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Chromatin memory

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https://www.readbyqxmd.com/read/28105774/stiffness-controlled-thermoresponsive-hydrogels-for-cell-harvesting-with-sustained-mechanical-memory
#1
Xingliang Fan, Lu Zhu, Ke Wang, Bingjie Wang, Yaozu Wu, Wei Xie, Chengyu Huang, Barbara Pui Chan, Yanan Du
Most mechanobiological investigations focused on in situ mechanical regulation of cells on stiffness-controlled substrates with few downstream applications, as it is still challenging to harvest and expand mechanically primed cells by enzymatic digestion (e.g., trypsin) without interrupting cellular mechanical memory between passages. This study develops thermoresponsive hydrogels with controllable stiffness to generate mechanically primed cells with intact mechanical memory for augmented wound healing. No significant cellular property alteration of the fibroblasts primed on thermoresponsive hydrogels with varied stiffness has been observed through thermoresponsive harvesting...
January 20, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28097824/mechanisms-of-metabolic-memory-and-renal-hypoxia-as-a-therapeutic-target-in-diabetic-kidney-disease
#2
REVIEW
Yosuke Hirakawa, Tetsuhiro Tanaka, Masaomi Nangaku
Diabetic kidney disease (DKD) is a worldwide public health problem. The definition of DKD is being under discussion. Although the term DKD was originally defined as "kidney disease specific to diabetes", DKD frequently means chronic kidney disease (CKD) with diabetes mellitus and includes not only classical diabetic nephropathy, but also kidney dysfunction due to nephrosclerosis and other causes. Metabolic memory plays a crucial role in the progression of various complications of diabetes, including DKD. The mechanisms of metabolic memory in DKD are supposed to include advanced glycation end products, DNA methylation, histone modifications, and non-coding RNA including microRNA...
January 17, 2017: Journal of Diabetes Investigation
https://www.readbyqxmd.com/read/28093507/mosaic-expression-of-atrx-in-the-central-nervous-system-causes-memory-deficits
#3
Renee J Tamming, Jennifer R Siu, Yan Jiang, Marco A M Prado, Frank Beier, Nathalie G Bérubé
The rapid modulation of chromatin organization is thought to play a critical role in cognitive processes such as memory consolidation. This is supported in part by the dysregulation of many chromatin remodeling proteins in neurodevelopmental and psychiatric disorders. A key example is ATRX, an X-linked gene commonly mutated in individuals with syndromic and non-syndromic intellectual disability (ID). The consequences of Atrx inactivation on learning and memory have been difficult to evaluate due to the early lethality of hemizygous-null animals...
January 12, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28076781/crtc1-nuclear-translocation-following-learning-modulates-memory-strength-via-exchange-of-chromatin-remodeling-complexes-on-the-fgf1-gene
#4
Shusaku Uchida, Brett J W Teubner, Charles Hevi, Kumiko Hara, Ayumi Kobayashi, Rutu M Dave, Tatsushi Shintaku, Pattaporn Jaikhan, Hirotaka Yamagata, Takayoshi Suzuki, Yoshifumi Watanabe, Stanislav S Zakharenko, Gleb P Shumyatsky
Memory is formed by synapse-to-nucleus communication that leads to regulation of gene transcription, but the identity and organizational logic of signaling pathways involved in this communication remain unclear. Here we find that the transcription cofactor CRTC1 is a critical determinant of sustained gene transcription and memory strength in the hippocampus. Following associative learning, synaptically localized CRTC1 is translocated to the nucleus and regulates Fgf1b transcription in an activity-dependent manner...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28071704/high-fat-diet-induced-changes-of-mouse-hepatic-transcription-and-enhancer-activity-can-be-reversed-by-subsequent-weight-loss
#5
Majken Siersbæk, Lyuba Varticovski, Shutong Yang, Songjoon Baek, Ronni Nielsen, Susanne Mandrup, Gordon L Hager, Jay H Chung, Lars Grøntved
Epigenetic factors have been suggested to play an important role in metabolic memory by trapping and maintaining initial metabolic changes within the transcriptional regulatory machinery. In this study we fed mice a high fat diet (HFD) for seven weeks followed by additional five weeks of chow, to identify HFD-mediated changes to the hepatic transcriptional program that may persist after weight loss. Mice fed a HFD displayed increased fasting insulin levels, hepatosteatosis and major changes in hepatic gene transcription associated with modulation of H3K27Ac at enhancers, but no significant changes in chromatin accessibility, indicating that HFD-regulated gene transcription is primarily controlled by modulating the activity of pre-established enhancers...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28057215/the-role-of-epigenetic-regulation-in-transcriptional-memory-in-the-immune-system
#6
A M Woodworth, A F Holloway
The immune system is exquisitely poised to identify, respond to, and eradicate pathogens from the body, as well as to produce a more rapid and augmented response to a subsequent encounter with the pathogen. These cellular responses rely on the highly coordinated and rapid activation of gene expression programs as well as the ability of the cell to retain a memory of the initial gene response. It is clear that chromatin structure and epigenetic mechanisms play a crucial role in determining these gene responses, and in fact the immune system has proved an instructive model for investigating the multifaceted mechanisms through which the chromatin landscape contributes to gene expression programs...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28057214/chromatin-remodeling-and-plant-immunity
#7
W Chen, Q Zhu, Y Liu, Q Zhang
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28045584/epigenetic-countermarks-in-mitotic-chromosome-condensation
#8
Karel H M van Wely, Carmen Mora Gallardo, Kendra R Vann, Tatiana G Kutateladze
Mitosis in metazoans is characterized by abundant phosphorylation of histone H3 and involves the recruitment of condensin complexes to chromatin. The relationship between the 2 phenomena and their respective contributions to chromosome condensation in vivo remain poorly understood. Recent studies have shown that H3T3 phosphorylation decreases binding of histone readers to methylated H3K4 in vitro and is essential to displace the corresponding proteins from mitotic chromatin in vivo. Together with previous observations, these data provide further evidence for a role of mitotic histone H3 phosphorylation in blocking transcriptional programs or preserving the 'memory' PTMs...
January 3, 2017: Nucleus
https://www.readbyqxmd.com/read/28026028/chromatin-priming-elements-establish-immunological-memory-in-t-cells-without-activating-transcription-t-cell-memory-is-maintained-by-dna-elements-which-stably-prime-inducible-genes-without-activating-steady-state-transcription
#9
Sarah L Bevington, Pierre Cauchy, Peter N Cockerill
We have identified a simple epigenetic mechanism underlying the establishment and maintenance of immunological memory in T cells. By studying the transcriptional regulation of inducible genes we found that a single cycle of activation of inducible factors is sufficient to initiate stable binding of pre-existing transcription factors to thousands of newly activated distal regulatory elements within inducible genes. These events lead to the creation of islands of active chromatin encompassing nearby enhancers, thereby supporting the accelerated activation of inducible genes, without changing steady state levels of transcription in memory T cells...
December 27, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28024185/in-the-loop-how-chromatin-topology-links-genome-structure-to-function-in-mechanisms-underlying-learning-and-memory
#10
REVIEW
L Ashley Watson, Li-Huei Tsai
Different aspects of learning, memory, and cognition are regulated by epigenetic mechanisms such as covalent DNA modifications and histone post-translational modifications. More recently, the modulation of chromatin architecture and nuclear organization is emerging as a key factor in dynamic transcriptional regulation of the post-mitotic neuron. For instance, neuronal activity induces relocalization of gene loci to 'transcription factories', and specific enhancer-promoter looping contacts allow for precise transcriptional regulation...
December 23, 2016: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28018147/receptor-signaling-directs-global-recruitment-of-pre-existing-transcription-factors-to-inducible-elements
#11
REVIEW
Peter N Cockerill
Gene expression programs are largely regulated by the tissue-specific expression of lineage-defining transcription factors or by the inducible expression of transcription factors in response to specific stimuli. Here I will review our own work over the last 20 years to show how specific activation signals also lead to the wide-spread re-distribution of pre-existing constitutive transcription factors to sites undergoing chromatin reorganization. I will summarize studies showing that activation of kinase signaling pathways creates open chromatin regions that recruit pre-existing factors which were previously unable to bind to closed chromatin...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/28018145/epigenetics-of-renal-development-and-disease
#12
REVIEW
Sylvia A Hilliard, Samir S El-Dahr
An understanding of epigenetics is indispensable to our understanding of gene regulation under normal and pathological states. This knowledge will help with designing better therapeutic approaches in regenerative tissue medicine. Epigenetics allows us to parse out the mechanisms by which transcriptional regulators gain access to specific gene loci thereby imprinting epigenetic information affecting chromatin function. This epigenetic memory forms the basis of cell lineage specification in multicellular organisms...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/28004446/is-h3k4me3-instructive-for-transcription-activation
#13
Françoise S Howe, Harry Fischl, Struan C Murray, Jane Mellor
Tri-methylation of lysine 4 on histone H3 (H3K4me3) is a near-universal chromatin modification at the transcription start site of active genes in eukaryotes from yeast to man and its levels reflect the amount of transcription. Because of this association, H3K4me3 is often described as an 'activating' histone modification and assumed to have an instructive role in the transcription of genes, but the field is lacking a conserved mechanism to support this view. The overwhelming finding from genome-wide studies is that actually very little transcription changes upon removal of most H3K4me3 under steady-state or dynamically changing conditions, including at mammalian CpG island promoters...
January 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27999180/a-ketogenic-diet-rescues-hippocampal-memory-defects-in-a-mouse-model-of-kabuki-syndrome
#14
Joel S Benjamin, Genay O Pilarowski, Giovanni A Carosso, Li Zhang, David L Huso, Loyal A Goff, Hilary J Vernon, Kasper D Hansen, Hans T Bjornsson
Kabuki syndrome is a Mendelian intellectual disability syndrome caused by mutations in either of two genes (KMT2D and KDM6A) involved in chromatin accessibility. We previously showed that an agent that promotes chromatin opening, the histone deacetylase inhibitor (HDACi) AR-42, ameliorates the deficiency of adult neurogenesis in the granule cell layer of the dentate gyrus and rescues hippocampal memory defects in a mouse model of Kabuki syndrome (Kmt2d(+/βGeo)). Unlike a drug, a dietary intervention could be quickly transitioned to the clinic...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27986499/targeting-chromatin-aging-the-epigenetic-impact-of-longevity-associated-interventions
#15
Adam E Field, Peter D Adams
A rapidly growing body of evidence has shown that chromatin undergoes radical alterations as an organism ages, but how these changes relate to aging itself is an open question. It is likely that these processes contribute to genomic instability and loss of transcriptional fidelity, which in turn drives deleterious age-related phenotypes. Interventions associated with increased healthspan and longevity such as reduced insulin/IGF signalling (IIS), inhibition of mTOR and energy depletion resulting in SIRT1/AMPK activation, all have beneficial effects which ameliorate multiple facets of age-associated decline...
December 13, 2016: Experimental Gerontology
https://www.readbyqxmd.com/read/27986453/cd8-t-cells-utilize-highly-dynamic-enhancer-repertoires-and-regulatory-circuitry-in-response-to-infections
#16
Bing He, Shaojun Xing, Changya Chen, Peng Gao, Li Teng, Qiang Shan, Jodi A Gullicksrud, Matthew D Martin, Shuyang Yu, John T Harty, Vladimir P Badovinac, Kai Tan, Hai-Hui Xue
Differentiation of effector and memory CD8(+) T cells is accompanied by extensive changes in the transcriptome and histone modifications at gene promoters; however, the enhancer repertoire and associated gene regulatory networks are poorly defined. Using histone mark chromatin immunoprecipitation coupled with deep sequencing, we mapped the enhancer and super-enhancer landscapes in antigen-specific naive, differentiated effector, and central memory CD8(+) T cells during LCMV infection. Epigenomics-based annotation revealed a highly dynamic repertoire of enhancers, which were inherited, de novo activated, decommissioned and re-activated during CD8(+) T cell responses...
December 20, 2016: Immunity
https://www.readbyqxmd.com/read/27939672/dynamic-changes-in-chromatin-accessibility-occur-in-cd8-t-cells-responding-to-viral-infection
#17
James P Scott-Browne, Isaac F López-Moyado, Sara Trifari, Victor Wong, Lukas Chavez, Anjana Rao, Renata M Pereira
In response to acute infection, naive CD8(+) T cells expand, differentiate into effector cells, and then contract to a long-lived pool of memory cells after pathogen clearance. During chronic infections or in tumors, CD8(+) T cells acquire an "exhausted" phenotype. Here we present genome-wide comparisons of chromatin accessibility and gene expression from endogenous CD8(+) T cells responding to acute and chronic viral infection using ATAC-seq and RNA-seq techniques. Acquisition of effector, memory, or exhausted phenotypes was associated with stable changes in chromatin accessibility away from the naive T cell state...
December 20, 2016: Immunity
https://www.readbyqxmd.com/read/27936378/genome-wide-identification-of-neuronal-activity-regulated-genes-in-drosophila
#18
Xiao Chen, Reazur Rahman, Fang Guo, Michael Rosbash
Activity-regulated genes (ARGs) are important for neuronal functions like long-term memory and are well-characterized in mammals but poorly studied in other model organisms like Drosophila. Here we stimulated fly neurons with different paradigms and identified ARGs using high-throughput sequencing from brains as well as from sorted neurons: they included a narrow set of circadian neurons as well as dopaminergic neurons. Surprisingly, many ARGs are specific to the stimulation paradigm and very specific to neuron type...
December 9, 2016: ELife
https://www.readbyqxmd.com/read/27931227/epigenetics-of-amphetamine-induced-sensitization-hdac5-expression-and-microrna-in-neural-remodeling
#19
Philip K Liu, Christina H Liu
BACKGROUND: Histone deacetylase (HDAC) activities modify chromatin structure and play a role in learning and memory during developmental processes. Studies of adult mice suggest HDACs are involved in neural network remodeling in brain repair, but its function in drug addiction is less understood. We aimed to examine in vivo HDAC5 expression in a preclinical model of amphetamine-induced sensitization (AIS) of behavior. We generated specific contrast agents to measure HDAC5 levels by in vivo molecular contrast-enhanced (MCE) magnetic resonance imaging (MRI) in amphetamine-naïve mice as well as in mice with AIS...
December 8, 2016: Journal of Biomedical Science
https://www.readbyqxmd.com/read/27920256/a-transcription-factor-pulse-can-prime-chromatin-for-heritable-transcriptional-memory
#20
Aimee Iberg-Badeaux, Samuel Collombet, Benoit Laurent, Chris van Oevelen, Kuo-Kai Chin, Denis Thieffry, Thomas Graf, Shi Yang
Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in post-mitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM), and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli...
December 5, 2016: Molecular and Cellular Biology
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