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https://www.readbyqxmd.com/read/29452937/epigenetic-chromatin-modification-by-amber-suppression-technology
#1
REVIEW
Heinz Neumann, Petra Neumann-Staubitz, Anna Witte, Daniel Summerer
The genetic incorporation of unnatural amino acids (UAAs) into proteins by amber suppression technology provides unique avenues to study protein structure, function and interactions both in vitro and in living cells and organisms. This approach has been particularly useful for studying mechanisms of epigenetic chromatin regulation, since these extensively involve dynamic changes in structure, complex formation and posttranslational modifications that are difficult to access by traditional approaches. Here, we review recent achievements in this field, emphasizing UAAs that help to unravel protein-protein interactions in cells by photo-crosslinking or that allow the biosynthesis of proteins with defined posttranslational modifications for studying their function and turnover in vitro and in cells...
February 13, 2018: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29451559/linking-chromatin-dynamics-cell-fate-plasticity-and-tissue-homeostasis-in-adult-mouse-hair-follicle-stem-cells
#2
Jayhun Lee, Tudorita Tumbar
Cellular plasticity for fate acquisition is associated with distinct chromatin states, which include histone modifications, dynamic association of chromatin factors with the DNA, and global chromatin compaction and nuclear organization. While embryonic stem cell (ESC) plasticity in vitro and its link with chromatin states have been characterized in depth, little is known about tissue stem cell plasticity in vivo , during adult tissue homeostasis. Recently, we reported a distinct globally low level of histone H3 K4/9/27me3 in mouse hair follicle stem cells (HFSCs) during quiescence...
July 2017: Mol Life
https://www.readbyqxmd.com/read/29449847/potential-epigenetic-regulation-in-the-germinal-center-reaction-of-lymphoid-tissues-in-hiv-siv-infection
#3
REVIEW
Xiaolei Wang, Huanbin Xu
The production of high-affinity and broadly neutralizing antibodies plays a key role in the defense against pathogens. These antibody responses require effective germinal center (GC) reaction within anatomical niches of GCs, where follicular helper T (Tfh) cells provide cognate help to B cells for T cell-dependent antibody responses. Emerging evidences indicate that GC reaction in normal state and perhaps establishment of latent Tfh cell reservoir in HIV/SIV infection are tightly regulated by epigenetic histone modifications, which are responsible for activating or silencing chromatin...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29447380/sirtuins-in-gamete-biology-and-reproductive-physiology-emerging-roles-and-therapeutic-potential-in-female-and-male-infertility
#4
Carla Tatone, Giovanna Di Emidio, Arcangelo Barbonetti, Gaspare Carta, Alberto M Luciano, Stefano Falone, Fernanda Amicarelli
BACKGROUND: Sirtuins (SIRT1-7) are a family of NAD+-dependent deacetylases that catalyze post-translational modifications of proteins. Together, they respond to metabolic challenges, inflammatory signals or hypoxic/oxidative stress, and are associated with aging and longevity. The role of Sirtuins in the regulation of fertility emerged in 2003 when a defective reproductive phenotype was observed in SIRT1-null mice. Although studies on Sirtuins in reproductive biology have been increasing in the last years, a recent comprehensive update on this issue is still lacking...
February 13, 2018: Human Reproduction Update
https://www.readbyqxmd.com/read/29444334/optimized-methods-of-chromatin-immunoprecipitation-chip-for-profiling-histone-modifications-in-industrial-microalgae-nannochloropsis-spp
#5
Li Wei, Jian Xu
Epigenetic factors such as histone modifications play integral roles in plant development and stress response, yet their implications in algae remain poorly understood. In the industrial oleaginous microalgae Nannochloropsis spp., the lack of an efficient methodology for chromatin immunoprecipitation (ChIP), which determines the specific genomic location of various histone modifications, has hindered probing the epigenetic basis of their photosynthetic carbon conversion and storage as oil. Here, a detailed ChIP protocol was developed for Nannochloropsis oceanica, which represents a reliable approach for the analysis of histone modifications, chromatin state, and transcription factor binding sites at the epigenetic level...
February 14, 2018: Journal of Phycology
https://www.readbyqxmd.com/read/29443090/native-chromatin-immunoprecipitation-using-murine-brain-tumor-neurospheres
#6
Flor M Mendez, Felipe J Núñez, Rocío I Zorrilla-Veloz, Pedro R Lowenstein, Maria G Castro
Epigenetic modifications may be involved in the development and progression of glioma. Changes in methylation and acetylation of promoters and regulatory regions of oncogenes and tumor suppressors can lead to changes in gene expression and play an important role in the pathogenesis of brain tumors. Native chromatin immunoprecipitation (ChIP) is a popular technique that allows the detection of modifications or other proteins tightly bound to DNA. In contrast to cross-linked ChIP, in native ChIP, cells are not treated with formaldehyde to covalently link protein to DNA...
January 29, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29443015/isolation-and-cultivation-of-neural-progenitors-followed-by-chromatin-immunoprecipitation-of-histone-3-lysine-79-dimethylation-mark
#7
Patrick Bovio, Deborah Roidl, Stefanie Heidrich, Tanja Vogel, Henriette Franz
Brain development is a complex process, which is controlled in a temporo-spatial manner by gradients of morphogens and different transcriptional programs. Additionally, epigenetic chromatin modifications, like histone methylation, have an important role for establishing and maintaining specific cell fates within this process. The vast majority of histone methylation occurs on the flexible histone tail, which is accessible to histone modifiers, erasers, and histone reader proteins. In contrast, H3K79 methylation is located in the globular domain of histone 3 and is implicated in different developmental functions...
January 26, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29442331/role-of-zic-family-proteins-in-transcriptional-regulation-and-chromatin-remodeling
#8
Minoru Hatayama, Jun Aruga
Proper functions of Zic proteins are essential for animals in health and disease. Here, we summarize our current understanding of the molecular properties and functions of the Zic family across animal species and paralog subtypes. Zics are basic proteins with some posttranslational modifications and can move to the cell nucleus via importin- and CRM1-based nucleocytoplasmic shuttling mechanisms. Degradation is mediated by the ubiquitin proteasome system. Many Zic proteins are capable of binding to two types of target DNA sequences (CTGCTG-core-type and GC-stretch-type)...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29440567/cellular-and-molecular-mechanisms-of-centromere-drive
#9
Michael A Lampson, Ben E Black
The asymmetric outcome of female meiosis I, whereby an entire set of chromosomes are discarded into a polar body, presents an opportunity for selfish genetic elements to cheat the process and disproportionately segregate to the egg. Centromeres, the chromosomal loci that connect to spindle microtubules, could potentially act as selfish elements and "drive" in meiosis. We review the current understanding of the genetic and epigenetic contributions to centromere identity and describe recent progress in a powerful model system to study centromere drive in mice...
February 12, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29438988/flavopiridol-inhibits-tgf-%C3%AE-stimulated-biglycan-synthesis-by-blocking-linker-region-phosphorylation-and-nuclear-translocation-of-smad2
#10
Muhamad Ashraf Rostam, Aravindra Shajimoon, Danielle Kamato, Partha Mitra, Terrence Piva, Robel Getachew, Yingnan Cao, Wenhua Zheng, Narin Osman, Peter James Little
Transforming Growth Factor (TGF) β is a pleiotropic growth factor implicated in the development of atherosclerosis for its role in mediating glycosaminoglycan (GAG) chain hyperelongation on the proteoglycan biglycan, a phenomenon that leads to increased binding of atherogenic lipoproteins in the wall of blood vessels. TGF-β signalling pathway components leading to the modification of GAG chains on biglcyan are therefore potential targets for the treatment of atherosclerosis. Phosphorylation of the transcription factor Smad has emerged as a critical step in the signalling pathways that control the synthesis of biglycan, both the core protein and the GAG chains...
February 9, 2018: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/29433067/rapid-induction-of-expression-by-lps-is-accompanied-by-favorable-chromatin-and-rapid-binding-of-c-jun
#11
Kelly Maurer, Swathi Ramen, Lihuaa Shi, Li Song, Kathleen E Sullivan
The response to infection is managed in mammals by a coordinated immune response. Innate responses are rapid and hard wired and have been demonstrated to be regulated at the level of chromatin accessibility. This study examined primary human monocyte responses to LPS as a model of innate responses to bacteria. We utilized inhibitors of chromatin modifying enzymes to understand the inter-relationships of the chromatin complexes regulating transcription. Multiplex digital gene detection was utilized to quantitate changes in mRNA levels for genes induced by LPS...
February 9, 2018: Molecular Immunology
https://www.readbyqxmd.com/read/29431122/poly-adp-ribose-polymerase-1-regulates-fibroblast-activation-in-systemic-sclerosis
#12
Yun Zhang, Sebastian Pötter, Chih-Wei Chen, Ruifang Liang, Kolja Gelse, Ingo Ludolph, Raymund E Horch, Oliver Distler, Georg Schett, Jörg H W Distler, Clara Dees
OBJECTIVES: The enzyme poly(ADP-ribose) polymerase-1 (PARP-1) transfers negatively charged ADP-ribose units to target proteins. This modification can have pronounced regulatory effects on target proteins. Recent studies showed that PARP-1 can poly(ADP-ribosyl)ate (PARylate) Smad proteins. However, the role of PARP-1 in the pathogenesis of systemic sclerosis (SSc) has not been investigated. METHODS: The expression of PARP-1 was determined by quantitative PCR and immunohistochemistry...
February 3, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29429572/mutations-in-the-baf-complex-subunit-dpf2-are-associated-with-coffin-siris-syndrome
#13
Georgia Vasileiou, Silvia Vergarajauregui, Sabine Endele, Bernt Popp, Christian Büttner, Arif B Ekici, Marion Gerard, Nuria C Bramswig, Beate Albrecht, Jill Clayton-Smith, Jenny Morton, Susan Tomkins, Karen Low, Astrid Weber, Maren Wenzel, Janine Altmüller, Yun Li, Bernd Wollnik, George Hoganson, Maria-Renée Plona, Megan T Cho, Christian T Thiel, Hermann-Josef Lüdecke, Tim M Strom, Eduardo Calpena, Andrew O M Wilkie, Dagmar Wieczorek, Felix B Engel, André Reis
Variants affecting the function of different subunits of the BAF chromatin-remodelling complex lead to various neurodevelopmental syndromes, including Coffin-Siris syndrome. Furthermore, variants in proteins containing PHD fingers, motifs recognizing specific histone tail modifications, have been associated with several neurological and developmental-delay disorders. Here, we report eight heterozygous de novo variants (one frameshift, two splice site, and five missense) in the gene encoding the BAF complex subunit double plant homeodomain finger 2 (DPF2)...
February 5, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29429518/epigenetic-status-of-buffalo-fibroblasts-treated-with-sodium-butyrate-a-chromatin-remodeling-agent
#14
Papori Sharma, A S Yadav, N L Selokar, Dharmendra Kumar, S S Dhaka, P S Yadav
The somatic cells having higher levels of DNA methylation and reducing it in donor cells before nuclear transfer (NT) by treating them with chemicals, may improve cloning efficiency of NT embryos by providing donor cells with similar epigenetic characteristics as in vivo embryos. Therefore, the present study was planned to understand mechanism of epigenetic changes in donor cells (buffalo fibroblasts) treated with different concentration of sodium butyrate (NaBu)-a chromatin remodeling agent. The cultured fibroblasts purity and lineage were confirmed by fibroblast specific protein and gene markers (Vimentin, Tubulin and Cytokeratin) at different passages using immuno-staining and qPCR respectively...
February 2018: Tissue & Cell
https://www.readbyqxmd.com/read/29429329/tandem-histone-binding-domains-enhance-the-activity-of-a-synthetic-chromatin-effector
#15
Stefan J Tekel, Daniel A Vargas, Lusheng Song, Joshua LaBear, Michael R Caplan, Karmella A Haynes
Fusion proteins that specifically interact with biochemical marks on chromosomes represent a new class of synthetic transcriptional regulators that decode cell state information rather than DNA sequences. In multicellular organisms, information relevant to cell state, tissue identity, and oncogenesis is often encoded as biochemical modifications of histones, which are bound to DNA in eukaryotic nuclei and regulate gene expression states. We have previously reported the development and validation of the "Polycomb-based transcription factor" (PcTF), a fusion protein that recognizes histone modifications through a protein-protein interaction between its polycomb chromodomain (PCD) motif and trimethylated lysine 27 of histone H3 (H3K27me3) at genomic sites...
February 12, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29429127/tissue-and-strain-specific-effects-of-a-genotoxic-carcinogen-1-3-butadiene-on-chromatin-and-transcription
#16
Jennifer W Israel, Grace A Chappell, Jeremy M Simon, Sebastian Pott, Alexias Safi, Lauren Lewis, Paul Cotney, Hala S Boulos, Wanda Bodnar, Jason D Lieb, Gregory E Crawford, Terrence S Furey, Ivan Rusyn
Epigenetic effects of environmental chemicals are under intense investigation to fill existing knowledge gaps between environmental/occupational exposures and adverse health outcomes. Chromatin accessibility is one prominent mechanism of epigenetic control of transcription, and understanding of the chemical effects on both could inform the causal role of epigenetic alterations in disease mechanisms. In this study, we hypothesized that baseline variability in chromatin organization and transcription profiles among various tissues and mouse strains influence the outcome of exposure to the DNA damaging chemical 1,3-butadiene...
February 10, 2018: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29427507/epigenetic-modifications-insight-into-oligodendrocyte-lineage-progression-regeneration-and-disease
#17
REVIEW
Alexander Gregath, Richard Q Lu
Myelination by oligodendrocytes in the central nervous system permits high fidelity saltatory conduction from neuronal cell bodies to axon terminals. Dysmyelinating and demyelinating disorders impair normal nervous system functions. Consequently, an understanding of oligodendrocyte differentiation that moves beyond the genetic code into the field of epigenetics is essential. Chromatin reprogramming is critical for steering stage-specific differentiation processes during oligodendrocyte development. Fine temporal control of chromatin remodeling through ATP-dependent chromatin remodelers and sequential histone modifiers shapes a chromatin regulatory landscape conducive to oligodendrocyte fate specification, lineage differentiation, and maintenance of cell identity...
February 10, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29425851/mechanistic-aspects-of-epigenetic-dysregulation-in-sle
#18
Christian Michael Hedrich
Epigenetic events have been linked with disease expression in individuals genetically predisposed to the development of systemic lupus erythematosus (SLE), a severe systemic autoimmune/inflammatory disease. Altered DNA methylation and hydroxymethylation as well as histone modifications mediate changes in chromatin accessibility and gene expression in immune cells from SLE patients. Defective epigenetic control contributes to uncontrolled expression of inflammatory mediators, including cytokines and co-receptors, resulting in systemic inflammation and tissue damage...
February 6, 2018: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/29423844/chromatin-immunoprecipitation-polymerase-chain-reaction-chip-pcr-detects-methylation-acetylation-and-ubiquitylation-in-s-pombe
#19
Valerie Migeot, Damien Hermand
The distribution of modified histones within the fission yeast Schizosaccharomyces pombe genome is ultimately dependent upon the transcriptional activity and in turn influences the ability of the polymerases to bind and progress through the chromatin template. The Chromatin Immunoprecipitation-Polymerase Chain Reaction (ChIP-PCR) method currently provides the highest resolution, accuracy, and reproducibility to characterize histones modifications within a defined region of the genome. The following protocol details the method applied to S...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29422688/lc-ms-ms-based-quantitative-study-of-the-acyl-group-and-site-selectivity-of-human-sirtuins-to-acylated-nucleosomes
#20
Kana Tanabe, Jiaan Liu, Daiki Kato, Hitoshi Kurumizaka, Kenzo Yamatsugu, Motomu Kanai, Shigehiro A Kawashima
Chromatin structure and gene expression are dynamically regulated by posttranslational modifications of histones. Recent advance in mass spectrometry has identified novel types of lysine acylations, such as butyrylation and malonylation, whose functions and regulations are likely different from those of acetylation. Sirtuins, nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases, catalyze various deacylations. However, it is poorly understood how distinct sirtuins regulate the histone acylation states of nucleosomes that have many lysine residues...
February 8, 2018: Scientific Reports
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