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https://www.readbyqxmd.com/read/29768178/trained-memory-of-human-uterine-nk-cells-enhances-their-function-in-subsequent-pregnancies
#1
Moriya Gamliel, Debra Goldman-Wohl, Batya Isaacson, Chamutal Gur, Natan Stein, Rachel Yamin, Michael Berger, Myriam Grunewald, Eli Keshet, Yoach Rais, Chamutal Bornstein, Eyal David, Adam Jelinski, Iris Eisenberg, Caryn Greenfield, Arbel Ben-David, Tal Imbar, Ronit Gilad, Ronit Haimov-Kochman, David Mankuta, Matan Elami-Suzin, Ido Amit, Jacob H Hanna, Simcha Yagel, Ofer Mandelboim
Natural killer cells (NKs) are abundant in the human decidua, regulating trophoblast invasion and angiogenesis. Several diseases of poor placental development are associated with first pregnancies, so we thus looked to characterize differences in decidual NKs (dNKs) in first versus repeated pregnancies. We discovered a population found in repeated pregnancies, which has a unique transcriptome and epigenetic signature, and is characterized by high expression of the receptors NKG2C and LILRB1. We named these cells Pregnancy Trained decidual NK cells (PTdNKs)...
May 15, 2018: Immunity
https://www.readbyqxmd.com/read/29752744/distinct-heat-shock-factors-and-chromatin-modifications-mediate-the-organ-autonomous-transcriptional-memory-of-heat-stress
#2
Hsiang-Chin Liu, Jörn Lämke, Siou-Ying Lin, Meng-Ju Hung, Kuan-Ming Liu, Yee-Yung Charng, Isabel Bäurle
Plants can be primed by a stress cue to mount a faster or stronger activation of defense mechanisms upon a subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress; however, the underlying mechanisms are poorly understood. Here, we report that dozens of Arabidopsis thaliana genes display transcriptional memory, i.e. stronger upregulation after a recurring heat stress, that lasts for at least three days. We define a set of transcription factors involved in this memory response and show that the transcriptional memory results in enhanced transcriptional activation within minutes after the onset of a heat stress cue...
May 11, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29715265/mice-lacking-the-transcriptional-regulator-bhlhe40-have-enhanced-neuronal-excitability-and-impaired-synaptic-plasticity-in-the-hippocampus
#3
Kelly A Hamilton, Yue Wang, Sophia M Raefsky, Sean Berkowitz, Ryan Spangler, Caitlin N Suire, Simonetta Camandola, Robert H Lipsky, Mark P Mattson
Bhlhe40 is a transcription factor that is highly expressed in the hippocampus; however, its role in neuronal function is not well understood. Here, we used Bhlhe40 null mice on a congenic C57Bl6/J background (Bhlhe40 KO) to investigate the impact of Bhlhe40 on neuronal excitability and synaptic plasticity in the hippocampus. Bhlhe40 KO CA1 neurons had increased miniature excitatory post-synaptic current amplitude and decreased inhibitory post-synaptic current amplitude, indicating CA1 neuronal hyperexcitability...
2018: PloS One
https://www.readbyqxmd.com/read/29712785/remote-memory-and-cortical-synaptic-plasticity-require-neuronal-ccctc-binding-factor-ctcf
#4
Somi Kim, Nam-Kyung Yu, Kyu-Won Shim, Ji-Il Kim, Hyopil Kim, Dae Hee Han, Ja Eun Choi, Seung-Woo Lee, Dong Il Choi, Myung Won Kim, Dong-Sung Lee, Kyungmin Lee, Niels Galjart, Yong-Seok Lee, Jae-Hyung Lee, Bong-Kiun Kaang
The molecular mechanism of long-term memory has been extensively studied in the context of the hippocampus-dependent recent memory examined within several days. However, months-old remote memory maintained in the cortex for long-term has not been investigated much at the molecular level yet. Various epigenetic mechanisms are known to be important for long-term memory, but how the three-dimensional (3D) chromatin architecture and its regulator molecules contribute to neuronal plasticity and systems consolidation are still largely unknown...
April 30, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29707792/maintenance-of-pre-existing-dna-methylation-states-through-recurring-excess-light-stress
#5
Diep R Ganguly, Peter A Crisp, Steven R Eichten, Barry J Pogson
The capacity for plant stress priming and memory, and the notion of this being underpinned by DNA methylation-mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought-induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess-light (EL) stress, can lead to robust programmable changes in newly developing leaf tissues...
April 29, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29703840/transcription-factor-id2-prevents-e-proteins-from-enforcing-a-na%C3%A3-ve-t-lymphocyte-gene-program-during-nk-cell-development
#6
Erin C Zook, Zhong-Yin Li, Yiying Xu, Renée F de Pooter, Mihalis Verykokakis, Aimee Beaulieu, Anna Lasorella, Mark Maienschein-Cline, Joseph C Sun, Mikael Sigvardsson, Barbara L Kee
All innate lymphoid cells (ILCs) require the small helix-loop-helix transcription factor ID2, but the functions of ID2 are not well understood in these cells. We show that mature natural killer (NK) cells, the prototypic ILCs, developed in mice lacking ID2 but remained as precursor CD27+ CD11b- cells that failed to differentiate into CD27- CD11b+ cytotoxic effectors. We show that ID2 limited chromatin accessibility at E protein binding sites near naïve T lymphocyte-associated genes including multiple chemokine receptors, cytokine receptors, and signaling molecules and altered the NK cell response to inflammatory cytokines...
April 27, 2018: Science Immunology
https://www.readbyqxmd.com/read/29686426/transcript-indexed-atac-seq-for-precision-immune-profiling
#7
Ansuman T Satpathy, Naresha Saligrama, Jason D Buenrostro, Yuning Wei, Beijing Wu, Adam J Rubin, Jeffrey M Granja, Caleb A Lareau, Rui Li, Yanyan Qi, Kevin R Parker, Maxwell R Mumbach, William S Serratelli, David G Gennert, Alicia N Schep, M Ryan Corces, Michael S Khodadoust, Youn H Kim, Paul A Khavari, William J Greenleaf, Mark M Davis, Howard Y Chang
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples...
April 23, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29669249/the-transcription-factor-runx3-establishes-chromatin-accessibility-of-cis-regulatory-landscapes-that-drive-memory-cytotoxic-t-lymphocyte-formation
#8
Dapeng Wang, Huitian Diao, Adam J Getzler, Walter Rogal, Megan A Frederick, Justin Milner, Bingfei Yu, Shane Crotty, Ananda W Goldrath, Matthew E Pipkin
T cell receptor (TCR) stimulation of naive CD8+ T cells initiates reprogramming of cis-regulatory landscapes that specify effector and memory cytotoxic T lymphocyte (CTL) differentiation. We mapped regions of hyper-accessible chromatin in naive cells during TCR stimulation and discovered that the transcription factor (TF) Runx3 promoted accessibility to memory CTL-specific cis-regulatory regions before the first cell division and was essential for memory CTL differentiation. Runx3 was specifically required for accessibility to regions highly enriched with IRF, bZIP and Prdm1-like TF motifs, upregulation of TFs Irf4 and Blimp1, and activation of fundamental CTL attributes in early effector and memory precursor cells...
April 17, 2018: Immunity
https://www.readbyqxmd.com/read/29657031/warming-induces-significant-reprogramming-of-beige-but-not-brown-adipocyte-cellular-identity
#9
Hyun Cheol Roh, Linus T Y Tsai, Mengle Shao, Danielle Tenen, Yachen Shen, Manju Kumari, Anna Lyubetskaya, Christopher Jacobs, Brian Dawes, Rana K Gupta, Evan D Rosen
Beige and brown adipocytes generate heat in response to reductions in ambient temperature. When warmed, both beige and brown adipocytes exhibit morphological "whitening," but it is unknown whether or to what extent this represents a true shift in cellular identity. Using cell-type-specific profiling in vivo, we uncover a unique paradigm of temperature-dependent epigenomic plasticity of beige, but not brown, adipocytes, with conversion from a brown to a white chromatin state. Despite this profound shift in cellular identity, warm whitened beige adipocytes retain an epigenomic memory of prior cold exposure defined by an array of poised enhancers that prime thermogenic genes for rapid response during a second bout of cold exposure...
April 5, 2018: Cell Metabolism
https://www.readbyqxmd.com/read/29628210/formation-of-chromatin-subcompartments-by-phase-separation
#10
REVIEW
Fabian Erdel, Karsten Rippe
Chromatin is partitioned on multiple length scales into subcompartments that differ from each other with respect to their molecular composition and biological function. It is a key question how these compartments can form even though diffusion constantly mixes the nuclear interior and rapidly balances concentration gradients of soluble nuclear components. Different biophysical concepts are currently used to explain the formation of "chromatin bodies" in a self-organizing manner and without consuming energy...
April 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29624006/intrinsic-and-extrinsic-molecular-determinants-or-modulators-for-epigenetic-remodeling-and-reprogramming-of-somatic-cell-derived-genome-in-mammalian-nuclear-transferred-oocytes-and-resultant-embryos
#11
M Samiec, M Skrzyszowska
The efficiency of somatic cell cloning in mammals remains disappointingly low. Incomplete and aberrant reprogramming of epigenetic memory of somatic cell nuclei in preimplantation nuclear- transferred (NT) embryos is one of the most important factors that limit the cloning effectiveness. The extent of epigenetic genome-wide alterations, involving histone or DNA methylation and histone deacetylation, that are mediated by histone-lysine methyltransferases (HMTs) or DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) can be modulated/reversed via exogenous inhibitors of these enzymes throughout in vitro culture of nuclear donor cells, nuclear recipient oocytes and/or cloned embryos...
March 2018: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/29615554/flying-the-rna-nest-drosophila-reveals-novel-insights-into-the-transcriptome-dynamics-of-early-development
#12
REVIEW
Fabio Alexis Lefebvre, Éric Lécuyer
Early development is punctuated by a series of pervasive and fast paced transitions. These events reshape a differentiated oocyte into a totipotent embryo and allow it to gradually mount a genetic program of its own, thereby framing a new organism. Specifically, developmental transitions that ensure the maternal to embryonic control of developmental events entail a deep remodeling of transcriptional and transcriptomic landscapes. Drosophila provides an elegant and genetically tractable system to investigate these conserved changes at a dazzling developmental pace...
March 7, 2018: Journal of Developmental Biology
https://www.readbyqxmd.com/read/29529924/the-ubiquitin-proteasome-system-and-memory-moving-beyond-protein-degradation
#13
Timothy J Jarome, Rishi K Devulapalli
Cellular models of memory formation have focused on the need for protein synthesis. Recently, evidence has emerged that protein degradation mediated by the ubiquitin-proteasome system (UPS) is also important for this process. This has led to revised cellular models of memory formation that focus on a balance between protein degradation and synthesis. However, protein degradation is only one function of the UPS. Studies using single-celled organisms have shown that non-proteolytic ubiquitin-proteasome signaling is involved in histone modifications and DNA methylation, suggesting that ubiquitin and the proteasome can regulate chromatin remodeling independent of protein degradation...
March 1, 2018: Neuroscientist: a Review Journal Bringing Neurobiology, Neurology and Psychiatry
https://www.readbyqxmd.com/read/29522656/how-polycomb-mediated-cell-memory-deals-with-a-changing-environment-variations-in-pcg-complexes-and-proteins-assortment-convey-plasticity-to-epigenetic-regulation-as-a-response-to-environment
#14
Federica Marasca, Beatrice Bodega, Valerio Orlando
Cells and tissues are continuously exposed to a changing microenvironment, hence the necessity of a flexible modulation of gene expression that in complex organism have been achieved through specialized chromatin mechanisms. Chromatin-based cell memory enables cells to maintain their identity by fixing lineage specific transcriptional programs, ensuring their faithful transmission through cell division; in particular PcG-based memory system evolved to maintain the silenced state of developmental and cell cycle genes...
April 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29514080/from-retina-to-stem-cell-and-back-again-memories-of-a-chromatin-journey
#15
Jacqueline M Roberts, Monica L Vetter
The use of retinal organoids requires efficient differentiation from induced pluripotent stem cells (iPSCs). In this issue of Cell Reports, Wang et al. (2018) examine how the chromatin landscape after iPSC programming predicts their ability to differentiate into retinal tissue.
March 6, 2018: Cell Reports
https://www.readbyqxmd.com/read/29507097/pioneer-transcription-factors-shape-the-epigenetic-landscape
#16
Alexandre Mayran, Jacques Drouin
Pioneer transcription factors have the unique and important role of unmasking chromatin domains during development to allow the implementation of new cellular programs. Compared to those of other transcription factors, this activity implies that pioneer factors can recognize their target DNA sequences in so-called compacted or "closed" heterochromatin and can trigger remodeling of the adjoining chromatin landscape to provide accessibility to non-pioneer transcription factors. Recent studies identified several steps of pioneer action, namely rapid but weak initial binding to heterochromatin, stabilization of binding followed by chromatin opening and loss of CpG methylation that provides epigenetic memory...
March 5, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29494759/transcriptional-co-repressor-sin3a-silencing-rescues-decline-in-memory-consolidation-during-scopolamine-induced-amnesia
#17
Sweta Srivas, Mahendra K Thakur
Epigenetic modifications through methylation of DNA and acetylation of histones modulate neuronal gene expression and regulate long-term memory. Earlier we demonstrated that scopolamine-induced decrease in memory consolidation is correlated with enhanced expression of hippocampal DNA methyltransferase 1 (DNMT1) and histone deacetylase 2 (HDAC2) in mice. DNMT1 and HDAC2 act together by recruiting a co-repressor complex and deacetylating the chromatin. The catalytic activity of HDACs is mainly dependent on its incorporation into multiprotein co-repressor complexes, among which SIN3A-HDAC2 co-repressor is widely studied to regulate synaptic plasticity...
May 2018: Journal of Neurochemistry
https://www.readbyqxmd.com/read/29477835/epigenetic-regulation-of-fgf1-transcription-by-crtc1-and-memory-enhancement
#18
REVIEW
Shusaku Uchida, Gleb P Shumyatsky
Recent evidence demonstrates that epigenetic regulation of gene transcription is critically involved in learning and memory. Here, we discuss the role of histone acetylation and DNA methylation, which are two best understood epigenetic processes in memory processes. More specifically, we focus on learning-strength-dependent changes in chromatin on the fibroblast growth factor 1 (Fgf1) gene and on the molecular events that modulate regulation of Fgf1 transcription, required for memory enhancement, with the specific focus on CREB-regulated transcription coactivator 1 (CRTC1)...
March 2, 2018: Brain Research Bulletin
https://www.readbyqxmd.com/read/29465625/spinal-bromodomain-containing-protein-4-contributes-to-neuropathic-pain-induced-by-hiv-glycoprotein-120-with-morphine-in-rats
#19
Keiya Takahashi, Hyun Yi, Ching-Hang Liu, Shue Liu, Yuta Kashiwagi, Dennis J Patin, Shuanglin Hao
The symptoms of HIV-sensory neuropathy are dominated by neuropathic pain. Recent data show that repeated use of opiates enhances the chronic pain states in HIV patients. Limited attention has so far been devoted to exploring the exact pathogenesis of HIV painful disorder and opiate abuse in vivo, for which there is no effective treatment. Bromodomain-containing protein 4 (Brd4) is a member of the bromodomain and extraterminal domain protein (BET) family and functions as a chromatin 'reader' that binds acetylated lysines in histones in brain neurons to mediate the transcriptional regulation underlying learning and memory...
April 11, 2018: Neuroreport
https://www.readbyqxmd.com/read/29462212/epstein-barr-virus-nuclear-antigen-ebna-lp-is-essential-for-transforming-na%C3%A3-ve-b-cells-and-facilitates-recruitment-of-transcription-factors-to-the-viral-genome
#20
Agnieszka Szymula, Richard D Palermo, Amr Bayoumy, Ian J Groves, Mohammed Ba Abdullah, Beth Holder, Robert E White
The Epstein-Barr virus (EBV) nuclear antigen leader protein (EBNA-LP) is the first viral latency-associated protein produced after EBV infection of resting B cells. Its role in B cell transformation is poorly defined, but it has been reported to enhance gene activation by the EBV protein EBNA2 in vitro. We generated EBNA-LP knockout (LPKO) EBVs containing a STOP codon within each repeat unit of internal repeat 1 (IR1). EBNA-LP-mutant EBVs established lymphoblastoid cell lines (LCLs) from adult B cells at reduced efficiency, but not from umbilical cord B cells, which died approximately two weeks after infection...
February 2018: PLoS Pathogens
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