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Chromatin memory

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https://www.readbyqxmd.com/read/27897969/satb2-determines-mirna-expression-and-long-term-memory-in-the-adult-central-nervous-system
#1
Clemens Jaitner, Chethan Reddy, Andreas Abentung, Nigel Whittle, Dietmar Rieder, Andrea Delekate, Martin Korte, Gaurav Jain, Andre Fischer, Farahnaz Sananbenesi, Isabella Cera, Nicolas Singewald, Georg Dechant, Galina Apostolova
SATB2 is a risk locus for schizophrenia and encodes a DNA-binding protein that regulates higher-order chromatin configuration. In the adult brain Satb2 is almost exclusively expressed in pyramidal neurons of two brain regions important for memory formation, the cerebral cortex and the CA1-hippocampal field. Here we show that Satb2 is required for key hippocampal functions since deletion of Satb2 from the adult mouse forebrain prevents the stabilization of synaptic long-term potentiation and markedly impairs long-term fear and object discrimination memory...
November 29, 2016: ELife
https://www.readbyqxmd.com/read/27880914/neuronal-ctcf-is-necessary-for-basal-and-experience-dependent-gene-regulation-memory-formation-and-genomic-structure-of-bdnf-and-arc
#2
Dev Sharan Sams, Stefano Nardone, Dmitriy Getselter, Dana Raz, Moran Tal, Prudhvi Raj Rayi, Hanoch Kaphzan, Ofir Hakim, Evan Elliott
CCCTC-binding factor (CTCF) is an organizer of higher-order chromatin structure and regulates gene expression. Genetic studies have implicated mutations in CTCF in intellectual disabilities. However, the role of CTCF-mediated chromatin structure in learning and memory is unclear. We show that depletion of CTCF in postmitotic neurons, or depletion in the hippocampus of adult mice through viral-mediated knockout, induces deficits in learning and memory. These deficits in learning and memory at the beginning of adulthood are correlated with impaired long-term potentiation and reduced spine density, with no changes in basal synaptic transmission and dendritic morphogenesis and arborization...
November 22, 2016: Cell Reports
https://www.readbyqxmd.com/read/27876548/the-effects-of-replication-stress-on-s-phase-histone-management-and-epigenetic-memory
#3
REVIEW
Saša Šviković, Julian E Sale
When a cell divides it must not only accurately duplicate its genome but must also recapitulate its programme of gene expression. A significant body of evidence suggests that an important fraction of the information specifying the transcriptional programme of vertebrate cells is carried epigenetically by post-translational modifications of histone proteins. For such a system to operate, propagation of key histone marks must be coupled to replication such that they remain correctly associated with the underlying DNA sequence, despite the huge disruption to chromatin structure generated by unwinding the parental DNA strands...
November 19, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27863463/the-chip-seq-tools-and-web-server-a-resource-for-analyzing-chip-seq-and-other-types-of-genomic-data
#4
Giovanna Ambrosini, René Dreos, Sunil Kumar, Philipp Bucher
BACKGROUND: ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. RESULTS: Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware...
November 18, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27863245/epigenetic-memory-underlies-cell-autonomous-heterogeneous-behavior-of-hematopoietic-stem-cells
#5
Vionnie W C Yu, Rushdia Z Yusuf, Toshihiko Oki, Juwell Wu, Borja Saez, Xin Wang, Colleen Cook, Ninib Baryawno, Michael J Ziller, Eunjung Lee, Hongcang Gu, Alexander Meissner, Charles P Lin, Peter V Kharchenko, David T Scadden
Stem cells determine homeostasis and repair of many tissues and are increasingly recognized as functionally heterogeneous. To define the extent of-and molecular basis for-heterogeneity, we overlaid functional, transcriptional, and epigenetic attributes of hematopoietic stem cells (HSCs) at a clonal level using endogenous fluorescent tagging. Endogenous HSC had clone-specific functional attributes over time in vivo. The intra-clonal behaviors were highly stereotypic, conserved under the stress of transplantation, inflammation, and genotoxic injury, and associated with distinctive transcriptional, DNA methylation, and chromatin accessibility patterns...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27815505/transcription-factor-ets-2-acts-as-a-pre-induction-repressor-of-interleukin-2-il-2-transcription-in-naive-t-helper-lymphocytes
#6
Ioannis Panagoulias, Tassos Georgakopoulos, Ioanna Aggeletopoulou, Marios Agelopoulos, Dimitris Thanos, Athanasia Mouzaki
IL-2 is the first cytokine produced when naive T helper (Th) cells are activated and differentiate into dividing pre-Th0 proliferating precursors. IL-2 expression is blocked in naive, but not activated or memory Th cells, by the transcription factor Ets-2 that binds to the ARRE-2 element of the proximal IL-2 promoter. Ets-2 acts as an independent pre-induction repressor in naive Th cells and does not interact physically with the transcription factor NFAT that binds to the ARRE-2 element in activated Th cells...
November 3, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27807647/epigenetic-transcriptional-memory
#7
REVIEW
Agustina D'Urso, Jason H Brickner
Organisms alter gene expression to adapt to changes in environmental conditions such as temperature, nutrients, inflammatory signals, and stress (Gialitakis et al. in Mol Cell Biol 30:2046-2056, 2010; Conrath in Trends Plant Sci 16:524-531, 2011; Avramova in Plant J 83:149-159, 2015; Solé et al. in Curr Genet 61:299-308, 2015; Ho and Gasch in Curr Genet 61:503-511, 2015; Bevington et al. in EMBO J 35:515-535, 2016; Hilker et al. in Biol Rev Camb Philos Soc 91:1118-1133, 2016). In some cases, organisms can "remember" a previous environmental condition and adapt to that condition more rapidly in the future (Gems and Partridge 2008)...
November 2, 2016: Current Genetics
https://www.readbyqxmd.com/read/27803663/environmental-enrichment-modified-epigenetic-mechanisms-in-samp8-mouse-hippocampus-by-reducing-oxidative-stress-and-inflammaging-and-achieving-neuroprotection
#8
Christian Griñan-Ferré, Dolors Puigoriol-Illamola, Verónica Palomera-Ávalos, David Pérez-Cáceres, Júlia Companys-Alemany, Antonio Camins, Daniel Ortuño-Sahagún, M Teresa Rodrigo, Mercè Pallàs
With the increase in life expectancy, aging and age-related cognitive impairments are becoming one of the most important issues for human health. At the same time, it has been shown that epigenetic mechanisms are emerging as universally important factors in life expectancy. The Senescence Accelerated Mouse P8 (SAMP8) strain exhibits age-related deterioration evidenced in learning and memory abilities and is a useful model of neurodegenerative disease. In SAMP8, Environmental Enrichment (EE) increased DNA-methylation levels (5-mC) and reduced hydroxymethylation levels (5-hmC), as well as increased histone H3 and H4 acetylation levels...
2016: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/27789799/the-epigenetic-landscape-of-t-cell-exhaustion
#9
Debattama R Sen, James Kaminski, R Anthony Barnitz, Makoto Kurachi, Ulrike Gerdemann, Kathleen B Yates, Hsiao-Wei Tsao, Jernej Godec, Martin W LaFleur, Flavian D Brown, Pierre Tonnerre, Raymond T Chung, Damien C Tully, Todd M Allen, Nicole Frahm, Georg M Lauer, E John Wherry, Nir Yosef, W Nicholas Haining
Exhausted T cells in cancer and chronic viral infection express distinctive patterns of genes, including sustained expression of programmed cell death protein 1 (PD-1). However, the regulation of gene expression in exhausted T cells is poorly understood. Here, we define the accessible chromatin landscape in exhausted CD8(+) T cells and show that it is distinct from functional memory CD8(+) T cells. Exhausted CD8(+) T cells in humans and a mouse model of chronic viral infection acquire a state-specific epigenetic landscape organized into functional modules of enhancers...
October 27, 2016: Science
https://www.readbyqxmd.com/read/27780875/molecular-mechanisms-of-innate-memory-and-tolerance-to-lps
#10
REVIEW
John J Seeley, Sankar Ghosh
LPS is a potent trigger of macrophage-mediated inflammation. However, prolonged exposure to LPS induces a state of tolerance that reprograms the inflammatory response, resulting in reduced inflammatory cytokine production in vitro and in vivo. Recent evidence suggests that LPS tolerance also increases the expression of a subset of genes that may protect animals from systemic infection while they are in the tolerized state. However, a molecular basis for these selective changes in inflammatory gene expression during LPS tolerance has remained elusive...
October 25, 2016: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/27766083/behavioral-neuroadaptation-to-alcohol-from-glucocorticoids-to-histone-acetylation
#11
Nicole Mons, Daniel Beracochea
A prime mechanism that contributes to the development and maintenance of alcoholism is the dysregulation of the hypothalamic-pituitary-adrenal axis activity and the release of glucocorticoids (cortisol in humans and primates, corticosterone in rodents) from the adrenal glands. In the brain, sustained, local elevation of glucocorticoid concentration even long after cessation of chronic alcohol consumption compromises functional integrity of a circuit, including the prefrontal cortex (PFC), the hippocampus (HPC), and the amygdala (AMG)...
2016: Frontiers in Psychiatry
https://www.readbyqxmd.com/read/27764097/dynamic-nucleosome-movement-provides-structural-information-of-topological-chromatin-domains-in-living-human-cells
#12
Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi
The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27727234/genome-wide-chromatin-and-gene-expression-profiling-during-memory-formation-and-maintenance-in-adult-mice
#13
Tonatiuh Pena Centeno, Orr Shomroni, Magali Hennion, Rashi Halder, Ramon Vidal, Raza-Ur Rahman, Stefan Bonn
Recent evidence suggests that the formation and maintenance of memory requires epigenetic changes. In an effort to understand the spatio-temporal extent of learning and memory-related epigenetic changes we have charted genome-wide histone and DNA methylation profiles, in two different brain regions, two cell types, and three time-points, before and after learning. In this data descriptor we provide detailed information on data generation, give insights into the rationale of experiments, highlight necessary steps to assess data quality, offer guidelines for future use of the data and supply ready-to-use code to replicate the analysis results...
October 11, 2016: Scientific Data
https://www.readbyqxmd.com/read/27713816/cgg-repeat-dynamics-and-fmr1-gene-silencing-in-fragile-x-syndrome-stem-cells-and-stem-cell-derived-neurons
#14
Yifan Zhou, Daman Kumari, Nicholas Sciascia, Karen Usdin
BACKGROUND: Fragile X syndrome (FXS), a common cause of intellectual disability and autism, results from the expansion of a CGG-repeat tract in the 5' untranslated region of the FMR1 gene to >200 repeats. Such expanded alleles, known as full mutation (FM) alleles, are epigenetically silenced in differentiated cells thus resulting in the loss of FMRP, a protein important for learning and memory. The timing of repeat expansion and FMR1 gene silencing is controversial. METHODS: We monitored the repeat size and methylation status of FMR1 alleles with expanded CGG repeats in patient-derived induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) that were grown for extended period of time either as stem cells or differentiated into neurons...
2016: Molecular Autism
https://www.readbyqxmd.com/read/27705745/rybp-stimulates-prc1-to-shape-chromatin-based-communication-between-polycomb-repressive-complexes
#15
Nathan R Rose, Hamish W King, Neil P Blackledge, Nadezda A Fursova, Katherine Ji Ember, Roman Fischer, Benedikt M Kessler, Robert J Klose
Polycomb group (PcG) proteins function as chromatin-based transcriptional repressors that are essential for normal gene regulation during development. However, how these systems function to achieve transcriptional regulation remains very poorly understood. Here, we discover that the histone H2AK119 E3 ubiquitin ligase activity of Polycomb repressive complex 1 (PRC1) is defined by the composition of its catalytic subunits and is highly regulated by RYBP/YAF2-dependent stimulation. In mouse embryonic stem cells, RYBP plays a central role in shaping H2AK119 mono-ubiquitylation at PcG targets and underpins an activity-based communication between PRC1 and Polycomb repressive complex 2 (PRC2) which is required for normal histone H3 lysine 27 trimethylation (H3K27me3)...
October 5, 2016: ELife
https://www.readbyqxmd.com/read/27684825/atorvastatin-inhibits-insulin-synthesis-by-inhibiting-the-ras-raf-erk-creb-pathway-in-ins-1-cells
#16
Hongxi Sun, Yu Li, Bei Sun, Ningning Hou, Juhong Yang, Miaoyan Zheng, Jie Xu, Jingyu Wang, Yi Zhang, Xianwei Zeng, Chunyan Shan, Bai Chang, Liming Chen, Baocheng Chang
BACKROUND: Type 2 diabetes has become a global epidemic disease. Atorvastatin has become a cornerstone in the prevention and treatment of atherosclerosis. However, increasing evidence showed that statins can dose-dependently increase the risk of diabetes mellitus. The mechanism is not clear. OBJECTIVE: The Ras complex pathway (Ras/Raf/extracellular signal-regulated kinase [ERK]/cAMP response element-binding protein [CREB]) is the major pathway that regulates the gene transcription...
September 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27680998/arabidopsis-forgetter1-mediates-stress-induced-chromatin-memory-through-nucleosome-remodeling
#17
Krzysztof Brzezinka, Simone Altmann, Hjördis Czesnick, Philippe Nicolas, Michal Gorka, Eileen Benke, Tina Kabelitz, Felix Jähne, Alexander Graf, Christian Kappel, Isabel Bäurle
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion...
September 28, 2016: ELife
https://www.readbyqxmd.com/read/27669308/making-sense-of-the-tangle-insights-into-chromatin-folding-and-gene-regulation
#18
REVIEW
Ill-Min Chung, Sarada Ketharnathan, Seung-Hyun Kim, Muthu Thiruvengadam, Mari Kavitha Rani, Govindasamy Rajakumar
Proximity ligation assays such as circularized chromosome conformation capture and high-throughput chromosome capture assays have shed light on the structural organization of the interphase genome. Functional topologically associating domains (TADs) that constitute the building blocks of genomic organization are disrupted and reconstructed during the cell cycle. Epigenetic memory, as well as the sequence of chromosomes, regulate TAD reconstitution. Sub-TAD domains that are invariant across cell types have been identified, and contacts between these domains, rather than looping, are speculated to drive chromatin folding...
2016: Genes
https://www.readbyqxmd.com/read/27642047/real-time-tracking-of-parental-histones-reveals-their-contribution-to-chromatin-integrity-following-dna-damage
#19
Salomé Adam, Juliette Dabin, Odile Chevallier, Olivier Leroy, Céline Baldeyron, Armelle Corpet, Patrick Lomonte, Olivier Renaud, Geneviève Almouzni, Sophie E Polo
Chromatin integrity is critical for cell function and identity but is challenged by DNA damage. To understand how chromatin architecture and the information that it conveys are preserved or altered following genotoxic stress, we established a system for real-time tracking of parental histones, which characterize the pre-damage chromatin state. Focusing on histone H3 dynamics after local UVC irradiation in human cells, we demonstrate that parental histones rapidly redistribute around damaged regions by a dual mechanism combining chromatin opening and histone mobilization on chromatin...
October 6, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27631330/accelerated-reduction-of-serum-thyroxine-and-hippocampal-histone-acetylation-links-to-exacerbation-of-spatial-memory-impairment-in-aged-cd-1-mice-pubertally-exposed-to-bisphenol-a
#20
Wei Jiang, Lei Cao, Fang Wang, Hai Ge, Peng-Chao Wu, Xue-Wei Li, Gui-Hai Chen
Age-related cognitive decline has been associated with changes in endogenous hormones and epigenetic modification of chromatin, including histone acetylation. Developmental exposure to endocrine disrupting chemicals, such as bisphenol-A (BPA) that produces endocrine disruption and epigenetic changes, may be a risk factor for accelerating cognitive deficits during aging. Thus, we exposed CD-1 mice to BPA (0, 1, and 100 mg/l BPA in the drinking water) orally during puberty (from postnatal days 28 to 56) and investigated whether pubertal BPA exposure exacerbates the age-related impairment of spatial cognition in old age (18 months old) and whether serum sex and thyroid hormones or hippocampal histone acetylation (H3K9ac and H4K8ac) are associated with cognitive effects...
September 9, 2016: Age (2005-)
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