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Epigenetic silencing

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https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#1
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29772549/long-non-coding-rna-and-polycomb-an-intricate-partnership-in-cancer-biology
#2
Cyrinne Achour, Francesca Aguilo
High-throughput analyses have revealed that the vast majority of the transcriptome does not code for proteins. These non-translated transcripts, when larger than 200 nucleotides, are termed long non-coding RNAs (lncRNAs), and play fundamental roles in diverse cellular processes. LncRNAs are subject to dynamic chemical modification, adding another layer of complexity to our understanding of the potential roles that lncRNAs play in health and disease. Many lncRNAs regulate transcriptional programs by influencing the epigenetic state through direct interactions with chromatin-modifying proteins...
June 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/29772433/lncrna-sox21-as1-is-associated-with-progression-of-hepatocellular-carcinoma-and-predicts-prognosis-through-epigenetically-silencing-p21
#3
Congxin Wei, Hong Wang, Fei Xu, Zeng Liu, Runde Jiang
Long non-coding RNAs (lncRNAs) have been widely reported in various cancers due to their special molecular mechanisms. LncRNA SOX21-AS1 has been discovered to be a tumor facilitator in several types of human cancers. However, the expression pattern, clinical value and biological effects in hepatocellular carcinoma (HCC) are still unknown. In this study, we detected the high expression level of SOX21-AS1 in tumor tissues and cell lines through performing qRT-PCR analysis. The prognostic value of SOX21-AS1 was identified...
May 14, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29771984/dna-methylation-of-hepatic-iron-sensing-genes-and-the-regulation-of-hepcidin-expression
#4
Paul A Sharp, Rachel Clarkson, Ahmed Hussain, Robert J Weeks, Ian M Morison
Production of the iron regulatory peptide hepcidin is tightly controlled by a network of proteins in hepatocytes that sense levels of iron in the circulation (as diferric-transferrin) and in tissues (in ferritin). Human studies show high variability in the normal range of serum hepcidin levels. We have postulated that this may, in part, be related to inter-individual variability in the expression of genes in the iron sensing pathway, potentially governed by epigenetic factors. Here, we have investigated whether genes encoding hepatic iron sensing proteins and hepcidin are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29769721/spatiotemporal-regulation-of-liquid-like-condensates-in-epigenetic-inheritance
#5
Gang Wan, Brandon D Fields, George Spracklin, Aditi Shukla, Carolyn M Phillips, Scott Kennedy
Non-membrane-bound organelles such as nucleoli, processing bodies, Cajal bodies and germ granules form by the spontaneous self-assembly of specific proteins and RNAs. How these biomolecular condensates form and interact is poorly understood. Here we identify two proteins, ZNFX-1 and WAGO-4, that localize to Caenorhabditis elegans germ granules (P granules) in early germline blastomeres. Later in germline development, ZNFX-1 and WAGO-4 separate from P granules to define an independent liquid-like condensate that we term the Z granule...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29763912/-a-succinate-ether-derivative-of-tocotrienol-enhances-dickkopf-1-gene-expression-through-epigenetic-alterations-in-malignant-mesothelioma-cells
#6
Ayami Sato, Haruka Ueno, Momoka Fusegi, Saki Kaneko, Kakeru Kohno, Nantiga Virgona, Akira Ando, Yuko Sekine, Tomohiro Yano
BACKGROUND: Wnt signaling plays an essential role in tumor cell growth, including the development of malignant mesothelioma (MM). Epigenetic silencing of negative Wnt regulators leading to constitutive Wnt signaling has been observed in various cancers and warrants further attention. We have reported that a succinate ether derivative of α-tocotrienol (T3E) has potent cytotoxic effects in MM cells. Thus, in this study, we investigated whether the anti-MM effect of T3E could be mediated via the epigenetic alteration of the Wnt antagonist gene, Dickkopf-1 (DKK1)...
May 15, 2018: Pharmacology
https://www.readbyqxmd.com/read/29760376/the-novel-19q13-krab-zinc-finger-tumour-suppressor-znf382-is-frequently-methylated-in-oesophageal-squamous-cell-carcinoma-and-antagonises-wnt-%C3%AE-catenin-signalling
#7
Chong Zhang, Tingxiu Xiang, Shuman Li, Lin Ye, Yixiao Feng, Lijiao Pei, Lili Li, Xiangyu Wang, Ran Sun, Qian Tao, Guosheng Ren
Zinc finger proteins (ZFPs) are the largest transcription factor family in mammals. About one-third of ZFPs are Krüppel-associated box domain (KRAB)-ZFPs and involved in the regulation of cell differentiation/proliferation/apoptosis and neoplastic transformation. We recently identified ZNF382 as a novel KRAB-ZFP epigenetically inactivated in multiple cancers due to frequent promoter CpG methylation. However, its epigenetic alterations, biological functions/mechanism and clinical significance in oesophageal squamous cell carcinoma (ESCC) are still unknown...
May 14, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29760177/epigenetic-promoter-dna-methylation-of-mir-124-promotes-hiv-1-tat-mediated-microglial-activation-via-mecp2-stat3-axis
#8
Palsamy Periyasamy, Annadurai Thangaraj, Ming-Lei Guo, Guoku Hu, Shannon Callen, Shilpa Buch
The present study demonstrates HIV-1 Tat-mediated epigenetic downregulation of microglial miR-124 and its association with microglial activation. Exposure of mouse primary microglia isolated from newborn pups of either sex to HIV-1 Tat resulted in decreased expression of primary miR-124-1, primary miR-124-2 as well as the mature miR-124. In parallel, HIV-1 Tat exposure to mouse primary microglial cells resulted in increased expression of DNA methylation enzymes, such as DNMT1, DNMT3A, and DNMT3B that were also accompanied by increased global DNA methylation...
May 14, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29759938/differentiation-therapy-by-epigenetic-reconditioning-exerts-antitumor-effects-on-liver-cancer-cells
#9
Luc Gailhouste, Lee Chuen Liew, Ken Yasukawa, Izuho Hatada, Yasuhito Tanaka, Hitoshi Nakagama, Takahiro Ochiya
Primary liver tumors are mainly represented by hepatocellular carcinoma (HCC), one of the most aggressive and resistant forms of cancer. Liver tumorigenesis is characterized by an accumulation of epigenetic abnormalities, leading to gene extinction and loss of hepatocyte differentiation. The aim of this work was to investigate the feasibility of converting liver cancer cells toward a less aggressive and differentiated phenotype using a process called epigenetic reconditioning. Here, we showed that an epigenetic regimen with non-cytotoxic doses of the demethylating compound 5-azacytidine (5-AZA) promoted an anti-cancer response by inhibiting HCC cell tumorigenicity...
April 26, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29759079/s-allylcysteine-suppresses-ovarian-cancer-cell-proliferation-by-dna-methylation-through-dnmt1
#10
Yasi Xu, Dan Su, Lucheng Zhu, Shirong Zhang, Shenglin Ma, Kan Wu, Qiang Yuan, Nengming Lin
BACKGROUND: The anti-tumor effects of S-allylcysteine (SAC), a water-soluble garlic derivative, on human ovarian cancer cells have been previous studied in vitro and in vivo models but the precise epigenetic molecular mechanisms are still unclear. This study aimed to investigate the epigenetic mechanism of SAC. METHODS: Human epithelial ovarian cancer cell line A2780 was selected. Cell proliferation and cell cycle was analyzed. DNA methylation, DNA methyltransferase (DNMT) activity, tumor suppressor gene expressions, as well as protein expression were analyzed...
May 14, 2018: Journal of Ovarian Research
https://www.readbyqxmd.com/read/29753027/jmjd3-inhibition-protects-against-isoproterenol-induced-cardiac-hypertrophy-by-suppressing-%C3%AE-mhc-expression
#11
Zhen Guo, Jing Lu, Jingyan Li, Panxia Wang, Zhenzhen Li, Yao Zhong, Kaiteng Guo, Junjian Wang, Jiantao Ye, Peiqing Liu
Jumonji domain-containing protein D3 (JMJD3), a histone 3 lysine 27 (H3K27) demethylase, has been extensively studied for their participation in development, cellular physiology and a variety of diseases. However, its potential roles in cardiovascular system remain unknown. In this study, we found that JMJD3 played a pivotal role in the process of cardiac hypertrophy. JMJD3 expression was elevated by isoproterenol (ISO) stimuli both in vitro and in vivo. Overexpression of wild-type JMJD3, but not the demethylase-defective mutant, promoted cardiomyocyte hypertrophy, as implied by increased cardiomyocyte surface area and the expression of hypertrophy marker genes...
May 9, 2018: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/29750270/peripheral-re-localization-of-constitutive-heterochromatin-advances-its-replication-timing-and-impairs-maintenance-of-silencing-marks
#12
Kathrin S Heinz, Corella S Casas-Delucchi, Timea Török, Dusan Cmarko, Alexander Rapp, Ivan Raska, M Cristina Cardoso
The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear DNA position remains unclear. We made use of the prominent structure and well-defined heterochromatic landscape of mouse pericentric chromosome domains as a well-studied example of late replicating constitutive heterochromatin...
May 10, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29748383/fshd2-and-bams-associated-mutations-confer-opposing-effects-on-smchd1-function
#13
Alexandra D Gurzau, Kelan Chen, Shifeng Xue, Weiwen Dai, Isabelle S Lucet, Thanh Thao Nguyen Ly, Bruno Reversade, Marnie E Blewitt, James M Murphy
Structural maintenance of chromosomes flexible hinge domain-containing 1 (Smchd1) plays important roles in epigenetic silencing and normal mammalian development. Recently, heterozygous mutations in SMCHD1 have been reported in two disparate disorders: facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS). FSHD2-associated mutations lead to loss of function, however whether BAMS is associated with loss or gain of function mutations in SMCHD1 is unclear. Here, we have assessed the effect of SMCHD1 missense mutations from FSHD2 and BAMS patients on ATP hydrolysis activity, protein conformation and the effect of BAMS mutations on craniofacial development in a Xenopus model...
May 10, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29747634/regulation-of-fibroblast-fas-expression-by-soluble-and-mechanical-pro-fibrotic-stimuli
#14
Amos E Dodi, Iyabode O Ajayi, Christine Chang, Meghan Beard, Shanna L Ashley, Steven K Huang, Victor J Thannickal, Daniel J Tschumperlin, Thomas H Sisson, Jeffrey C Horowitz
BACKGROUND: Fibroblast apoptosis is a critical component of normal repair and the acquisition of an apoptosis-resistant phenotype contributes to the pathogenesis of fibrotic repair. Fibroblasts from fibrotic lungs of humans and mice demonstrate resistance to apoptosis induced by Fas-ligand and prior studies have shown that susceptibility to apoptosis is enhanced when Fas (CD95) expression is increased in these cells. Moreover, prior work shows that Fas expression in fibrotic lung fibroblasts is reduced by epigenetic silencing of the Fas promoter...
May 10, 2018: Respiratory Research
https://www.readbyqxmd.com/read/29747401/the-dna-methylome-and-association-of-differentially-methylated-regions-with-differential-gene-expression-during-heat-stress-in-brassica-rapa
#15
Gaofeng Liu, Yudong Xia, Tongkun Liu, Shaojun Dai, Xilin Hou
Cytosine DNA methylation is a critical epigenetic mechanism in the silencing of transposable elements, imprinting and regulating gene expression. However, little is known about the potential role of mC in response to heat stress. To determine and explore the functions of the dynamic DNA methylome during heat stress, we characterized single-base resolution methylome maps of Brassica rapa and assessed the dynamic changes of mC under heat stress using whole genome bisulfite sequencing. On average, the DNA methylation levels of CG, CHG and CHH are 39...
May 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29743404/-epigenetic-aberrations-in-adult-t-cell-leukemia-lymphoma-and-development-of-a-novel-ezh1-2-inhibitor
#16
Makoto Yamagishi
Histone H3 lysine 27 tri-methylation (H3K27me3) -dependent transcription regulation is a fundamental process of gene control. Although EZH2 mutation is observed in certain lymphoma types, many other cancers show global H3K27me3 accumulation irrespective of mutation. However, the underlying mechanisms of gene silencing and therapeutic efficacies of epigenetic drugs remain unclear. In this study, we showed that globally-accumulated H3K27me3 is induced by both cis-bound EZH1 and EZH2 in mature lymphocyte-derived malignancies...
2018: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/29742286/study-of-promoter-hypomethylation-profiles-of-ras-oncogenes-in-hepatocellular-carcinoma-derived-from-hepatitis-c-virus-genotype-3a-in-pakistani-population
#17
Maria Maryam, Muhammad Idrees
Epigenetic modifications such as DNA methylation contribute to progression of Hepatitis C virus (HCV) infection to life-threatening hepatocellular carcinoma (HCC), by promoting the silencing of tumor suppressor genes due to DNA hypermethylation and by causing genomic instability due to global hypomethylation. However few studies addressed promoter region hypomethylation status of the oncogenes involved in HCV derived HCC. In this study, we analyzed the promoter region methylation pattern of RAS oncogenes (HRAS, KRAS, NRAS) using methylation-specific PCR (MSP) for 50 Chronic HCV patients infected with genotype 3a (27 HCC patients and 23 Control non-HCC patients)...
May 9, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29739907/clag3-self-associates-in-malaria-parasites-and-quantitatively-determines-nutrient-uptake-channels-at-the-host-membrane
#18
Ankit Gupta, Praveen Balabaskaran-Nina, Wang Nguitragool, Gagandeep S Saggu, Marc A Schureck, Sanjay A Desai
Malaria parasites increase host erythrocyte permeability to ions and nutrients via a broad-selectivity channel known as the plasmodial surface anion channel (PSAC), linked to parasite-encoded CLAG3 and two associated proteins. These proteins lack the multiple transmembrane domains typically present in channel-forming proteins, raising doubts about their precise roles. Using the virulent human Plasmodium falciparum parasite, we report that CLAG3 undergoes self-association and that this protein's expression determines channel phenotype quantitatively...
May 8, 2018: MBio
https://www.readbyqxmd.com/read/29734353/knockdown-of-cdk2ap1-in-human-embryonic-stem-cells-reduces-the-threshold-of-differentiation
#19
Khaled N Alsayegh, Steven D Sheridan, Shilpa Iyer, Raj Raghavendra Rao
Recent studies have suggested a role for the Cyclin Dependent Kinase-2 Associated Protein 1 (CDK2AP1) in stem cell differentiation and self-renewal. In studies with mouse embryonic stem cells (mESCs) derived from generated mice embryos with targeted deletion of the Cdk2ap1 gene, CDK2AP1 was shown to be required for epigenetic silencing of Oct4 during differentiation, with deletion resulting in persistent self-renewal and reduced differentiation potential. Differentiation capacity was restored in these cells following the introduction of a non-phosphorylatible form of the retinoblastoma protein (pRb) or exogenous Cdk2ap1...
2018: PloS One
https://www.readbyqxmd.com/read/29734178/long-non-coding-rna-sh3pxd2a-as1-promotes-cell-progression-partly-through-epigenetic-silencing-p57-and-klf2-in-colorectal-cancer
#20
Zhonghua Ma, Peng Peng, Jing Zhou, Bingqing Hui, Hao Ji, Juan Wang, Keming Wang
BACKGROUND/AIMS: Colorectal cancer (CRC) is one of the most commonly diagnosed malignancies worldwide. Current evidence has revealed the key roles of long non-coding RNAs (IncRNAs) in multiple cancers, including CRC. In this study we identified the lncRNA SH3PXD2A-AS1 as a novel molecule associated with CRC progression by analyzing the publicly available data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. METHODS: Quantitative real-time polymerase chain reaction (qRT-PCR) assays were performed to examine the expression levels of SH3PXD2A-AS1 in CRC tissue samples and CRC cell lines...
May 3, 2018: Cellular Physiology and Biochemistry
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