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DNA demethylation

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https://www.readbyqxmd.com/read/29053963/hydrilla-verticillata-employs-two-different-ways-to-affect-dna-methylation-under-excess-copper-stress
#1
Danlu Shi, Kai Zhuang, Yan Xia, Changhua Zhu, Chen Chen, Zhubing Hu, Zhenguo Shen
Because of the accumulation of heavy metals, Hydrilla verticillata (L.f.) Royle, a rooted submerged perennial aquatic herb, is being developed as a potential tool to clean the aquatic ecosystem polluted by heavy metals. However, its physiological responses for heavy metal remain to be elucidated. Here, through employing proteomics approach, we found that excess Cu significantly induced the expressions of four DNA methylation related proteins in H. verticillata, which were the homologues of two domains rearranged methyltransferases (DRM), a methyltransferases chromomethylase (CMT) and a histone H3 lysine-9 specific SUVH6-like (SUVH6)...
October 14, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/29050069/-mir-449a-is-a-potential-epigenetic-biomarker-for-wnt-subtype-of-medulloblastoma
#2
Y X Li, L W Shao, T Jiang, Y Liu, Q Chang
Objective: To identify the candidate epigenetic biomarkers of Wnt subtype of medulloblastoma(MB). Methods: MicroRNAs(miRNAs) expression array was used to detect the expression of miRNAs in MB cell lines with or without treatment by demethylation reagent. Nanostring gene expression array was used to detect the expression level of mRNA in 45 samples of primary MB. Molecular subtyping was performed based on the NanoString data. The status of methylation was confirmed by methylation specific PCR. The expression of candidate miRNA was confirmed by real-time PCR...
October 8, 2017: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/29048538/improvement-of-foxp3-stability-through-cns2-demethylation-by-tet-enzyme-induction-and-activation
#3
Kazue Someya, Hiroko Nakatsukasa, Minako Ito, Taisuke Kondo, Kenn-Ichi Tateda, Takashi Akanuma, Ikuko Koya, Tsukasa Sanosaka, Jun Kohyama, Yu-Ichi Tsukada, Takeji Takamura-Enya, Akihiko Yoshimura
Since induced regulatory T cells (iTregs) can be produced in a large quantity in vitro, these cells are expected to be clinically useful to induce immunological tolerance in various immunological diseases. Foxp3 (Forkhead box P3) expression in iTregs is, however, unstable due to the lack of demethylation of the CpG island in the conserved non-coding sequence 2 (CNS2) of the Foxp3 locus. To facilitate the demethylation of CNS2, we over-expressed the catalytic domain (CD) of the ten-eleven translocation (TET) protein, which catalyzes the steps of the iterative demethylation of 5-methylcytosine...
August 1, 2017: International Immunology
https://www.readbyqxmd.com/read/29045493/the-sequence-preference-of-dna-methylation-variation-in-mammalians
#4
Ling Zhang, Chan Gu, Lijiang Yang, Fuchou Tang, Yi Qin Gao
Methylation of cytosine at the 5 position of the pyrimidine ring is the most prevalent and significant epigenetic modifications in mammalian DNA. The CpG methylation level shows a bimodal distribution but the bimodality can be overestimated due to the heterogeneity of per-base depth. Here, we developed an algorithm to eliminate the effect of per-base depth inhomogeneity on the bimodality and obtained a random CpG methylation distribution. By quantifying the deviation of the observed methylation distribution and the random one using the information formula, we find that in tetranucleotides 5'-N5CGN3-3' (N5, N3 = A, C, G or T), GCGN3 and CCGN3 show less apparent deviation than ACGN3 and TCGN3, indicating that GCGN3 and CCGN3 are less variant in their level of methylation...
2017: PloS One
https://www.readbyqxmd.com/read/29042941/epigallocatechin-gallate-inhibits-the-growth-and-promotes-the-apoptosis-of-bladder-cancer-cells
#5
Chenchen Feng, Yatfaat Ho, Chuanyu Sun, Guowei Xia, Qiang Ding, Bin Gu
Epigallocatechin gallate (EGCG) has been revealed to inhibit the proliferation and induce the apoptosis of several types of tumor, in addition to inhibiting DNA methyltransferase activity, leading to CpG demethylation. Tissue factor pathway inhibitor 2 (TFPI-2) expression is downregulated in bladder cancer. The present study revealed that this downregulation was partly due to hypermethylation of the TFPI-2 gene promoter, which was decreased by EGCG treatment. In addition, the present study demonstrated that EGCG could inhibit the viability and invasion, and induce the apoptosis, of bladder cancer T24 cells...
October 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29039788/impact-of-natural-compounds-on-dna-methylation-levels-of-the-tumor-suppressor-gene-rassf1a-in-cancer
#6
REVIEW
Reinhard H Dammann, Antje M Richter, Adriana P Jiménez, Michelle Woods, Miriam Küster, Chamindri Witharana
Epigenetic inactivation of tumor suppressor genes (TSG) is a fundamental event in the pathogenesis of human cancer. This silencing is accomplished by aberrant chromatin modifications including DNA hypermethylation of the gene promoter. One of the most frequently hypermethylated TSG in human cancer is the Ras Association Domain Family 1A (RASSF1A) gene. Aberrant methylation of RASSF1A has been reported in melanoma, sarcoma and carcinoma of different tissues. RASSF1A hypermethylation has been correlated with tumor progression and poor prognosis...
October 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29037838/expression-and-epigenetic-regulation-of-cystatin-b-in-lung-cancer-and-colorectal-cancer
#7
Yunxia Ma, Yuan Chen, Iver Petersen
AIMS: Dysregulated expression of cystatin B (CSTB) has been implicated in various cancers. The aims of this study were to analyze the CSTB expression and investigate the epigenetic regulation of CSTB in lung and colon cancer cell lines, and also evaluate the clinical outcome of CSTB in primary lung and colorectal tumors. METHODS: CSTB expression in lung and colon cancer cell lines was analyzed by real-time RT-PCR and western blotting. Epigenetic regulation of CSTB was examined by demethylation, deacetylation tests and bisulfite sequencing (BS)...
June 6, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/29037594/epigenetic-modification-of-microrna-200b-contributes-to-diabetic-vasculopathy
#8
Kanhaiya Singh, Durba Pal, Mithun Sinha, Subhadip Ghatak, Surya C Gnyawali, Savita Khanna, Sashwati Roy, Chandan K Sen
Hyperglycemia (HG) induces genome-wide cytosine demethylation. Our previous work recognized miR-200b as a critical angiomiR, which must be transiently downregulated to initiate wound angiogenesis. Under HG, miR-200b downregulation is not responsive to injury. Here, we demonstrate that HG may drive vasculopathy by epigenetic modification of a miR promoter. In human microvascular endothelial cells (HMECs), HG also lowered DNA methyltransferases (DNMT-1 and DNMT-3A) and compromised endothelial function as manifested by diminished endothelial nitric oxide (eNOS), lowered LDL uptake, impaired Matrigel tube formation, lower NO production, and compromised VE-cadherin expression...
September 12, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29036598/global-dna-methylation-analysis-reveals-mir-214-3p-contributes-to-cisplatin-resistance-in-pediatric-intracranial-nongerminomatous-malignant-germ-cell-tumors
#9
Tsung-Han Hsieh, Yun-Ru Liu, Ting-Yu Chang, Muh-Lii Liang, Hsin-Hung Chen, Hsei-Wei Wang, Yun Yen, Tai-Tong Wong
Background: Pediatric central nervous system germ cell tumors (CNSGCTs) are rare and heterogeneous neoplasms, and they can be divided into germinomas and nongerminomatous GCTs (NGGCTs). NGGCTs are further subdivided into mature teratomas and nongerminomatous malignant GCTs (NGMGCTs). Clinical outcomes suggest that NGMGCTs have poor prognosis and survival, and that they require more extensive radiotherapy and adjuvant chemotherapy. However, the mechanisms underlying this difference are still unclear...
October 3, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29036586/epigenetic-mechanisms-underlie-the-crosstalk-between-growth-factors-and-a-steroid-hormone
#10
Yehoshua Enuka, Morris E Feldman, Animesh Chowdhury, Swati Srivastava, Moshit Lindzen, Aldema Sas-Chen, Renaud Massart, David Cheishvili, Matthew J Suderman, Yoav Zaltsman, Chiara A Mazza, Kirti Shukla, Cindy Körner, Noa Furth, Mattia Lauriola, Moshe Oren, Stefan Wiemann, Moshe Szyf, Yosef Yarden
Crosstalk between growth factors (GFs) and steroid hormones recurs in embryogenesis and is co-opted in pathology, but underlying mechanisms remain elusive. Our data from mammary cells imply that the crosstalk between the epidermal GF and glucocorticoids (GCs) involves transcription factors like p53 and NF-κB, along with reduced pausing and traveling of RNA polymerase II (RNAPII) at both promoters and bodies of GF-inducible genes. Essentially, GCs inhibit positive feedback loops activated by GFs and stimulate the reciprocal inhibitory loops...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29031162/dna-demethylation-activates-genes-in-seed-maternal-integument-development-in-rice-oryza-sativa-l
#11
Yifeng Wang, Haiyan Lin, Xiaohong Tong, Yuxuan Hou, Yuxiao Chang, Jian Zhang
DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development...
September 27, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29029465/alterations-in-dna-methylation-demethylation-intermediates-predict-clinical-outcome-in-chronic-lymphocytic-leukemia
#12
Cristina Bagacean, Adrian Tempescul, Christelle Le Dantec, Anne Bordron, Audrey Mohr, Hussam Saad, Valerie Olivier, Mihnea Zdrenghea, Victor Cristea, Pierre-François Cartron, Nathalie Douet-Guilbert, Christian Berthou, Yves Renaudineau
Cytosine derivative dysregulations represent important epigenetic modifications whose impact on the clinical outcome in chronic lymphocytic leukemia (CLL) is incompletely understood. Hence, global levels of 5-methylcytosine (5-mCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-CaCyt) and 5-hydroxymethyluracil were tested in purified B cells from CLL patients (n = 55) and controls (n = 17). The DNA methylation 'writers' (DNA methyltransferases [DNMT1/3A/3B]), 'readers' (methyl-CpG-binding domain [MBD2/4]), 'editors' (ten-eleven translocation [TET1/2/3]) and 'modulators' (SAT1) were also evaluated...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29028111/dna-methylation-of-methylation-complex-genes-in-relation-to-stress-and-genome-wide-methylation-in-mother-newborn-dyads
#13
Christopher J Clukay, David A Hughes, Nicole C Rodney, Darlene A Kertes, Connie J Mulligan
OBJECTIVES: Early life stress is known to have enduring biological effects, particularly with respect to health. Epigenetic modifications, such as DNA methylation, are a possible mechanism to mediate the biological effect of stress. We previously found correlations between maternal stress, newborn birthweight, and genome-wide measures of DNA methylation. Here we investigate ten genes related to the methylation/demethylation complex in order to better understand the impact of stress on health...
October 13, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29026973/active-dna-demethylation-mechanism-and-role-in-plant-development
#14
REVIEW
Yan Li, Suresh Kumar, Weiqiang Qian
Active DNA demethylation (enzymatic removal of methylated cytosine) regulates many plant developmental processes. In Arabidopsis, active DNA demethylation entails the base excision repair pathway initiated by the Repressor of silencing 1/Demeter family of bifunctional DNA glycosylases. In this review, we first present an introduction to the recent advances in our understanding about the mechanisms of active DNA demethylation. We then focus on the role of active DNA demethylation in diverse developmental processes in various plant species, including the regulation of seed development, pollen tube formation, stomatal development, fruit ripening, and nodule development...
October 12, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29020633/erasure-of-tet-oxidized-5-methylcytosine-by-a-srap-nuclease
#15
Soo-Mi Kweon, Bing Zhu, Yibu Chen, L Aravind, Shuang-Yong Xu, Douglas E Feldman
Enzymatic oxidation of 5-methylcytosine (5mC) in DNA by the Tet dioxygenases reprograms genome function in embryogenesis and postnatal development. Tet-oxidized derivatives of 5mC such as 5-hydroxymethylcytosine (5hmC) act as transient intermediates in DNA demethylation or persist as durable marks, yet how these alternative fates are specified at individual CpGs is not understood. Here, we report that the SOS response-associated peptidase (SRAP) domain protein Srap1, the mammalian ortholog of an ancient protein superfamily associated with DNA damage response operons in bacteria, binds to Tet-oxidized forms of 5mC in DNA and catalyzes turnover of these bases to unmodified cytosine by an autopeptidase-coupled nuclease...
October 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/29020412/emerging-role-of-one-carbon-metabolism-and-dna-methylation-enrichment-on-%C3%AE-containing-gabaa-receptor-expression-in-the-cerebellum-of-subjects-with-alcohol-use-disorders-aud
#16
Eleonora Gatta, James Auta, David P Gavin, Dulal K Bhaumik, Dennis R Grayson, Subhash C Pandey, Alessandro Guidotti
BACKGROUND: Cerebellum is an area of the brain particularly sensitive to the effects of acute and chronic alcohol consumption. Alcohol exposure decreases cerebellar Purkinje cell output by increasing GABA release from Golgi cells onto extrasynaptic α6/δ-containing GABAA receptors located on glutamatergic granule cells. Here, we studied whether chronic alcohol consumption induces changes in GABAA receptor subunit expression and whether these changes are associated with alterations in epigenetic mechanisms via DNA methylation...
August 19, 2017: International Journal of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29018507/down-regulation-of-mbd4-contributes-to-hypomethylation-and-overexpression-of-cd70-in-cd4-t-cells-in-systemic-lupus-erythematosus
#17
Wei Liao, Mengying Li, Haijing Wu, Sujie Jia, Nu Zhang, Yong Dai, Ming Zhao, Qianjin Lu
BACKGROUND: Systemic lupus erythematosus (SLE) is an autoimmune disease that is characterized by lymphocytic infiltration and overproduction of autoantibodies, leading to significant morbidity and mortality. However, the pathogenesis of this disorder has not yet been completely elucidated. It has been reported that CD70, a B cell costimulatory molecule encoded by the gene TNFSF7 (tumor necrosis factor ligand superfamily member 7), is overexpressed in CD4(+) T cells from patients with SLE due to the demethylation of its promoter...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28993426/effect-of-diabetes-status-and-hyperglycemia-on-global-dna-methylation-and-hydroxymethylation
#18
Jairo Arturo Pinzón-Cortés, Angelina Perna-Chaux, Nicolás Steven Rojas-Villamizar, Angelica Diaz-Basabe, Diana Carolina Polania-Villanueva, María Fernanda Jacome, Carlos Olimpo Mendivil, Helena Groot, Valeriano López-Segura
Type 2 diabetes mellitus (T2DM) is characterized by oxidative stress that could lead to chronic micro- and macro-vascular complications. We hypothesized that some of the target organ damage is mediated by oxidative alterations in epigenetic mechanisms involving DNA methylation (5mC) and DNA hydroxymethylation (5hmC). We analyzed global DNA methylation and hydroxymethylation in peripheral blood cells in well-controlled and poorly controlled patients with type 2 diabetes mellitus and compared them to healthy controls...
October 9, 2017: Endocrine Connections
https://www.readbyqxmd.com/read/28992291/retinoic-acid-inhibits-white-adipogenesis-by-disrupting-gadd45a-mediated-zfp423-dna-demethylation
#19
B Wang, Xing Fu, Mei-Jun Zhu, Min Du
Retinoic acid (RA), a bioactive metabolite of vitamin A, is a critical mediator of cell differentiation. RA blocks adipogenesis, but mechanisms remain to be established. ZFP423 is a key transcription factor maintaining white adipose identity. We found that RA inhibits Zfp423 expression and adipogenesis via blocking DNA demethylation in the promoter of Zfp423, a process mediated by growth arrest and DNA-damage-inducible protein alpha (GADD45A). RA induces the partnering between retinoic acid receptor (RAR) and tumor suppressor inhibitor of growth protein 1 (ING1), which prevents the formation of GADD45A and ING1 complex necessary for locus-specific Zfp423 DNA demethylation...
August 1, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28986802/re-expressing-epigenetically-silenced-genes-by-inducing-dna-demethylation-through-targeting-of-ten-eleven-translocation-2-to-any-given-genomic-locus
#20
Julio Cesar Rendón, David Cano-Rodríguez, Marianne G Rots
Epigenetic editing is a novel methodology to modify the epigenetic landscape of any genomic location. As such, the approach might reprogram expression profiles, without altering the DNA sequence. Epigenetic alterations, including promoter hypermethylation, are associated with an increasing number of human diseases. To exploit this situation, epigenetic editing rises as a new alternative to specifically demethylate abnormally hypermethylated regions. Here, we describe a methodology to actively demethylate the hypermethylated ICAM-1 promoter...
2017: Methods in Molecular Biology
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