keyword
MENU ▼
Read by QxMD icon Read
search

active DNA demethylation

keyword
https://www.readbyqxmd.com/read/29791079/overexpression-of-tet3-in-donor-cells-enhances-goat-somatic-cell-nuclear-transfer-efficiency
#1
Chengquan Han, Ruizhi Deng, Tingchao Mao, Yan Luo, Biao Wei, Peng Meng, Lu Zhao, Qing Zhang, Fusheng Quan, Liu Jun, Yong Zhang
Ten-eleven translocation 3 (TET3) mediates active DNA demethylation of paternal genomes during mouse embryonic development. However, the mechanism of DNA demethylation in goat embryos remains unknown. In addition, aberrant DNA methylation reprogramming prevalently occurs in cloned embryos by somatic cell nuclear transfer (SCNT). In this study, we reported that TET3 is a key factor in DNA demethylation in goat pre-implantation embryos. Knockdown of Tet3 hindered DNA demethylation at 2-4-cell stage in goat embryos and decreased Nanog expression in blastocysts...
May 23, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29784956/dynamics-and-function-of-dna-methylation-in-plants
#2
REVIEW
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu
DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions...
May 21, 2018: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29784784/uncovering-universal-rules-governing-the-selectivity-of-the-archetypal-dna-glycosylase-tdg
#3
Thomas Dodd, Chunli Yan, Bradley R Kossmann, Kurt Martin, Ivaylo Ivanov
Thymine DNA glycosylase (TDG) is a pivotal enzyme with dual roles in both genome maintenance and epigenetic regulation. TDG is involved in cytosine demethylation at CpG sites in DNA. Here we have used molecular modeling to delineate the lesion search and DNA base interrogation mechanisms of TDG. First, we examined the capacity of TDG to interrogate not only DNA substrates with 5-carboxyl cytosine modifications but also G:T mismatches and nonmismatched (A:T) base pairs using classical and accelerated molecular dynamics...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29780504/gene-specific-loci-quantitative-and-single-base-resolution-analysis-of-5-formylcytosine-by-compound-mediated-polymerase-chain-reaction
#4
Yafen Wang, Chaoxing Liu, Xiong Zhang, Wei Yang, Fan Wu, Guangrong Zou, Xiaocheng Weng, Xiang Zhou
5-Formylcytosine (5fC) is known as one of the key players in the process of active DNA demethylation and displays essential epigenetic functions in mammals. In spite of the blooming development of whole genome sequencing methods for this modified cytosine base, the easily operated gene specific-loci detection of 5fC has rarely been reported. Herein, we present a compound-mediated analysis of the content and site of 5fC by the polymerase chain reaction (PCR) assay. The molecule, namely azi-BP, which can selectively label 5fC and form a huge group through a click chemistry reaction, hindering the amplification activity of Taq DNA polymerase, acts as a "roadblock" and enables the quantitative analysis of 5fC by quantitative polymerase chain reaction (qPCR)...
April 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29774579/integrative-epigenetic-analysis-reveals-therapeutic-targets-to-the-dna-methyltransferase-inhibitor-sgi-110-in-hepatocellular-carcinoma
#5
Minmin Liu, Lian Zhang, Hongtao Li, Toshinori Hinoue, Wanding Zhou, Hitoshi Ohtani, Anthony El-Khoueiry, John Daniels, Casey O'Connell, Tanya B Dorff, Qianjin Lu, Daniel J Weisenberger, Gangning Liang
There is an urgent need for developing more effective therapies for hepatocellular carcinoma (HCC) because of its aggressiveness. Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi) currently in clinical trials for HCC and shows greater stability and performance over first generation DNMTis. In order to identify potential therapeutic targets of SGI-110 for clinical trials, HCC cell lines (SNU398, HepG2 and SNU475) were used to evaluate effects of transient SGI-110 treatment by an integrative analysis of DNA methylation, nucleosome accessibility, gene expression profiles and its clinical relevance by comparisons to TCGA HCC clinical data...
May 18, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29774027/clinical-remission-of-sight-threatening-non-infectious-uveitis-is-characterized-by-an-upregulation-of-peripheral-t-regulatory-cell-polarized-towards-t-bet-and-tigit
#6
Rose M Gilbert, Xiaozhe Zhang, Robert D Sampson, Michael R Ehrenstein, Dao X Nguyen, Mahid Chaudhry, Charles Mein, Nadiya Mahmud, Grazyna Galatowicz, Oren Tomkins-Netzer, Virginia L Calder, Sue Lightman
Background: Non-infectious uveitis can cause chronic relapsing and remitting ocular inflammation, which may require high dose systemic immunosuppression to prevent severe sight loss. It has been classically described as an autoimmune disease, mediated by pro-inflammatory Th1 and Th17 T-cell subsets. Studies suggest that natural immunosuppressive CD4+ CD25+ FoxP3+ T-regulatory cells (Tregs) are involved in resolution of inflammation and may be involved in the maintenance of clinical remission...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29773648/ten-eleven-translocation-2-demethylates-the-mmp9-promoter-and-its-down-regulation-in-preeclampsia-impairs-trophoblast-migration-and-invasion
#7
Xiaoliang Li, Chunlian Wu, Ying Shen, Ke Wang, Li Tang, Mi Zhou, Ming Yang, Tianying Pan, Xinghui Liu, Wenming Xu
Preeclampsia is the most common clinical disorder in pregnancy and might result from disordered uterine environments caused by epigenetic modifications, including deregulation of DNA methylation/demethylation. Recent research has indicated that 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC) via oxidation by ten-eleven translocation (TET) enzymes, is involved in DNA methylation-related plasticity. Here, we report that TET2 expression and 5hmC abundance are significantly altered in the placentas from preeclampsia patients...
May 17, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29762710/base-flipping-dynamics-from-an-intrahelical-to-an-extrahelical-state-exerted-by-thymine-dna-glycosylase-during-dna-repair-process
#8
Lin-Tai Da, Jin Yu
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29757674/eicosapentaenoic-acid-induces-dna-demethylation-in-carcinoma-cells-through-a-tet1-dependent-mechanism
#9
Veronica Ceccarelli, Virginia Valentini, Simona Ronchetti, Lorenza Cannarile, Monia Billi, Carlo Riccardi, Laura Ottini, Vincenzo Nicola Talesa, Francesco Grignani, Alba Vecchini
In cancer cells, global genomic hypomethylation is found together with localized hypermethylation of CpG islands within the promoters and regulatory regions of silenced tumor suppressor genes. Demethylating agents may reverse hypermethylation, thus promoting gene re-expression. Unfortunately, demethylating strategies are not efficient in solid tumor cells. DNA demethylation is mediated by ten-eleven translocation enzymes (TETs). They sequentially convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which is associated with active transcription; 5-formylcytosine; and finally, 5-carboxylcytosine...
May 14, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29747586/selective-modulation-of-local-linkages-between-active-transcription-and-oxidative-demethylation-activity-shapes-cardiomyocyte-specific-gene-body-epigenetic-status-in-mice
#10
Mayumi Oda, Shunichi Wakabayashi, N Ari Wijetunga, Shinsuke Yuasa, Hirokazu Enomoto, Ruri Kaneda, Sung Han Yoon, Nishant Mittal, Qiang Jing, Masako Suzuki, John M Greally, Keiichi Fukuda, Shinji Makino
BACKGROUND: Cell-type-specific genes exhibit heterogeneity in genomic contexts and may be subject to different epigenetic regulations through different gene transcriptional processes depending on the cell type involved. The gene-body regions (GBRs) of some cardiomyocyte (CM)-specific genes are long and highly hypomethylated in CMs. To explore the cell-type specificities of epigenetic patterns and functions, multiple epigenetic modifications of GBRs were compared among CMs, liver cells and embryonic stem cells (ESCs)...
May 10, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29739797/epigenetic-regulation-of-aldosterone-synthase-gene-by-sodium-and-angiotensin-ii
#11
Yoshimichi Takeda, Masashi Demura, Fen Wang, Shigehiro Karashima, Takashi Yoneda, Mitsuhiro Kometani, Atsushi Hashimoto, Daisuke Aono, Shin-Ichi Horike, Makiko Meguro-Horike, Masakazu Yamagishi, Yoshiyu Takeda
BACKGROUND: DNA methylation is believed to be maintained in adult somatic cells. Recent findings, however, suggest that all methylation patterns are not stable. We demonstrate that stimulatory signals can change the DNA methylation status around transcription factor binding sites and a transcription start site and activate expression of the aldosterone synthase gene ( CYP11B2 ). METHODS AND RESULTS: DNA methylation of CYP11B2 was analyzed in aldosterone-producing adenomas, nonfunctioning adrenal adenomas, and adrenal glands and compared with the gene expression levels...
May 8, 2018: Journal of the American Heart Association
https://www.readbyqxmd.com/read/29732371/hippocampal-tet1-and-tet2-expression-and-dna-hydroxymethylation-are-affected-by-physical-exercise-in-aged-mice
#12
Peter Jessop, Maria Toledo-Rodriguez
The function of 5-hydroxymethylcytosine (5hmC) is poorly understood. 5hmC is an epigenetic modification of DNA, resulting from the oxidation of 5-methylcytosine (5mC) by the Fe2+ , and 2-oxoglutarate-dependent, 10-11 translocation methylcytosine dioxygenases (TET1, TET2, and TET3). Recent evidence suggests that, in addition to being an intermediate in active demethylation, 5hmC may also have an epigenetic role. 5hmC is enriched in the adult brain, where it has been implicated in regulating neurogenesis. The rate of adult neurogenesis decreases with age, however physical exercise has been shown to counteract this deficit...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29721644/morphology-oriented-epigenetic-research
#13
REVIEW
Sohei Kitazawa, Ryuma Haraguchi, Riko Kitazawa
Cytosine methylation plays a major role in the regulation of sequential and tissue-specific expression of genes. De novo aberrant DNA methylation and demethylation are also crucial processes in tumorigenesis and tumor progression. The mechanisms of how and when such aberrant methylation and demethylation occur in tumor cells are still obscure, however. To evaluate subtle epigenetic alteration among minor subclonal populations, morphology-oriented epigenetic analysis is requisite, especially where heterogeneity and flexibility are as notable as in the process of cancer progression and cellular differentiation at critical stages...
May 2, 2018: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/29717211/up-regulation-of-microrna-203-in-influenza-a-virus-infection-inhibits-viral-replication-by-targeting-dr1
#14
Sen Zhang, Jing Li, Junfeng Li, Yinhui Yang, Xiaoping Kang, Yuchang Li, Xiaoyan Wu, Qingyu Zhu, Yusen Zhou, Yi Hu
MicroRNAs (miRNAs) are small noncoding RNA molecules that play important roles in various biological processes. Much evidence shows that miRNAs are closely associated with numerous virus infections; however, involvement of cellular miRNAs in influenza A virus (IAV) infection is unclear. Here, we found that expression of miR-203 was up-regulated markedly via two different mechanisms during IAV infection. First, we examined the effects of type I interferon induced by IAV on direct activation of miR-203 expression...
May 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29712855/fact-complex-is-required-for-dna-demethylation-at-heterochromatin-during-reproduction-in-arabidopsis
#15
Jennifer M Frost, M Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J H Lin, Hyunjin Yoo, Jaemyung Choi, Yoko Ikeda, Tetsu Kinoshita, Yeonhee Choi, Daniel Zilberman, Robert L Fischer
The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29710792/epigenetic-modulation-of-cd8%C3%A2-%C2%BA-t-cell-function-in-lentivirus-infections-a-review
#16
REVIEW
Mukta Nag, Kristina De Paris, Jonathan E Fogle
CD8⁺ T cells are critical for controlling viremia during human immunodeficiency virus (HIV) infection. These cells produce cytolytic factors and antiviral cytokines that eliminate virally- infected cells. During the chronic phase of HIV infection, CD8⁺ T cells progressively lose their proliferative capacity and antiviral functions. These dysfunctional cells are unable to clear the productively infected and reactivated cells, representing a roadblock in HIV cure. Therefore, mechanisms to understand CD8⁺ T cell dysfunction and strategies to boost CD8⁺ T cell function need to be investigated...
April 28, 2018: Viruses
https://www.readbyqxmd.com/read/29705354/effect-of-tet2-on-the-pathogenesis-of-diabetic-nephropathy-through-activation-of-transforming-growth-factor-%C3%AE-1-expression-via-dna-demethylation
#17
Yang Liling, Zhang Qian, Wu Qiong, Wei Yi, Yu Jiawei, Mu Jiao, Zhang Jun, Zeng Wei, Feng Bing
AIMS: Transforming growth factor β1 (TGFβ1) plays a pivotal role in the pathogenesis of diabetic nephropathy (DN). However, the mechanism of its expression and activation induced by high glucose (HG) is still unclear. We mainly explored the role of ten-eleven translocation enzyme-2 (TET2) in regulating TGFβ1 expression in the process of DN. MAIN METHODS: Human mesangial cells (HMCs) and db/db mice were used to analyze the biological effects of hyperglycemia both in vivo and in vitro...
April 26, 2018: Life Sciences
https://www.readbyqxmd.com/read/29686419/dynamics-of-the-epigenetic-landscape-during-the-maternal-to-zygotic-transition
#18
REVIEW
Melanie A Eckersley-Maslin, Celia Alda-Catalinas, Wolf Reik
A remarkable epigenetic remodelling process occurs shortly after fertilization, which restores totipotency to the zygote. This involves global DNA demethylation, chromatin remodelling, genome spatial reorganization and substantial transcriptional changes. Key to these changes is the transition from the maternal environment of the oocyte to an embryonic-driven developmental expression programme, a process termed the maternal-to-zygotic transition (MZT). Zygotic genome activation occurs predominantly at the two-cell stage in mice and the eight-cell stage in humans, yet the dynamics of its control are still mostly obscure...
April 23, 2018: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29686265/reprogramming-of-h3k9me3-dependent-heterochromatin-during-mammalian-embryo-development
#19
Chenfei Wang, Xiaoyu Liu, Yawei Gao, Lei Yang, Chong Li, Wenqiang Liu, Chuan Chen, Xiaochen Kou, Yanhong Zhao, Jiayu Chen, Yixuan Wang, Rongrong Le, Hong Wang, Tao Duan, Yong Zhang, Shaorong Gao
H3K9me3-dependent heterochromatin is a major barrier of cell fate changes that must be reprogrammed after fertilization. However, the molecular details of these events are lacking in early embryos. Here, we map the genome-wide distribution of H3K9me3 modifications in mouse early embryos. We find that H3K9me3 exhibits distinct dynamic features in promoters and long terminal repeats (LTRs). Both parental genomes undergo large-scale H3K9me3 reestablishment after fertilization, and the imbalance in parental H3K9me3 signals lasts until blastocyst...
May 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29685105/chilling-induced-dna-demethylation-is-associated-with-the-cold-tolerance-of-hevea-brasiliensis
#20
Xiao Tang, Qichao Wang, Hongmei Yuan, Xi Huang
BACKGROUND: Low temperature influences the development and latex production of rubber trees (Hevea brasiliensis) when extension to suboptimal high-latitude areas. The successful extension of Hevea brasiliensis cultivation to high-latitude areas has long believed to benefit from the breeding of cold-tolerant cultivars. A puzzling incongruity is the variation in cold tolerance among the cultivated clones despite their similar genetic make-up. RESULTS: To investigate this, we first transferred cultivar Reyan 7-33-97 to short-term cold treatment, and showed that cold-related genes (such as HbICE1 and HbCBF2), cold-responsive (COR) genes, and DNA-methylation related genes (such as HbMET1) were induced by cold treatment...
April 23, 2018: BMC Plant Biology
keyword
keyword
23560
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"