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histone acetylation

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https://www.readbyqxmd.com/read/28448740/sequencing-on-the-solid-5500xl-system-in-depth-characterization-of-the-gc-bias
#1
Simone Roeh, Peter Weber, Monika Rex-Haffner, Jan M Deussing, Elisabeth B Binder, Mira Jakovcevski
Different types of sequencing biases have been described and subsequently improved for a variety of sequencing systems, mostly focusing on the widely used Illumina systems. Similar studies are missing for the SOLiD 5500xl system, a sequencer which produced many data sets available to researchers today. Describing and understanding the bias is important to accurately interpret and integrate these published data in various ongoing research projects. We report a particularly strong GC bias for this sequencing system when analyzing a defined gDNA mix of five microbes with a wide range of different GC contents (20-72%) when comparing to the expected distribution and Illumina MiSeq data from the same DNA pool...
April 27, 2017: Nucleus
https://www.readbyqxmd.com/read/28447752/islet-1-induces-the-differentiation-of-mesenchymal-stem-cells-into-cardiomyocyte-like-cells-through-the-regulation-of-gcn5-and-dnmt-1
#2
Qin Yi, Hao Xu, Ke Yang, Yue Wang, Bin Tan, Jie Tian, Jing Zhu
Previous studies from this group demonstrated that insulin gene enhancer binding protein ISL-1 (Islet-1) specifically induces the differentiation of mesenchymal stem cells (MSCs) into cardiomyocyte‑like cells through histone acetylation. However, the underlying mechanisms remain unclear. In the present study, the role of the histone acetylation and DNA methylation on the regulatory mechanism of the Islet‑1 was further investigated by methylation‑specific polymerase chain reaction (PCR), chromatin immunoprecipitation quantitative PCR and western blot analysis...
March 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447718/role-of-histone-deacetylase-expression-levels-and-activity-in-the-inflammatory-responses-of-patients-with-chronic-hepatitis-b
#3
Haiyue Zhang, Xun Li, Qian Zhang, Fan Yang, Xiaogang Chu, Di Zhang, Luwen Wang, Zuojiong Gong
Histone acetylation has been demonstrated to serve a pivotal role in numerous inflammatory diseases. The present study examined histone acetylation in patients with chronic hepatitis B (CHB) and CHB with liver failure by detecting histone deacetylase (HDAC) activity. Mice with acute liver failure (ALF) were treated with the HDAC inhibitor entinostat (MS275) and alterations in HDAC activity and pro‑inflammatory cytokine expression levels were detected. The effect of HDAC1 silencing on LPS-treated RAW264.7 murine macrophages was examined using specific small interfering RNA sequences, and the acetylation level of the non‑histone nuclear factor‑κB (NF‑κB) p65 subunit was additionally examined...
March 7, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447071/the-effects-of-reduced-rpd3-levels-on-fly-physiology
#4
Jared K Woods, Tahereh Ziafazeli, Blanka Rogina
BACKGROUND: Rpd3 is a conserved histone deacetylase that removes acetyl groups from lysine residues within histones and other proteins. Reduction or inhibition of Rpd3 extends longevity in yeast, worms, and flies. Previous studies in flies suggest an overlap with the mechanism of lifespan extension by dietary restriction. However, the mechanism of rpd3's effects on longevity remains unclear. OBJECTIVES: In this study we investigated how rpd3 reduction affects fly spontaneous physical activity, fecundity, and stress resistance...
March 31, 2017: Nutrition and Healthy Aging
https://www.readbyqxmd.com/read/28445736/systematic-epigenomic-analysis-reveals-chromatin-states-associated-with-melanoma-progression
#5
Petko Fiziev, Kadir C Akdemir, John P Miller, Emily Z Keung, Neha S Samant, Sneha Sharma, Christopher A Natale, Christopher J Terranova, Mayinuer Maitituoheti, Samirkumar B Amin, Emmanuel Martinez-Ledesma, Mayura Dhamdhere, Jacob B Axelrad, Amiksha Shah, Christine S Cheng, Harshad Mahadeshwar, Sahil Seth, Michelle C Barton, Alexei Protopopov, Kenneth Y Tsai, Michael A Davies, Benjamin A Garcia, Ido Amit, Lynda Chin, Jason Ernst, Kunal Rai
The extent and nature of epigenomic changes associated with melanoma progression is poorly understood. Through systematic epigenomic profiling of 35 epigenetic modifications and transcriptomic analysis, we define chromatin state changes associated with melanomagenesis by using a cell phenotypic model of non-tumorigenic and tumorigenic states. Computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer-regulatory genes in important melanoma-driving cell signaling pathways...
April 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28444663/transcriptional-coactivator-p300-and-silent-information-regulator-1-sirt1-gene-polymorphism-associated-with-diabetic-kidney-disease-in-a-chinese-cohort
#6
Kang Tang, Mingfang Sun, Jing Shen, Bo Zhou
One of the most serious complications of diabetes mellitus, which could lead to end-stage renal disease across all demographics, is 'diabetic kidney disease'. However, how diabetic kidney disease develops remains unclear. Studies conducted thus far suggest that a major factor in the origination and development of the disease occurs through histone acetylation modifications. This study aims to examine the probable relationship in Chinese patients suffering from type 2 diabetes. A case-control study was conducted in the Chongqing region of China on the Chinese Han population...
April 25, 2017: Experimental and Clinical Endocrinology & Diabetes
https://www.readbyqxmd.com/read/28444370/identification-of-hda15-pif1-as-a-key-repression-module-directing-the-transcriptional-network-of-seed-germination-in-the-dark
#7
Dachuan Gu, Chia-Yang Chen, Minglei Zhao, Linmao Zhao, Xuewu Duan, Jun Duan, Keqiang Wu, Xuncheng Liu
Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated transcription regulation remains largely unclear. Here, we identified that histone deacetylase15 (HDA15) is a negative component of PHYB-dependent seed germination. Overexpression of HDA15 in Arabidopsis inhibits PHYB-dependent seed germination, whereas loss of function of HDA15 increases PHYB-dependent seed germination...
April 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28443467/effect-of-irinotecan-on-hmgb1-mmp9-expression-cell-cycle-and-cell-growth-in-breast-cancer-mcf-7-cells
#8
Saeedeh Keyvani-Ghamsari, Azra Rabbani-Chadegani, Javad Sargolzaei, Maryam Shahhoseini
Irinotecan is a natural alkaloid agent widely used in cancer therapy. High-mobility group protein B1 as a non-histone chromosomal protein plays a fundamental role in gene expression and inflammation. In this study, the effect of irinotecan on high-mobility group protein B1 and MMP9 content, gene expression, cell cycle, and cell growth in human breast cancer cells (MCF-7) was investigated. The cells were exposed to various concentrations of irinotecan and the viability determined by trypan blue exclusion and 3-(4,5-dimethylthiazal-2-yl)-2,5-diphenyltetrazolium bromide assays...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28442993/alcohol-induced-neuroadaptation-is-orchestrated-by-the-histone-acetyltransferase-cbp
#9
Alfredo Ghezzi, Xiaolei Li, Linda K Lew, Thilini P Wijesekera, Nigel S Atkinson
Homeostatic neural adaptations to alcohol underlie the production of alcohol tolerance and the associated symptoms of withdrawal. These adaptations have been shown to persist for relatively long periods of time and are believed to be of central importance in promoting the addictive state. In Drosophila, a single exposure to alcohol results in long-lasting alcohol tolerance and symptoms of withdrawal following alcohol clearance. These persistent adaptations involve mechanisms such as long-lasting changes in gene expression and perhaps epigenetic restructuring of chromosomal regions...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28442629/blocking-a-signal-to-host-cell-histones
#10
Alexandra A Mushegian
A plant pathogen suppresses the host immune response by preventing histone acetylation.
April 25, 2017: Science Signaling
https://www.readbyqxmd.com/read/28442255/acetanilide-and-bromoacetyl-lysine-derivatives-as-activators-for-human-histone-deacetylase-8
#11
Yusif M Mukhtar, Yajun Huang, Jiajia Liu, Di Chen, Weiping Zheng
In the current study, seven compounds (i.e. 1-7) were found to be novel activators for the N(ε)-acetyl-lysine deacetylation reaction catalyzed by human histone deacetylase 8 (HDAC8). When assessed with the commercially available HDAC8 peptide substrate Fluor-de-Lys®-HDAC8 that harbors the unnatural 7-amino-4-methylcoumarin (AMC) residue immediately C-terminal to the N(ε)-acetyl-lysine residue to be deacetylated, our compounds exhibited comparable activation potency to that of TM-2-51, the strongest HDAC8 activator reported in the current literature...
April 13, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28442024/intracytoplasmic-oxidative-stress-reverses-epigenetic-modifications-in-polycystic-ovary-syndrome
#12
Fatemeh Eini, Marefat Ghaffari Novin, Khojasteh Joharchi, Ahmad Hosseini, Hamid Nazarian, Abbas Piryaei, Arash Bidadkosh
In polycystic ovary syndrome (PCOS), substantial genetic and environmental alterations, along with hyperandrogenism, affect the quality of oocytes and decrease ovulation rates. To determine the mechanisms underlying these alterations caused specifically by an increase in plasma androgens, the present study was performed in experimentally-induced PCOS mice. As the study model, female B6D2F1 mice were treated with dehydroepiandrosterone (DHEA, 6mg per 100g bodyweight). After 20 days, oocytes at the germinal vesicle and metaphase II stages were retrieved from isolated ovaries and subsequent analyses of oocyte quality were performed for each mouse...
April 26, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28440559/a-phase-2-study-of-mocetinostat-a-histone-deacetylase-inhibitor-in-relapsed-or-refractory-lymphoma
#13
Connie L Batlevi, Michael Crump, Charalambos Andreadis, David Rizzieri, Sarit E Assouline, Susan Fox, Richard H C van der Jagt, Amanda Copeland, Diane Potvin, Richard Chao, Anas Younes
Deregulation of histone deacetylase (HDAC) is important in the pathogenesis of follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Mocetinostat, an isotype-selective HDAC inhibitor, induces accumulation of acetylated histones, cell cycle arrest and apoptosis in several cancers. This phase 2 study evaluated mocetinostat in patients with relapsed/refractory (R/R) DLBCL and FL. Seventy-two patients received mocetinostat (starting doses: 70-110 mg TIW, 4-week cycles). The best overall response rate (95% CI) was 18·9% (7·2, 32·2) for the DLBCL cohort (n = 41), and 11·5% (1·7, 20·7) for the FL cohort (n = 31)...
April 25, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28436938/geminin-facilitates-foxo3-deacetylation-to-promote-breast-cancer-cell-metastasis
#14
Lei Zhang, Meizhen Cai, Zhicheng Gong, Bingchang Zhang, Yuanpei Li, Li Guan, Xiaonan Hou, Qing Li, Gang Liu, Zengfu Xue, Muh-Hua Yang, Jing Ye, Y Eugene Chin, Han You
Geminin expression is essential for embryonic development and the maintenance of chromosomal integrity. In spite of this protective role, geminin is also frequently overexpressed in human cancers and the molecular mechanisms underlying its role in tumor progression remain unclear. The histone deacetylase HDAC3 modulates transcription factors to activate or suppress transcription. Little is known about how HDAC3 specifies substrates for modulation among highly homologous transcription factor family members. Here, we have demonstrated that geminin selectively couples the transcription factor forkhead box O3 (FoxO3) to HDAC3, thereby specifically facilitating FoxO3 deacetylation...
April 24, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28435027/exercise-modulated-epigenetic-markers-and-inflammatory-response-in-copd-individuals-a-pilot-study
#15
Ivy Reichert Vital da Silva, Cintia Laura Pereira de Araujo, Gilson Pires Dorneles, Alessandra Peres, Andreia Luciana Bard, Gustavo Reinaldo, Paulo José Zimermann Teixeira, Pedro Dal Lago, Viviane Rostirola Elsner
The study investigated the effects of exercise on epigenetic signals and systemic cytokine levels in chronic obstructive pulmonary disease (COPD) individuals. Ten participants of a pulmonary rehabilitation program were submitted to 24 sessions of a supervisioned exercise protocol thrice-weekly (90min/session). Blood samples were collected at baseline, after the 1st session, before and after the 24th session. A DNA hypomethylation status was observed after the 1st session when compared at baseline, while global histone H4 acetylation status was unaltered in any time-points evaluated...
April 19, 2017: Respiratory Physiology & Neurobiology
https://www.readbyqxmd.com/read/28434780/total-chemical-synthesis-of-methylated-analogues-of-histone-3-revealed-kdm4d-as-a-potential-regulator-of-h3k79me3
#16
Muhammad Jbara, Noga Guttmann-Raviv, Suman Kumar Maity, Nabieh Ayoub, Ashraf Brik
Histone H3 methylation plays an important role in regulating gene expression. In histones in general, this mark is dynamically regulated via various demethylases, which found to control cell fate decisions as well as linked to several diseases, including neurological and cancer. Despite major progress in studying methylation mark at various positions in H3 histone proteins, less is known about the regulation of methylated H3 at Lys79. Methylation at this site is known to have direct cross-talk with monoubiquitination of histone H2B at positions Lys120 and 34, as well as with acetylated H3 at Lys9...
April 12, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28433423/prefrontal-cortex-expression-of-chromatin-modifier-genes-in-male-wsp-and-wsr-mice-changes-across-ethanol-dependence-withdrawal-and-abstinence
#17
Joel G Hashimoto, David P Gavin, Kristine M Wiren, John C Crabbe, Marina Guizzetti
Alcohol-use disorder (AUD) is a relapsing disorder associated with excessive ethanol consumption. Recent studies support the involvement of epigenetic mechanisms in the development of AUD. Studies carried out so far have focused on a few specific epigenetic modifications. The goal of this project was to investigate gene expression changes of epigenetic regulators that mediate a broad array of chromatin modifications after chronic alcohol exposure, chronic alcohol exposure followed by 8 h withdrawal, and chronic alcohol exposure followed by 21 days of abstinence in Withdrawal-Resistant (WSR) and Withdrawal Seizure-Prone (WSP) selected mouse lines...
March 14, 2017: Alcohol
https://www.readbyqxmd.com/read/28433418/binge-alcohol-alters-pnpla3-levels-in-liver-through-epigenetic-mechanism-involving-histone-h3-acetylation
#18
REVIEW
Ricardo J Restrepo, Robert W Lim, Ronald J Korthuis, Shivendra D Shukla
The human PNPLA3 (patatin-like phospholipase domain-containing 3) gene codes for a protein which is highly expressed in adipose tissue and liver, and is implicated in lipid homeostasis. While PNPLA3 protein contains regions homologous to functional lipolytic proteins, the regulation of its tissue expression is reflective of lipogenic genes. A naturally occurring genetic variant of PNPLA3 in humans has been linked to increased susceptibility to alcoholic liver disease. We have examined the modulatory effect of alcohol on PNPLA3 protein and mRNA expression as well as the association of its gene promoter with acetylated histone H3K9 by chromatin immunoprecipitation (ChIP) assay in rat hepatocytes in vitro, and in vivo in mouse and rat models of acute binge, chronic, and chronic followed by acute binge ethanol administration...
March 12, 2017: Alcohol
https://www.readbyqxmd.com/read/28432877/maternal-low-protein-diet-decreases-brain-derived-neurotrophic-factor-expression-in-the-brains-of-the-neonatal-rat-offspring
#19
Gurdeep Marwarha, Kate Claycombe-Larson, Jared Schommer, Othman Ghribi
Prenatal exposure to a maternal low-protein (LP) diet has been known to cause cognitive impairment, learning and memory deficits. However, the underlying mechanisms have not been identified. Herein, we demonstrate that a maternal LP diet causes, in the brains of the neonatal rat offspring, an attenuation in the basal expression of the brain-derived neurotrophic factor (BDNF), a neurotrophin indispensable for learning and memory. Female rats were fed either a 20% normal protein (NP) diet or an 8% LP 3 weeks before breeding and during the gestation period...
April 6, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28432707/suberoylanilide-hydroxamic-acid-a-novel-histone-deacetylase-inhibitor-improves-the-development-and-acetylation-level-of-miniature-porcine-handmade-cloning-embryos
#20
J M Sun, K Q Cui, Z P Li, X R Lu, Z F Xu, Q Y Liu, B Huang, D S Shi
Histone deacetylase inhibitors (HDACis) can change the histone acetylation and significantly enhance the developmental competence of the pre-implantation SCNT embryo. To select a proper histone deacetylase inhibitor to improve the success rate and potentially developmental ability of handmade cloning (HMC) embryos of miniature porcine, we compared the effect of two histone deacetylase inhibitors (SAHA vs. VPA) on HMC embryo development, their histone acetylation level and the expression level of relevant genes...
April 22, 2017: Reproduction in Domestic Animals, Zuchthygiene
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