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Histone modification

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https://www.readbyqxmd.com/read/29350772/arsenite-induced-histone-h3-modification-and-its-effects-on-egr1-and-fos-expression-in-hela-cells
#1
Toshihide Suzuki, Hiroshi Watanabe, Kayoko Kita, Taro Honma, Takafumi Ochi
It is evident that trivalent arsenicals do not have mutagenicity, but they are human carcinogens. Recently, epigenetic modification has been considered as one of the important causes of arsenical carcinogenicity. Here we examined global histone H3 modification by trivalent inorganic arsenite (iAs(III)) and its contribution to gene expression in HeLa cells. iAs(III) induced histone H3K9 dimethylation (H3K9me2) and trimethylation (H3K9me3), histone H3S10 phosphorylation (H3S10p), histone H3T11 phosphorylation (H3T11p) and histone H3K9S10 trimethyl-phosphorylation (H3K9me3S10p)...
January 19, 2018: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/29348483/cell-type-specific-survey-of-epigenetic-modifications-by-tandem-chromatin-immunoprecipitation-sequencing
#2
Mari Mito, Mitsutaka Kadota, Kaori Tanaka, Yasuhide Furuta, Kuniya Abe, Shintaro Iwasaki, Shinichi Nakagawa
The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29345920/acetylation-by-eis-and-deacetylation-by-rv1151c-of-mycobacterium-tuberculosis-hupb-biochemical-and-structural-insight
#3
Keith D Green, Tapan Biswas, Allan H Pang, Melisa J Willby, Matthew S Reed, Olga Stuchlik, Jan Pohl, James E Posey, Oleg V Tsodikov, Sylvie Garneau-Tsodikova
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29343059/top-down-characterization-of-heavily-modified-histones-using-193-nm-ultraviolet-photodissociation-uvpd-mass-spectrometry
#4
Sylvester M Greer, Jennifer S Brodbelt
The characterization of protein post-translational modifications (PTMs) remains a significant challenge for traditional bottom-up proteomics methods owing to the lability of PTMs and the difficulty of mapping combinatorial patterns of PTMs based on analysis of small peptides. These shortcomings have accelerated interest in top-down MS/MS methods which focus on analysis of intact proteins. Mapping all protein PTMs simultaneously requires the ability to obtain extensive sequence coverage to allow confident localization of the modifications...
January 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29340707/vrk1-and-aurkb-form-a-complex-that-cross-inhibit-their-kinase-activity-and-the-phosphorylation-of-histone-h3-in-the-progression-of-mitosis
#5
David S Moura, Ignacio Campillo-Marcos, Marta Vázquez-Cedeira, Pedro A Lazo
Regulation of cell division requires the integration of signals implicated in chromatin reorganization and coordination of its sequential changes in mitosis. Vaccinia-related kinase 1 (VRK1) and Aurora B (AURKB) are two nuclear kinases involved in different steps of cell division. We have studied whether there is any functional connection between these two nuclear kinases, which phosphorylate histone H3 in Thr3 and Ser10, respectively. VRK1 and AURKB are able to form a stable protein complex, which represents only a minor subpopulation of each kinase within the cell and is detected following nocodazole release...
January 16, 2018: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/29339751/jmjc-domain-proteins-modulate-circadian-behaviors-and-sleep-in-drosophila
#6
Nevine A Shalaby, Jorge H Pinzon, Anjana S Narayanan, Eugene Jennifer Jin, Morgan P Ritz, Rachel J Dove, Heike Wolfenberg, Aylin R Rodan, Michael Buszczak, Adrian Rothenfluh
Jumonji (JmjC) domain proteins are known regulators of gene expression and chromatin organization by way of histone demethylation. Chromatin modification and remodeling provides a means to modulate the activity of large numbers of genes, but the importance of this class of predicted histone-modifying enzymes for different aspects of post-developmental processes remains poorly understood. Here we test the function of all 11 non-lethal members in the regulation of circadian rhythms and sleep. We find loss of every Drosophila JmjC gene affects different aspects of circadian behavior and sleep in a specific manner...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339543/genes-predisposed-to-dna-hypermethylation-during-acquired-resistance-to-chemotherapy-are-identified-in-ovarian-tumors-by-bivalent-chromatin-domains-at-initial-diagnosis
#7
Edward Curry, Constanze Zeller, Nahal Masrour, Darren Patten, John Gallon, Charlotte S Wilhelm-Benartzi, Sadaf Ghaem-Maghami, David D L Bowtell, Robert Brown
Bivalent chromatin domains containing both active H3K4me3 and repressive H3K27me3 histone marks define gene sets poised for expression or silencing in differentiating embryonic stem (ES) cells. In cancer cells aberrantly poised genes may facilitate changes in transcriptional states after exposure to anti-cancer drugs. In this study, we used ChIP-seq to characterize genome-wide positioning of H3K4me3 and H3K27me3-associated chromatin in primary high-grade serous ovarian carcinomas and in normal ovarian surface and fallopian tube tissue...
January 16, 2018: Cancer Research
https://www.readbyqxmd.com/read/29339515/mers-cov-and-h5n1-influenza-virus-antagonize-antigen-presentation-by-altering-the-epigenetic-landscape
#8
Vineet D Menachery, Alexandra Schäfer, Kristin E Burnum-Johnson, Hugh D Mitchell, Amie J Eisfeld, Kevin B Walters, Carrie D Nicora, Samuel O Purvine, Cameron P Casey, Matthew E Monroe, Karl K Weitz, Kelly G Stratton, Bobbie-Jo M Webb-Robertson, Lisa E Gralinski, Thomas O Metz, Richard D Smith, Katrina M Waters, Amy C Sims, Yoshihiro Kawaoka, Ralph S Baric
Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems-based approach, we examined differential regulation of IFN-γ-dependent genes following infection with robust respiratory viruses including influenza viruses [A/influenza/Vietnam/1203/2004 (H5N1-VN1203) and A/influenza/California/04/2009 (H1N1-CA04)] and coronaviruses [severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV)]...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29337990/clustering-gene-expression-time-series-data-using-an-infinite-gaussian-process-mixture-model
#9
Ian C McDowell, Dinesh Manandhar, Christopher M Vockley, Amy K Schmid, Timothy E Reddy, Barbara E Engelhardt
Transcriptome-wide time series expression profiling is used to characterize the cellular response to environmental perturbations. The first step to analyzing transcriptional response data is often to cluster genes with similar responses. Here, we present a nonparametric model-based method, Dirichlet process Gaussian process mixture model (DPGP), which jointly models cluster number with a Dirichlet process and temporal dependencies with Gaussian processes. We demonstrate the accuracy of DPGP in comparison to state-of-the-art approaches using hundreds of simulated data sets...
January 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29337851/transcriptional-regulation-by-cpg-sites-methylation-in-the-core-promoter-region-of-the-bovine-six1-gene-roles-of-histone-h4-and-e2f2
#10
Dawei Wei, Anning Li, Chunping Zhao, Hongbao Wang, Chugang Mei, Rajwali Khan, Linsen Zan
DNA methylation is a major epigenetic modification of the genome and has an essential role in muscle development. The SIX1 gene is thought to play a principal role in mediating skeletal muscle development. In the present study, we determined that bovine SIX1 expression levels were significantly higher in the fetal bovine group (FB) and in undifferentiated Qinchuan cattle muscle cells (QCMCs) than in the adult bovine group (AB) and in differentiated QCMCs. Moreover, a bisulfite sequencing polymerase chain reaction (BSP) analysis of DNA methylation levels showed that three CpG sites in the core promoter region (-216/-28) of the bovine SIX1 gene exhibited significantly higher DNA methylation levels in the AB and differentiated QCMCs groups...
January 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29337423/the-next-generation-of-melanocyte-data-genetic-epigenetic-and-transcriptional-resource-datasets-and-analysis-tools
#11
Stacie K Loftus
Genomics is a common thread linking all aspects of pigment cell biology, including melanocyte- and melanosome-related functions, pigmentary disorders, normal human pigmentation variation and melanoma. Recently, genomic-scale Next Generation Sequencing (NGS) analyses have rapidly expanded, because of reductions in sequencing costs, increased assay sensitivity, and smaller sample requirement. These NGS technologies have been adapted to assay RNA transcript expression, chromatin accessibility, DNA methylation, histone modifications, and transcription factor binding...
January 16, 2018: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/29337251/chromatin-organization-regulated-by-ezh2-mediated-h3k27me3-is-required-for-opn-induced-migration-of-bone-marrow-derived-mesenchymal-stem-cells
#12
Lingling Liu, Qing Luo, Jinghui Sun, Yang Ju, Yasuyuki Morita, Guanbin Song
Osteopontin (OPN) is a chemokine-like extracellular matrix-associated protein involved in the migration of bone marrow-derived mesenchymal stem cells (BMSCs). An increasing number of studies have found that chromatin organization may affect cellular migration. However, whether OPN regulates chromatin organization is not understood, nor are the underlying molecular mechanisms. In this study, we investigated the link between chromatin organization and BMSC migration and demonstrated that OPN-mediated BMSC migration leads to elevated levels of heterochromatin marker histone H3 lysine 27 trimethylation (H3K27me3) through the methyltransferase EZH2...
January 11, 2018: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29336373/advances-of-long-noncoding-rnas-mediated-regulation-in-reproduction
#13
REVIEW
Kang-Sheng Liu, Tai-Ping Li, Hua Ton, Xiao-Dong Mao, Ya-Jun Chen
OBJECTIVE: Advances in genomics and molecular biology have led to the discovery of a large group of uncharacterized long noncoding RNAs (lncRNAs). Emerging evidence indicated that many lncRNAs function in multiple biological processes and its dysregulation often causes diseases. Recent studies suggested that almost all regulatory lncRNAs interact with biological macromolecules such as DNA, RNA, and protein. LncRNAs regulate gene expression mainly on three levels, including epigenetic modification, transcription, and posttranscription, through DNA methylation, histone modification, and chromatin remodeling...
January 20, 2018: Chinese Medical Journal
https://www.readbyqxmd.com/read/29335608/n6-methyladenosine-rna-modification-regulates-embryonic-neural-stem-cell-self-renewal-through-histone-modifications
#14
Yang Wang, Yue Li, Minghui Yue, Jun Wang, Sandeep Kumar, Robert J Wechsler-Reya, Zhaolei Zhang, Yuya Ogawa, Manolis Kellis, Gregg Duester, Jing Crystal Zhao
Internal N6-methyladenosine (m6A) modification is widespread in messenger RNAs (mRNAs) and is catalyzed by heterodimers of methyltransferase-like protein 3 (Mettl3) and Mettl14. To understand the role of m6A in development, we deleted Mettl14 in embryonic neural stem cells (NSCs) in a mouse model. Phenotypically, NSCs lacking Mettl14 displayed markedly decreased proliferation and premature differentiation, suggesting that m6A modification enhances NSC self-renewal. Decreases in the NSC pool led to a decreased number of late-born neurons during cortical neurogenesis...
January 15, 2018: Nature Neuroscience
https://www.readbyqxmd.com/read/29335368/in-medio-stat-virtus-unanticipated-consequences-of-telomere-dysequilibrium
#15
REVIEW
Lea Harrington, Fabio Pucci
The integrity of chromosome ends, or telomeres, depends on myriad processes that must balance the need to compact and protect the telomeric, G-rich DNA from detection as a double-stranded DNA break, and yet still permit access to enzymes that process, replicate and maintain a sufficient reserve of telomeric DNA. When unable to maintain this equilibrium, erosion of telomeres leads to perturbations at or near the telomeres themselves, including loss of binding by the telomere protective complex, shelterin, and alterations in transcription and post-translational modifications of histones...
March 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29335024/sex-differences-in-the-late-first-trimester-human-placenta-transcriptome
#16
Tania L Gonzalez, Tianyanxin Sun, Alexander F Koeppel, Bora Lee, Erica T Wang, Charles R Farber, Stephen S Rich, Lauren W Sundheimer, Rae A Buttle, Yii-Der Ida Chen, Jerome I Rotter, Stephen D Turner, John Williams, Mark O Goodarzi, Margareta D Pisarska
BACKGROUND: Development of the placenta during the late first trimester is critical to ensure normal growth and development of the fetus. Developmental differences in this window such as sex-specific variation are implicated in later placental disease states, yet gene expression at this time is poorly understood. METHODS: RNA-sequencing was performed to characterize the transcriptome of 39 first trimester human placentas using chorionic villi following genetic testing (17 females, 22 males)...
January 15, 2018: Biology of Sex Differences
https://www.readbyqxmd.com/read/29332244/structural-insights-into-the-function-of-elongator
#17
REVIEW
Udit Dalwadi, Calvin K Yip
Conserved from yeast to humans, Elongator is a protein complex implicated in multiple processes including transcription regulation, α-tubulin acetylation, and tRNA modification, and its defects have been shown to cause human diseases such as familial dysautonomia. Elongator consists of two copies of six core subunits (Elp1, Elp2, Elp3, Elp4, Elp5, and Elp6) that are organized into two subcomplexes: Elp1/2/3 and Elp4/5/6 and form a stable assembly of ~ 850 kDa in size. Although the catalytic subunit of Elongator is Elp3, which contains a radical S-adenosyl-L-methionine (SAM) domain and a putative histone acetyltransferase domain, the Elp4/5/6 subcomplex also possesses ATP-modulated tRNA binding activity...
January 13, 2018: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/29331887/idh1r132h-promotes-malignant-transformation-of-benign-prostatic-epithelium-by-dysregulating-micrornas-involvement-of-igf1r-akt-stat3-signaling-pathway
#18
Lili Zhang, Mei Qi, Tingting Feng, Jing Hu, Lin Wang, Xinjun Li, Wei Gao, Hui Liu, Meng Jiao, Zhen Wu, Xinnuo Bai, Yifan Bie, Long Liu, Bo Han
Risk stratification using molecular features could potentially help distinguish indolent from aggressive prostate cancer (PCa). Mutations in isocitrate dehydrogenase (IDH) acquire an abnormal enzymatic activity, resulting in the production of 2-hydroxyglutarate and alterations in cellular metabolism, histone modification, and DNA methylation. Mutant IDH1 has been identified in various human malignancies, and IDH1R132H constituted the vast majority of mutational events of IDH1. Most recent studies suggested that IDH1 mutations define a methylator subtype in PCa...
January 11, 2018: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29330124/manipulating-the-epigenome-for-the-treatment-of-disorders-with-thrombotic-complications
#19
REVIEW
Faith A A Kwa, Denise E Jackson
The haemostatic system is tightly regulated to maintain homeostasis to avoid unwanted bleeding or thrombotic complications. Recent research has highlighted the importance of epigenetic changes, such as DNA methylation, histone modifications, and miRNA-based mechanisms, that alter gene expression. This can give rise to dysregulated haemostatic or vascular expressed molecules contributing to the development of thrombotic complications. Targeting these epigenetic changes could provide a new avenue for the treatment of pathological blood clots...
January 9, 2018: Drug Discovery Today
https://www.readbyqxmd.com/read/29330049/the-histone-demethylase-phf8-promotes-adult-acute-lymphoblastic-leukemia-through-interaction-with-the-mek-erk-signaling-pathway
#20
Yue Fu, Yaling Yang, Xiaoming Wang, Xiaolin Yin, Minran Zhou, Siqi Wang, Lin Yang, Tao Huang, Man Xu, Chunyan Chen
Adult acute lymphoblastic leukemia (ALL) is a malignant disorder of lymphoid progenitor cells that is associated with a high risk of relapse and poor prognosis. Thus, novel pathogenic mechanisms and therapeutic targets need to be explored. Histone methylation is one of the most significant chromatin post-translational modifications. Here, we show that the histone demethylase PHF8 is highly expressed in a large number of ALL clinical specimens and that PHF8 expression is associated with ALL progression. PHF8 knockdown inhibits proliferation and promotes the apoptosis of ALL cells in vitro as well as attenuates tumor growth in vivo...
January 9, 2018: Biochemical and Biophysical Research Communications
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