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https://www.readbyqxmd.com/read/28812986/epigenome-aberrations-emerging-driving-factors-of-the-clear-cell-renal-cell-carcinoma
#1
REVIEW
Ali Mehdi, Yasser Riazalhosseini
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28808893/epigenetics-and-bone-remodeling
#2
REVIEW
Ali Husain, Matlock A Jeffries
PURPOSE OF REVIEW: Bone remodeling is a diverse field of study with many direct clinical applications; past studies have implicated epigenetic alterations as key factors of both normal bone tissue development and function and diseases of pathologic bone remodeling. The purpose of this article is to review the most important recent advances that link epigenetic changes to the bone remodeling field. RECENT FINDINGS: Epigenetics describes three major phenomena: DNA modification via methylation, histone side chain modifications, and short non-coding RNA sequences which work in concert to regulate gene transcription in a heritable fashion...
August 14, 2017: Current Osteoporosis Reports
https://www.readbyqxmd.com/read/28808264/knockdown-of-lncrna-mir31hg-inhibits-adipocyte-differentiation-of-human-adipose-derived-stem-cells-via-histone-modification-of-fabp4
#3
Yiping Huang, Chanyuan Jin, Yunfei Zheng, Xiaobei Li, Shan Zhang, Yixin Zhang, Lingfei Jia, Weiran Li
Adipogenesis plays an important role in the regulation of whole-body energy homeostasis and is inextricably related to obesity. Several studies have highlighted the relevance of microRNAs in adipocyte differentiation, but the contributions of long non-coding RNAs (lncRNAs) are still largely uncharacterized. Here, we determined that lncRNA MIR31HG is related to adipocyte lineage commitment. We demonstrated that knockdown of MIR31HG inhibited adipocyte differentiation, whereas overexpression of MIR31HG promoted adipogenesis in vitro and in vivo...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807921/candida-albicans-swi-snf-and-mediator-complexes-differentially-regulate-mrr1-induced-mdr1-expression-and-fluconazole-resistance
#4
Zhongle Liu, Lawrence C Myers
Long-term azole treatment of patients with chronic Candida albicans infections can lead to drug resistance. Gain-of-function (GOF) mutations in the transcription factor Mrr1 and the consequent transcriptional activation of MDR1, a drug efflux coding gene, is a common pathway by which this human fungal pathogen acquires fluconazole resistance. This work elucidates the previously unknown downstream transcription mechanisms utilized by hyperactive Mrr1. We've identified the Swi/Snf chromatin remodeling complex as a key co-activator for Mrr1, which is required to maintain basal and induced 'open' chromatin, and Mrr1 occupancy, at the MDR1 promoter...
August 14, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28799233/stochastics-of-cellular-differentiation-explained-by-epigenetics-the-case-of-t-cell-differentiation-and-functional-plasticity
#5
REVIEW
Jaydeep Bhat, Johannes Helmuth, Guranda Chitadze, Léonce Kouakanou, Christian Peters, Martin Vingron, Ole Ammerpohl, Dieter Kabelitz
Epigenetic marks including histone modifications and DNA methylation are associated to the regulation of gene expression and activity. In addition, an increasing number of non-coding RNAs with regulatory activity on gene expression have been identified. Alongside, technological advancements allow for the analysis of these mechanisms with high resolution - up to the single-cell level. For instance, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) simultaneously probes for chromatin accessibility and nucleosome positioning...
August 10, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28798233/the-atad2-bromodomain-binds-different-acetylation-marks-on-the-histone-h4-in-similar-fuzzy-complexes
#6
Cassiano Langini, Amedeo Caflisch, Andreas Vitalis
Bromodomains are protein modules adopting conserved helix-bundle folds. Some bromodomain-containing proteins, such as ATPase family AAA domain-containing protein 2 (ATAD2), isoform A, have attracted much interest because they are overexpressed in many types of cancer. Bromodomains bind to acetylated lysine residues on histone tails and thereby facilitate the reading of the histone code. Epigenetic regulators in general have been implicated as indicators, mediators, or causes of a large number of diseases and disorders...
August 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28793054/revealing-potential-long-non-coding-rna-biomarkers-in-lung-adenocarcinoma-using-long-non-coding-rna-mediated-competitive-endogenous-rna-network
#7
T-G Zhu, X Xiao, Q Wei, M Yue, L-X Zhang
In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value >0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure...
August 7, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28791254/transcriptional-profiling-defines-histone-acetylation-as-a-regulator-of-gene-expression-during-human-to-mosquito-transmission-of-the-malaria-parasite-plasmodium-falciparum
#8
Che J Ngwa, Meike J Kiesow, Olga Papst, Lindsey M Orchard, Michael Filarsky, Alina N Rosinski, Till S Voss, Manuel Llinás, Gabriele Pradel
Transmission of the malaria parasite Plasmodium falciparum from the human to the mosquito is mediated by the intraerythrocytic gametocytes, which, once taken up during a blood meal, become activated to initiate sexual reproduction. Because gametocytes are the only parasite stages able to establish an infection in the mosquito, they are crucial for spreading the tropical disease. During gametocyte maturation, different repertoires of genes are switched on and off in a well-coordinated sequence, pointing to regulatory mechanisms of gene expression...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28783101/analysis-of-argonaute-4-associated-long-non-coding-rna-in-arabidopsis-thaliana-sheds-novel-insights-into-gene-regulation-through-rna-directed-dna-methylation
#9
Phil Chi Khang Au, Elizabeth S Dennis, Ming-Bo Wang
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28780716/epigenetics-a-potential-key-mechanism-involved-in-the-pathogenesis-of-cardiorenal-syndromes
#10
REVIEW
Grazia Maria Virzì, Anna Clementi, Alessandra Brocca, Massimo de Cal, Claudio Ronco
Epigenetics is defined as the heritable changes in gene expression patterns which are not directly encoded by modifications in the nucleotide DNA sequence of the genome, including higher order chromatin organization, DNA methylation, cytosine modifications, covalent histone tail modifications, and short non-coding RNA molecules. Recently, much attention has been paid to the role and the function of epigenetics and epimutations in the cellular and subcellular pathways and in the regulation of genes in the setting of both kidney and cardiovascular disease...
August 5, 2017: Journal of Nephrology
https://www.readbyqxmd.com/read/28760199/major-satellite-repeat-rna-stabilize-heterochromatin-retention-of-suv39h-enzymes-by-rna-nucleosome-association-and-rna-dna-hybrid-formation
#11
Oscar Velazquez Camacho, Carmen Galan, Kalina Swist-Rosowska, Reagan Ching, Michael Gamalinda, Fethullah Karabiber, Inti De La Rosa-Velazquez, Bettina Engist, Birgit Koschorz, Nicholas Shukeir, Megumi Onishi-Seebacher, Suzanne van de Nobelen, Thomas Jenuwein
The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes...
August 1, 2017: ELife
https://www.readbyqxmd.com/read/28758277/fusion-of-the-genes-brd8-and-phf1-in-endometrial-stromal-sarcoma
#12
Francesca Micci, Marta Brunetti, Paola Dal Cin, Marisa R Nucci, Ludmila Gorunova, Sverre Heim, Ioannis Panagopoulos
We present a new endometrial stromal sarcoma (ESS)-associated genomic rearrangement involving chromosome arms 5p and 6p and leading to the formation of a BRD8-PHF1 fusion gene. The PHF1 (PHD finger protein 1) gene, from 6p21, is known to be rearranged in ESS in a promiscuous way inasmuch as it has been shown to recombine with JAZF1, EPC1, MEAF6, and now also with BRD8, in tumors of this type. In all rearrangements of PHF1, including the present one, a recurrent theme is that the entire coding part of PHF1 constitutes the 3' end of the fusion...
July 30, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28756022/histone-methylase-mll1-coordinates-with-hif-and-regulate-lncrna-hotair-expression-under-hypoxia
#13
Arunoday Bhan, Paromita Deb, Nadine Shihabeddin, Khairul I Ansari, Marco Brotto, Subhrangsu S Mandal
Hypoxia signaling plays a critical role in tumor growth, angiogenesis, metastasis cancer, and aging. Under hypoxia, hypoxia-inducible factors (HIFs) are stabilized and they coordinate the process of hypoxia-induced gene expression and cell signaling leading to increased tumor growth. Recent studies indicate that non-coding RNAs which are closely associated with cancer are abnormally expressed under hypoxia. Here, we have investigated the transcriptional regulation of a cancer associated long non-coding RNA (lncRNA), HOTAIR, under hypoxic conditions...
July 26, 2017: Gene
https://www.readbyqxmd.com/read/28744016/anti-inflammatory-and-chondroprotective-effects-of-the-s-adenosylhomocysteine-hydrolase-inhibitor-3-deazaneplanocin-a-in-human-articular-chondrocytes
#14
Juliette Aury-Landas, Céline Bazille, Lyess Allas, Sara Bouhout, Christophe Chesneau, Sylvain Leclercq, Karim Boumédiene, Catherine Baugé
3-Deazaneplanocin A (DZNep) is an inhibitor of S-Adenosyl-L-Homocysteine Hydrolase (SAHH) known to inhibit EZH2, a histone methylase upregulated during osteoarthritis. In this study, we assessed its effects in human articular chondrocytes. Anti-inflammatory effects were assessed by Nitric Oxide (NO), Prostaglandin E2 (PGE2) and Metalloprotease (MMP) release in IL-1β-stimulated chondrocytes. MAPK and NFκB activation was analyzed by western blotting. Differentially expressed genes (DEG) regulated by DZNep were identified by whole-transcriptome microarray...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743737/real-time-visualization-of-chromatin-modification-in-isolated-nuclei
#15
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/28741489/epigenomic-consequences-of-coding-and-noncoding-driver-mutations
#16
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/28733365/contrasting-determinants-of-mutation-rates-in-germline-and-soma
#17
Chen Chen, Hongjian Qi, Yufeng Shen, Joseph Pickrell, Molly Przeworski
Recent studies of somatic and germline mutations have led to the identification of a number of factors that influence point mutation rates, including CpG methylation, expression levels, replication timing and GC content. Intriguingly, some of the effects appear to differ between soma and germline: in particular, whereas mutation rates have been reported to decrease with expression levels in tumors, no clear effect has been detected in the germline. Distinct approaches were taken to analyze the data, however, so it is hard to know whether these apparent differences are real...
July 21, 2017: Genetics
https://www.readbyqxmd.com/read/28724449/novel-promoters-and-coding-first-exons-in-dlg2-linked-to-developmental-disorders-and-intellectual-disability
#18
Claudio Reggiani, Sandra Coppens, Tayeb Sekhara, Ivan Dimov, Bruno Pichon, Nicolas Lufin, Marie-Claude Addor, Elga Fabia Belligni, Maria Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gerard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
BACKGROUND: Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play...
July 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28720323/rapid-divergence-of-histones-in-hydrozoa-cnidaria-and-evolution-of-a-novel-histone-involved-in-dna-damage-response-in-hydra
#19
Puli Chandramouli Reddy, Suyog Ubhe, Neha Sirwani, Rasika Lohokare, Sanjeev Galande
Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra...
June 15, 2017: Zoology: Analysis of Complex Systems, ZACS
https://www.readbyqxmd.com/read/28718505/immunogenomic-approaches-to-understand-the-function-of-immune-disease-variants
#20
REVIEW
Dafni Anna Glinos, Blagoje Soskic, Gosia Trynka
Mapping hundreds of genetic variants through genome wide association studies provided an opportunity to gain insights into the pathobiology of immune mediated diseases. However, since most of the disease variants fall outside the gene coding sequences, thereby implicating gene expression regulation as the causal mechanism, the functional interpretation of the exact role of the associated variants remains to be determined. Despite these challenges, integration of disease associated variants with large scale genomic maps of cell type specific gene regulation both at chromatin and transcript levels deliver examples of functionally prioritised causal variants and genes...
July 17, 2017: Immunology
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