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https://www.readbyqxmd.com/read/28747748/the-epigenetic-landscape-of-promoter-genome-wide-analysis-in-breast-cancer
#1
Seher Karsli-Ceppioglu, Aslihan Dagdemir, Gaëlle Judes, André Lebert, Frédérique Penault-Llorca, Yves-Jean Bignon, Dominique Bernard-Gallon
Breast cancer is a heterogeneous disease due to its clinico-pathological features and response to therapy. The classification of breast tumors based on their hormone receptor status and pathologic features. Post-translational histone modifications come into prominence for regulation of gene expression in cancer pathogenesis. Here, we analyzed dysregulation of H3K9ac and H3K27me3-enriched subtype-specific genes using ChIP-on-chip assay in breast cancer tumors and matched normal tissue samples. Breast cancer tumors were classified according to St Gallen Consensus 2013...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747563/the-h3k27me3-demethylase-kdm6a-is-suppressed-in-breast-cancer-stem-like-cells-and-enables-the-resolution-of-bivalency-during-the-mesenchymal-epithelial-transition
#2
Joseph H Taube, Nathalie Sphyris, Kelsey S Johnson, Keighley N Reisenauer, Taylor A Nesbit, Robiya Joseph, Geraldine V Vijay, Tapasree R Sarkar, Neeraja A Bhangre, Joon Jin Song, Jeffrey T Chang, Min Gyu Lee, Rama Soundararajan, Sendurai A Mani
The deposition of the activating H3K4me3 and repressive H3K27me3 histone modifications within the same promoter, forming a so-called bivalent domain, maintains gene expression in a repressed but transcription-ready state. We recently reported a significantly increased incidence of bivalency following an epithelial-mesenchymal transition (EMT), a process associated with the initiation of the metastatic cascade. The reverse process, known as the mesenchymal-epithelial transition (MET), is necessary for efficient colonization...
July 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28746399/coordination-of-matrix-attachment-and-atp-dependent-chromatin-remodeling-regulate-auxin-biosynthesis-and-arabidopsis-hypocotyl-elongation
#3
Kyounghee Lee, Pil Joon Seo
Hypocotyl elongation is extensively controlled by hormone signaling networks. In particular, auxin metabolism and signaling play key roles in light-dependent hypocotyl growth. The nuclear matrix facilitates organization of DNA within the nucleus, and dynamic interactions between nuclear matrix and DNA are related to gene regulation. Conserved scaffold/matrix attachment regions (S/MARs) are anchored to the nuclear matrix by the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) proteins in Arabidopsis. Here, we found that ESCAROLA (ESC)/AHL27 and SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3)/AHL29 redundantly regulate auxin biosynthesis in the control of hypocotyl elongation...
2017: PloS One
https://www.readbyqxmd.com/read/28743737/real-time-visualization-of-chromatin-modification-in-isolated-nuclei
#4
Luca Sardo, Angel Lin, Svetlana Khakhina, Lucas Beckman, Luis Ricon, Weam Elbezanti, Tara Jaison, Harshad Vishwasrao, Hari Shroff, Christopher Janetopoulos, Zachary A Klase
Chromatin modification is traditionally queried by biochemical assays that provide average measurements of static events since the analysis requires components from many cells. Microscopy can visualize single cells, but the cell body and organelles can hamper staining and visualization of the nucleus. Normally, chromatin is visualized by immunostaining a fixed sample or by expressing exogenous fluorescently tagged proteins in a live cell. Alternative microscopy tools to observe changes of endogenous chromatin in real-time are needed...
July 25, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28743695/ectopic-application-of-the-repressive-histone-modification-h3k9me2-establishes-post-zygotic-reproductive-isolation-in-arabidopsis-thaliana
#5
Hua Jiang, Jordi Moreno-Romero, Juan Santos-González, Geert De Jaeger, Kris Gevaert, Eveline Van De Slijke, Claudia Köhler
Hybrid seed lethality as a consequence of interspecies or interploidy hybridizations is a major mechanism of reproductive isolation in plants. This mechanism is manifested in the endosperm, a dosage-sensitive tissue supporting embryo growth. Deregulated expression of imprinted genes such as ADMETOS (ADM) underpin the interploidy hybridization barrier in Arabidopsis thaliana; however, the mechanisms of their action remained unknown. In this study, we show that ADM interacts with the AT hook domain protein AHL10 and the SET domain-containing SU(VAR)3-9 homolog SUVH9 and ectopically recruits the heterochromatic mark H3K9me2 to AT-rich transposable elements (TEs), causing deregulated expression of neighboring genes...
July 25, 2017: Genes & Development
https://www.readbyqxmd.com/read/28743023/principles-of-transgenerational-small-rna-inheritance-in-caenorhabditis-elegans
#6
REVIEW
Oded Rechavi, Itamar Lev
Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations...
July 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28742579/a-review-of-the-epigenetic-contributions-to-endometriosis
#7
Frances W Grimstad, Alan Decherney
Epigenetic influences have been postulated to affect the course of endometriosis. DNA methyltransferases, estrogen and progesterone receptors, micro-RNAs, and histone deacetylators, have shown differential expression in endometriosis compared with normal endometrium. Others such as aromatase, Steroid Factor-1, COX-2, and Homeobox A10 also have epigenetic modifications in endometriosis. Limitations in this area of research include heterogeneity in study design, patient populations, and methods of analysis. Larger, controlled studies are needed...
September 2017: Clinical Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28741489/epigenomic-consequences-of-coding-and-noncoding-driver-mutations
#8
REVIEW
Xiaosai Yao, Manjie Xing, Wen Fong Ooi, Patrick Tan, Bin Tean Teh
Chromatin alterations are integral to the pathogenic process of cancer, as demonstrated by recent discoveries of frequent mutations in chromatin-modifier genes and aberrant DNA methylation states in different cancer types. Progress is being made on elucidating how chromatin alterations, and how proteins catalyzing these alterations, mechanistically contribute to tissue-specific tumorigenesis. In parallel, technologies enabling the genome-wide profiling of histone modifications have revealed the existence of noncoding driver genetic alterations in cancer...
October 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28741224/comparative-analysis-of-histone-modifications-and-dna-methylation-at-osbz8-locus-under-salinity-stress-in-ir64-and-nonabokra-rice-varieties
#9
Amit Paul, Pratiti Dasgupta, Dipan Roy, Shubho Chaudhuri
Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. In this study, we have compared the salinity-induced changes in chromatin modifications at the OsBZ8 locus in salt-tolerant Nonabokra and salt-sensitive IR64 rice varieties...
July 24, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28739643/histone-methyltransferase-dot1l-is-a-coactivator-for-thyroid-hormone-receptor-during-xenopus-development
#10
Luan Wen, Liezhen Fu, Yun-Bo Shi
Histone modifications are associated with transcriptional regulation by diverse transcription factors. Genome-wide correlation studies have revealed that histone activation marks and repression marks are associated with activated and repressed gene expression, respectively. Among the histone activation marks is histone H3 K79 methylation, which is carried out by only a single methyltransferase, disruptor of telomeric silencing-1-like (DOT1L). We have been studying thyroid hormone (T3)-dependent amphibian metamorphosis in two highly related species, the pseudo-tetraploid Xenopus laevis and diploid Xenopus tropicalis, as a model for postembryonic development, a period around birth in mammals that is difficult to study...
July 24, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28738802/histological-and-transcriptomic-effects-of-17%C3%AE-methyltestosterone-on-zebrafish-gonad-development
#11
Stephanie Ling Jie Lee, Julia A Horsfield, Michael A Black, Kim Rutherford, Amanda Fisher, Neil J Gemmell
BACKGROUND: Sex hormones play important roles in teleost ovarian and testicular development. In zebrafish, ovarian differentiation appears to be dictated by an oocyte-derived signal via Cyp19a1a aromatase-mediated estrogen production. Androgens and aromatase inhibitors can induce female-to-male sex reversal, however, the mechanisms underlying gonadal masculinisation are poorly understood. We used histological analyses together with RNA sequencing to characterise zebrafish gonadal transcriptomes and investigate the effects of 17α-methyltestosterone on gonadal differentiation...
July 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28737980/nitration-of-h2b-histone-elicits-an-immune-response-in-experimental-animals
#12
Md Asad Khan, Khursheed Alam, Syed Mehdi Hassan, M Moshahid A Rizvi
Histone H2B is an autoantigen that appears in circulation due to altered apoptosis/or insufficient clearance and is likely to be involved in the induction and progression of autoimmune diseases since modified-H2B is immunogenic. Our studies demonstrate that tyrosines of H2B histone spontaneously converts to free and nitrotyrosine bound protein in vivo. Commercially available H2B histone was modified with peroxynitrite in vitro. Modified H2B was found to be more immunogenic than native form in experimental animals...
July 24, 2017: Autoimmunity
https://www.readbyqxmd.com/read/28736194/the-epigenetic-drug-trichostatin-a-ameliorates-experimental-autoimmune-encephalomyelitis-via-t-cell-tolerance-induction-and-impaired-influx-of-t-cells-into-the-spinal-cord
#13
Arathi Jayaraman, Advait Soni, Bellur Prabhakar, Mark Holterman, Sundararajan Jayaraman
Multiple sclerosis is a T cell mediated chronic demyelinating disease of the central nervous system. Although currently available therapies reduce relapses, they do not facilitate tolerization of myelin antigen-specific T lymphocytes to ensure prolonged protection against multiple sclerosis. Here, we show that treatment of NOD mice with the histone deacetylase inhibitor, Trichostatin A affords robust protection against myelin peptide induced experimental autoimmune encephalomyelitis, a mouse model of multiple sclerosis...
July 20, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28735518/the-possible-prognostic-role-of-histone-deacetylase-and-transforming-growth-factor-%C3%AE-smad-signaling-in-high-grade-gliomas-treated-by-radio-chemotherapy-a-preliminary-immunohistochemical-study
#14
Roberta Sferra, Simona Pompili, Claudio Festuccia, Francesco Marampon, Giovanni L Gravina, Luca Ventura, Ernesto Di Cesare, Sara Cicchinelli, Eugenio Gaudio, Antonella Vetuschi
Glioblastoma (GBM) is the most common and aggressive tumor of the central nervous system. Unfortunately, patients affected by this disease have a very poor prognosis, due to high level of invasiveness and resistance to standard therapies. Although the molecular profile of GBM has been extensively investigated, the events responsible for its pathogenesis and progression remain largely unknown. Histone Deacetylases (HDAC) dependent epigenetic modifications and transforming growth factor (TGF)-β/Smad pathway seem to play an important role in GBM tumorigenesis, resistance to common therapies and poor clinical outcome...
May 16, 2017: European Journal of Histochemistry: EJH
https://www.readbyqxmd.com/read/28735395/chip-seq-analysis-for-identifying-genome-wide-histone-modifications-associated-with-stress-responsive-genes-in-plants
#15
Guosheng Li, Guru Jagadeeswaran, Andrew Mort, Ramanjulu Sunkar
Histone modifications represent the crux of epigenetic gene regulation essential for most biological processes including abiotic stress responses in plants. Thus, identification of histone modifications at the genome-scale can provide clues for how some genes are 'turned-on' while some others are "turned-off" in response to stress. This chapter details a step-by-step protocol for identifying genome-wide histone modifications associated with stress-responsive gene regulation using chromatin immunoprecipitation (ChIP) followed by sequencing of the DNA (ChIP-seq)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28734945/the-epigenomic-revolution-in-breast-cancer-from-single-gene-to-genome-wide-next-generation-approaches
#16
REVIEW
Veronica Davalos, Anna Martinez-Cardus, Manel Esteller
From the first identification of aberrant DNA methylation in primary human tumors more than three decades ago, exponential progress in cancer epigenetics research has been made. For many years, cancer epigenetics studies relied on identification of DNA methylation and histone modifications at specific genes. These studies laid the foundation for the field and revealed the epigenetic alterations as hallmark of cancer, as well as the crucial role of epigenetic mechanisms in tumorigenesis. The introduction of next-generation sequencing and array-based technologies for analyzing epigenetic states has accelerated our understanding about cancer and nowadays have become potent tools in our fight against the disease...
July 19, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28734548/ubiquitin-like-modifications-in-the-dna-damage-response
#17
REVIEW
Zhifeng Wang, Wei-Guo Zhu, Xingzhi Xu
Genomic DNA is damaged at an extremely high frequency by both endogenous and environmental factors. An improper response to DNA damage can lead to genome instability, accelerate the aging process and ultimately cause various human diseases, including cancers and neurodegenerative disorders. The mechanisms that underlie the cellular DNA damage response (DDR) are complex and are regulated at many levels, including at the level of post-translational modification (PTM). Since the discovery of ubiquitin in 1975 and ubiquitylation as a form of PTM in the early 1980s, a number of ubiquitin-like modifiers (UBLs) have been identified, including small ubiquitin-like modifiers (SUMOs), neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), interferon-stimulated gene 15 (ISG15), human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10), ubiquitin-fold modifier 1 (UFRM1), URM1 ubiquitin-related modifier-1 (URM1), autophagy-related protein 12 (ATG12), autophagy-related protein 8 (ATG8), fan ubiquitin-like protein 1 (FUB1) and histone mono-ubiquitylation 1 (HUB1)...
July 11, 2017: Mutation Research
https://www.readbyqxmd.com/read/28733645/hdac3-is-a-molecular-brake-of-the-metabolic-switch-supporting-white-adipose-tissue-browning
#18
Alessandra Ferrari, Raffaella Longo, Erika Fiorino, Rui Silva, Nico Mitro, Gaia Cermenati, Federica Gilardi, Béatrice Desvergne, Annapaola Andolfo, Cinzia Magagnotti, Donatella Caruso, Emma De Fabiani, Scott W Hiebert, Maurizio Crestani
White adipose tissue (WAT) can undergo a phenotypic switch, known as browning, in response to environmental stimuli such as cold. Post-translational modifications of histones have been shown to regulate cellular energy metabolism, but their role in white adipose tissue physiology remains incompletely understood. Here we show that histone deacetylase 3 (HDAC3) regulates WAT metabolism and function. Selective ablation of Hdac3 in fat switches the metabolic signature of WAT by activating a futile cycle of de novo fatty acid synthesis and β-oxidation that potentiates WAT oxidative capacity and ultimately supports browning...
July 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28733598/role-of-hdac9-foxo1-axis-in-the-transcriptional-program-associated-with-hepatic-gluconeogenesis
#19
Jizheng Chen, Zhilei Zhang, Ning Wang, Min Guo, Xiumei Chi, Yu Pan, Jing Jiang, Junqi Niu, Sulaiman Ksimu, John Zhong Li, Xinwen Chen, Qian Wang
Histone deacetylase 9 (HDAC9) regulates hepatic gluconeogenesis by deacetylating Forkhead box O 1 (FoxO1). HDAC9 upregulation is involved in hepatitis C virus (HCV)-associated exaggerated gluconeogenesis. Herein, we found in addition to FoxO1, HDAC9 also regulates other gluconeogenic transcription factors, including peroxisomeproliferator-activated receptor-γ coactivator-1α (PGC-1α), cyclic AMP-responsive element-binding protein (CREB), and glucocorticoid receptor (GR). Unlike FoxO1, which is regulated by post-translational modification responses to HDAC9, HDAC9 regulates PGC-1α, CREB and GR by altering gene expression...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733487/the-stat4-mll1-epigenetic-axis-regulates-the-antimicrobial-functions-of-murine-macrophages
#20
William F Carson, Karen A Cavassani, Elyara M Soares, Soichiro Hirai, Nicolai A Kittan, Matthew A Schaller, Melissa M Scola, Amrita Joshi, Akihiro Matsukawa, David M Aronoff, Craig N Johnson, Yali Dou, Katherine A Gallagher, Steven L Kunkel
Macrophages are critical immune cells for the clearance of microbial pathogens and cellular debris from peripheral tissues. Macrophage inflammatory responses are governed by gene expression patterns, and these patterns are often subject to epigenetic control. Chromatin modifications, such as histone methylation, regulate gene accessibility in macrophages, and macrophage polarization is governed in part by the expression and function of chromatin-modifying enzymes. The histone methyltransferase mixed-lineage leukemia 1 (MLL1) preferentially modifies lysine residue 4 on the unstructured protein tail of histone H3...
July 21, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
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