "ON CALL" molecules that can combat stressors to which the body has never been exposed, via cross-tolerance mechanisms (heat acclimation-mediated cross-tolerance-HACT). The foundation of HACT lies in the sharing of generic stress signaling, combined with tissue/organ- specific protective responses. HACT becomes apparent when acclimatory homeostasis is achieved, lasts for several weeks, and has a memory...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28799233/stochastics-of-cellular-differentiation-explained-by-epigenetics-the-case-of-t-cell-differentiation-and-functional-plasticity
#12
REVIEW
Jaydeep Bhat, Johannes Helmuth, Guranda Chitadze, Léonce Kouakanou, Christian Peters, Martin Vingron, Ole Ammerpohl, Dieter Kabelitz
Epigenetic marks including histone modifications and DNA methylation are associated to the regulation of gene expression and activity. In addition, an increasing number of non-coding RNAs with regulatory activity on gene expression have been identified. Alongside, technological advancements allow for the analysis of these mechanisms with high resolution - up to the single-cell level. For instance, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) simultaneously probes for chromatin accessibility and nucleosome positioning...
August 10, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28771884/hmgb2-expression-is-associated-with-transition-from-a-quiescent-to-an-activated-state-of-adult-neural-stem-cells
#13
Ayaka Kimura, Taito Matsuda, Atsuhiko Sakai, Naoya Murao, Kinichi Nakashima
BACKGROUND: Although quiescent neural stem cells (NSCs) in the adult hippocampus proliferate in response to neurogenic stimuli and subsequently give rise to new neurons continuously throughout life, misregulation of NSCs in pathological conditions, including aging, leads to the impairment of learning and memory. High mobility group B family 1 (HMGB1) and HMGB2, HMG family proteins that function as transcriptional activators through the modulation of chromatin structure, have been assumed to play some role in the regulation of adult NSCs; however, their precise functions and even expression patterns in the adult hippocampus remain elusive...
August 2, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28771465/ebv-epigenetically-suppresses-the-b-cell-to-plasma-cell-differentiation-pathway-while-establishing-long-term-latency
#14
Christine T Styles, Quentin Bazot, Gillian A Parker, Robert E White, Kostas Paschos, Martin J Allday
Mature human B cells infected by Epstein-Barr virus (EBV) become activated, grow, and proliferate. If the cells are infected ex vivo, they are transformed into continuously proliferating lymphoblastoid cell lines (LCLs) that carry EBV DNA as extra-chromosomal episomes, express 9 latency-associated EBV proteins, and phenotypically resemble antigen-activated B-blasts. In vivo similar B-blasts can differentiate to become memory B cells (MBC), in which EBV persistence is established. Three related latency-associated viral proteins EBNA3A, EBNA3B, and EBNA3C are transcription factors that regulate a multitude of cellular genes...
August 2017: PLoS Biology
https://www.readbyqxmd.com/read/28764817/the-rpmi-1640-vitamin-mixture-promotes-bovine-blastocyst-development-in-vitro-and-downregulates-gene-expression-of-txnip-with-epigenetic-modification-of-associated-histones
#15
S Ikeda, M Sugimoto, S Kume
Diverse environmental conditions surrounding preimplantation embryos, including available nutrients, affect their metabolism and development in both short- and long-term manner. Thioredoxin-interacting protein (TXNIP) is a possible marker for preimplantation stress that is implicated in in vitro fertilization- (IVF) induced long-term DOHaD effects. B vitamins, as participants in one-carbon metabolism, may affect preimplantation embryos by epigenetic alterations of metabolically and developmentally important genes...
August 2, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28704368/mouse-models-of-17q21-31-microdeletion-and-microduplication-syndromes-highlight-the-importance-of-kansl1-for-cognition
#16
Thomas Arbogast, Giovanni Iacono, Claire Chevalier, Nurudeen O Afinowi, Xander Houbaert, Matthijs C van Eede, Christine Laliberte, Marie-Christine Birling, Katrin Linda, Hamid Meziane, Mohammed Selloum, Tania Sorg, Nael Nadif Kasri, David A Koolen, Henk G Stunnenberg, R Mark Henkelman, Maksym Kopanitsa, Yann Humeau, Bert B A De Vries, Yann Herault
Koolen-de Vries syndrome (KdVS) is a multi-system disorder characterized by intellectual disability, friendly behavior, and congenital malformations. The syndrome is caused either by microdeletions in the 17q21.31 chromosomal region or by variants in the KANSL1 gene. The reciprocal 17q21.31 microduplication syndrome is associated with psychomotor delay, and reduced social interaction. To investigate the pathophysiology of 17q21.31 microdeletion and microduplication syndromes, we generated three mouse models: 1) the deletion (Del/+); or 2) the reciprocal duplication (Dup/+) of the 17q21...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28702178/the-development-prospection-of-hdac-inhibitors-as-a-potential-therapeutic-direction-in-alzheimer-s-disease
#17
REVIEW
Shuang-Shuang Yang, Rui Zhang, Gang Wang, Yong-Fang Zhang
Alzheimer's disease (AD) is a chronic neurodegenerative disease, which is associated with learning and memory impairment in the elderly. Recent studies have found that treating AD in the way of chromatin remodeling via histone acetylation is a promising therapeutic regimen. In a number of recent studies, inhibitors of histone deacetylase (HDACs) have been found to be a novel promising therapeutic agents for neurological disorders, particularly for AD and other neurodegenerative diseases. Although HDAC inhibitors have the ability to ameliorate cognitive impairment, successful treatments in the classic AD animal model are rarely translated into clinical trials...
2017: Translational Neurodegeneration
https://www.readbyqxmd.com/read/28701956/administration-of-a-histone-deacetylase-inhibitor-into-the-basolateral-amygdala-enhances-memory-consolidation-delays-extinction-and-increases-hippocampal-bdnf-levels
#18
Fernanda E Valiati, Mailton Vasconcelos, Martina Lichtenfels, Fernanda S Petry, Rosa M M de Almeida, Gilberto Schwartsmann, Nadja Schröder, Caroline B de Farias, Rafael Roesler
Gene expression related to the formation and modification of memories is regulated epigenetically by chromatin remodeling through histone acetylation. Memory formation and extinction can be enhanced by treatment with inhibitors of histone deacetylases (HDACs). The basolateral amygdala (BLA) is a brain area critically involved in regulating memory for inhibitory avoidance (IA). However, previous studies have not examined the effects of HDAC inhibition in the amygdala on memory for IA. Here we show that infusion of an HDAC inhibitor (HDACi), trichostatin A (TSA), into the BLA, enhanced consolidation of IA memory in rats when given at 1...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28681984/brd4-promotes-gastric-cancer-progression-through-the-transcriptional-and-epigenetic-regulation-of-c-myc
#19
Mingchen Ba, Hui Long, Zhaofei Yan, Shuai Wang, Yinbing Wu, Yinuo Tu, Yuanfeng Gong, Shuzhong Cui
Although the significance of BRD4 in the epigenetic memory and cancer genesis has been intensively investigated, little is known about its function and potential roles during the generation and progression of gastric cancer. We report here that BRD4 increases the proliferation and represses the apoptosis of gastric cancer cells through activating c-MYC via transcriptional and epigenetic regulation mechanisms. Expression analyses in both small and large cohort of sample show that BRD4 is highly expressed in gastric cancer tissues/cells when compared with the adjacent non-tumor tissues/normal cells...
July 6, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28670349/epigenetic-mechanisms-during-ageing-and-neurogenesis-as-novel-therapeutic-avenues-in-human-brain-disorders
#20
REVIEW
Raúl Delgado-Morales, Roberto Carlos Agís-Balboa, Manel Esteller, María Berdasco
Ageing is the main risk factor for human neurological disorders. Among the diverse molecular pathways that govern ageing, epigenetics can guide age-associated decline in part by regulating gene expression and also through the modulation of genomic instability and high-order chromatin architecture. Epigenetic mechanisms are involved in the regulation of neural differentiation as well as in functional processes related to memory consolidation, learning or cognition during healthy lifespan. On the other side of the coin, many neurodegenerative diseases are associated with epigenetic dysregulation...
2017: Clinical Epigenetics
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