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histone modification chromatin

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https://www.readbyqxmd.com/read/29163371/cofactors-as-metabolic-sensors-driving-cell-adaptation-in-physiology-and-disease
#1
REVIEW
Nabil Rabhi, Sarah Anissa Hannou, Philippe Froguel, Jean-Sébastien Annicotte
Chromatin architectures and epigenetic fingerprint regulation are fundamental for genetically determined biological processes. Chemical modifications of the chromatin template sensitize the genome to intracellular metabolism changes to set up diverse functional adaptive states. Accumulated evidence suggests that the action of epigenetic modifiers is sensitive to changes in dietary components and cellular metabolism intermediates, linking nutrition and energy metabolism to gene expression plasticity. Histone posttranslational modifications create a code that acts as a metabolic sensor, translating changes in metabolism into stable gene expression patterns...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29162512/mmp9-gene-expression-regulation-by-intragenic-epigenetic-modifications-in-breast-cancer
#2
Liliane M B Klassen, Andressa Chequin, Graciele C M Manica, Isis V Biembengut, Mariana B Toledo, Valter A Baura, Fábio de O Pedrosa, Edneia A S Ramos, Fabrício F Costa, Emanuel M De Souza, Giseli Klassen
Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death among women worldwide. Metastasis remains a major challenge for the clinical management and prognosis of patients with cancer. The metalloprotease MMP-9 plays a critical role in the first step of metastasis through extracellular matrix degradation. In this study, our goal was to determine the effect of epigenetic mechanisms in the promoter and intragenic region of this gene and to correlate it to the levels of expression of MMP9 in breast cancer cell lines...
November 18, 2017: Gene
https://www.readbyqxmd.com/read/29161272/global-transcriptome-profile-reveals-abundance-of-dna-damage-response-and-repair-genes-in-individuals-from-high-level-natural-radiation-areas-of-kerala-coast
#3
Vinay Jain, Birajalaxmi Das
The high level natural radiation areas (HLNRA) of Kerala coast in south west India is unique for its wide variation in the background radiation dose (<1.0mGy to 45mGy/year) and vast population size. Several biological studies conducted in this area did not reveal any adverse effects of chronic low dose and low dose rate radiation on human population. In the present study, global transcriptome analysis was carried out in peripheral blood mono-nuclear cells of 36 individuals belonging to different background dose groups [NLNRA, (Group I, ≤1...
2017: PloS One
https://www.readbyqxmd.com/read/29159235/trimethylation-of-histone-3-lysine-27-h3k27me3-chip-pcr-and-transcriptional-expression-data-of-ef1-alpha-cyp26a-hoxc10-hoxd10-and-hoxd11-in-the-xenopus-xtc-cell-line
#4
Warren Vieira, Hande Sahin, Kaylee Wells, Catherine McCusker
Trimethylation of Histone 3 lysine 27 (H3K27me3) is a chromatin modification that is associated with transcriptional repression (Cao et al., 2002; Sarma et al., 2008; Pengelly et al., 2013) [1], [2], [3]. In this article we performed anti-H3K27me3 Chromosomal Immunoprecipitation (ChIP-PCR), to detect the abundance of H3K27me3 marks on Ef1-alpha, cyp26A, HoxC10, HoxD10 and HoxD11 in the Xenopus XTC cell line. We also performed RT-PCR for these genes to determine whether their expression is detectable in the XTC cell culture...
December 2017: Data in Brief
https://www.readbyqxmd.com/read/29158493/structural-and-spatial-chromatin-features-at-developmental-gene-loci-in-human-pluripotent-stem-cells
#5
Hiroki Ikeda, Masamitsu Sone, Shinya Yamanaka, Takuya Yamamoto
Higher-order chromatin organization controls transcriptional programs that govern cell properties and functions. In order for pluripotent stem cells (PSCs) to appropriately respond to differentiation signals, developmental gene loci should be structurally and spatially regulated to be readily available for immediate transcription, even though these genes are hardly expressed in PSCs. Here, we show that both chromatin interaction profiles and nuclear positions at developmental gene loci differ between human somatic cells and hPSCs, and that changes in the chromatin interactions are closely related to the nuclear repositioning...
November 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29158132/deciphering-the-histone-code-to-build-the-genome-structure
#6
Kirti Prakash, David Fournier
Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutralisation, molecular specificity, robustness and evolvability. Next, we present evidence for the association among different histone modifications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replication and cell division...
November 17, 2017: Bio Systems
https://www.readbyqxmd.com/read/29156705/upregulation-of-cd11b-and-cd86-through-lsd1-inhibition-promotes-myeloid-differentiation-and-suppresses-cell-proliferation-in-human-monocytic-leukemia-cells
#7
Jianwu Fang, Haiyan Ying, Ting Mao, Yanjia Fang, Yuan Lu, He Wang, Irene Zang, Zhaofu Wang, Ying Lin, Mengxi Zhao, Xiao Luo, Zongyao Wang, Yan Zhang, Chao Zhang, Wei Xiao, Yan Wang, Wei Tan, Zhui Chen, Chris Lu, Peter Atadja, En Li, Kehao Zhao, Jianfeng Liu, Justin Gu
LSD1 (Lysine Specific Demethylase1)/KDM1A (Lysine Demethylase 1A), a flavin adenine dinucleotide (FAD)-dependent histone H3K4/K9 demethylase, sustains oncogenic potential of leukemia stem cells in primary human leukemia cells. However, the pro-differentiation and anti-proliferation effects of LSD1 inhibition in acute myeloid leukemia (AML) are not yet fully understood. Here, we report that small hairpin RNA (shRNA) mediated LSD1 inhibition causes a remarkable transcriptional activation of myeloid lineage marker genes (CD11b/ITGAM and CD86), reduction of cell proliferation and decrease of clonogenic ability of human AML cells...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156681/the-histone-demethylase-kdm3a-is-required-for-normal-epithelial-proliferation-ductal-elongation-and-tumor-growth-in-the-mouse-mammary-gland
#8
Li Qin, Yixiang Xu, Xiaobin Yu, Michael J Toneff, Dabing Li, Lan Liao, Jarrod D Martinez, Yi Li, Jianming Xu
Histone modification alters chromatin architecture to regulate gene transcription. KDM3A is a histone demethylase in the JmjC domain-containing protein family. It removes di- and mono- methyl residues from di- or mono-methylated lysine 9 of histone H3 (H3K9me2/me1). Recent studies have shown that Kdm3a plays an important role in self-renewal of embryonic stem cells, spermatogenesis, metabolism, sex determination and tumor angiogenesis. However, its role in mammary gland development and breast carcinogenesis remains unclear...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155791/improved-protocol-for-chromatin-immunoprecipitation-from-mouse-skeletal-muscle
#9
Shilpy Joshi, Vanessa Ueberschlag-Pitiot, Daniel Metzger, Irwin Davidson
We describe an efficient and reproducible protocol for the preparation of chromatin from adult mouse skeletal muscle, a physically resistant tissue with a high content of structural proteins. Dissected limb muscles from adult mice are physically disrupted by mechanical homogenisation, or a combination of mincing and douncing, in a hypotonic buffer before formaldehyde fixation of the cell lysate. The fixed nuclei are purified by further cycles of mechanical homogenisation or douncing and sequential filtrations to remove cell debris...
November 6, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29151149/impact-of-xist-rna-on-chromatin-modifications-and-transcriptional-silencing-maintenance-at-different-stages-of-imprinted-x-chromosome-inactivation-in-vole-microtus-levis
#10
Alexander I Shevchenko, Elena V Grigor'eva, Sergey P Medvedev, Irina S Zakharova, Elena V Dementyeva, Eugeny A Elisaphenko, Anastasia A Malakhova, Sophia V Pavlova, Suren M Zakian
In vole Microtus levis, cells of preimplantation embryo and extraembryonic tissues undergo imprinted X chromosome inactivation (iXCI) which is triggered by a long non-coding nuclear RNA, Xist. At early stages of iXCI, chromatin of vole inactive X chromosome is enriched with the HP1 heterochromatin-specific protein, trimethylated H3K9 and H4K20 attributable to constitutive heterochromatin. In the study, using vole trophoblast stem (TS) cells as a model of iXCI, we further investigated chromatin of the inactive X chromosome of M...
November 18, 2017: Chromosoma
https://www.readbyqxmd.com/read/29149419/changes-in-chromatin-state-reveal-arnt2-at-a-node-of-a-tumorigenic-transcription-factor-signature-driving-glioblastoma-cell-aggressiveness
#11
Alexandra Bogeas, Ghislaine Morvan-Dubois, Elias A El-Habr, François-Xavier Lejeune, Matthieu Defrance, Ashwin Narayanan, Klaudia Kuranda, Fanny Burel-Vandenbos, Salwa Sayd, Virgile Delaunay, Luiz G Dubois, Hugues Parrinello, Stéphanie Rialle, Sylvie Fabrega, Ahmed Idbaih, Jacques Haiech, Ivan Bièche, Thierry Virolle, Michele Goodhardt, Hervé Chneiweiss, Marie-Pierre Junier
Although a growing body of evidence indicates that phenotypic plasticity exhibited by glioblastoma cells plays a central role in tumor development and post-therapy recurrence, the master drivers of their aggressiveness remain elusive. Here we mapped the changes in active (H3K4me3) and repressive (H3K27me3) histone modifications accompanying the repression of glioblastoma stem-like cells tumorigenicity. Genes with changing histone marks delineated a network of transcription factors related to cancerous behavior, stem state, and neural development, highlighting a previously unsuspected association between repression of ARNT2 and loss of cell tumorigenicity...
November 17, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/29149060/epigenetic-regulation-of-viral-biological-processes
#12
REVIEW
Lata Balakrishnan, Barry Milavetz
It is increasingly clear that DNA viruses exploit cellular epigenetic processes to control their life cycles during infection. This review will address epigenetic regulation in members of the polyomaviruses, adenoviruses, human papillomaviruses, hepatitis B, and herpes viruses. For each type of virus, what is known about the roles of DNA methylation, histone modifications, nucleosome positioning, and regulatory RNA in epigenetic regulation of the virus infection will be discussed. The mechanisms used by certain viruses to dysregulate the host cell through manipulation of epigenetic processes and the role of cellular cofactors such as BRD4 that are known to be involved in epigenetic regulation of host cell pathways will also be covered...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29142071/chromatin-histone-modifications-and-rigidity-affect-nuclear-morphology-independent-of-lamins
#13
Andrew D Stephens, Patrick Z Liu, Edward J Banigan, Luay M Almassalha, Vadim Backman, Stephen A Adam, Robert D Goldman, John F Marko
Nuclear shape and architecture influence gene localization, mechanotransduction, transcription, and cell function. Abnormal nuclear morphology and protrusions termed "blebs" are diagnostic markers for many human afflictions including heart disease, aging, progeria, and cancer. Nuclear blebs are associated with both lamin and chromatin alterations. A number of prior studies suggest that lamins dictate nuclear morphology, but the contributions of altered chromatin compaction remain unclear. We show that chromatin histone modification state dictates nuclear rigidity, and modulating it is sufficient to both induce and suppress nuclear blebs...
November 15, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29141987/brachyury-directs-histone-acetylation-to-target-loci-during-mesoderm-development
#14
Arica Beisaw, Pavel Tsaytler, Frederic Koch, Sandra U Schmitz, Maria-Theodora Melissari, Anna D Senft, Lars Wittler, Tracie Pennimpede, Karol Macura, Bernhard G Herrmann, Phillip Grote
T-box transcription factors play essential roles in multiple aspects of vertebrate development. Here, we show that cooperative function of BRACHYURY (T) with histone-modifying enzymes is essential for mouse embryogenesis. A single point mutation (T(Y88A)) results in decreased histone 3 lysine 27 acetylation (H3K27ac) at T target sites, including the T locus, suggesting that T autoregulates the maintenance of its expression and functions by recruiting permissive chromatin modifications to putative enhancers during mesoderm specification...
November 15, 2017: EMBO Reports
https://www.readbyqxmd.com/read/29141961/chromatin-accessibility-dynamics-reveal-novel-functional-enhancers-in-c-elegans
#15
Aaron C Daugherty, Robin W Yeo, Jason D Buenrostro, William J Greenleaf, Anshul Kundaje, Anne Brunet
Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism Caenorhabditis elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29138512/proteome-wide-identification-of-lysine-2-hydroxyisobutyrylation-reveals-conserved-and-novel-histone-modifications-in-physcomitrella-patens
#16
Zhiming Yu, Jun Ni, Wei Sheng, Zhikun Wang, Yuhuan Wu
Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly identified post-translational modification found in animal and yeast cells. Previous research suggested that histone Khib is involved in male cell differentiation and plays a critical role in the regulation of chromatin functions in animals. However, information regarding protein Khib in plants is still limited. In this study, using a specific antibody and LC-MS/MS methods, we identified 11,976 Khib sites in 3,001 proteins in Physcomitrella patens. The bioinformatics analysis indicated that these Khib-modified proteins were involved in a wide range of molecular functions and cellular processes, and showed diverse subcellular localizations...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#17
Oluwatosin Oluwadare, Jianlin Cheng
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29133310/convergent-origination-of-a-drosophila-like-dosage-compensation-mechanism-in-a-reptile-lineage
#18
Ray Marin, Diego Cortez, Francesco Lamanna, Madapura M Pradeepa, Evgeny Leushkin, Philippe Julien, Angélica Liechti, Jean Halbert, Thoomke Brüning, Katharina Mössinger, Timo Trefzer, Christian Conrad, Halie N Kerver, Juli Wade, Patrick Tschopp, Henrik Kaessmann
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage...
November 13, 2017: Genome Research
https://www.readbyqxmd.com/read/29133298/functional-redundancy-of-variant-and-canonical-histone-h3-lysine-9-modification-in-drosophila
#19
Taylor J R Penke, Daniel J McKay, Brian D Strahl, A Gregory Matera, Robert J Duronio
Histone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for "active" histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin...
November 13, 2017: Genetics
https://www.readbyqxmd.com/read/29133117/application-of-mixed-peptide-arrays-to-study-combinatorial-readout-of-chromatin-modifications
#20
Rebekka Mauser, Goran Kungulovski, David Meral, Daniel Maisch, Albert Jeltsch
The N-terminal tails of histone proteins are massively decorated with post-translational modifications (PTMs), which play important roles in the regulation of gene expression. Several highly conserved chromatin interacting proteins can bind to histone modifications in a sequence and modification specific manner employing specific reading domains. These proteins often contain several reading domains, which can cooperate in the readout of different PTMs. To gain a better insight into the combinatorial readout of PTMs, we developed a method to study the binding of double reading domains to mixed peptide arrays containing two different peptides in each spot...
November 10, 2017: Biochimie
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