keyword
MENU ▼
Read by QxMD icon Read
search

Dna hydroxymethylation

keyword
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#1
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29750267/base-modifications-affecting-rna-polymerase-and-reverse-transcriptase-fidelity
#2
Vladimir Potapov, Xiaoqing Fu, Nan Dai, Ivan R Corrêa, Nathan A Tanner, Jennifer L Ong
Ribonucleic acid (RNA) is capable of hosting a variety of chemically diverse modifications, in both naturally-occurring post-transcriptional modifications and artificial chemical modifications used to expand the functionality of RNA. However, few studies have addressed how base modifications affect RNA polymerase and reverse transcriptase activity and fidelity. Here, we describe the fidelity of RNA synthesis and reverse transcription of modified ribonucleotides using an assay based on Pacific Biosciences Single Molecule Real-Time sequencing...
May 10, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29743892/epigenetic-regulations-in-neural-stem-cells-and-neurological-diseases
#3
REVIEW
Hang Zhou, Bin Wang, Hao Sun, Xingshun Xu, Yongxiang Wang
Among the regulatory mechanisms of the renewal and differentiation of neural stem cells, recent evidences support that epigenetic modifications such as DNA methylation, histone modification, and noncoding RNAs play critical roles in the regulation on the proliferation and differentiation of neural stem cells. In this review, we discussed recent advances of DNA modifications on the regulative mechanisms of neural stem cells. Among these epigenetic modifications, DNA 5-hydroxymethylcytosine (5hmC) modification is emerging as an important modulator on the proliferation and differentiation of neural stem cells...
2018: Stem Cells International
https://www.readbyqxmd.com/read/29732371/hippocampal-tet1-and-tet2-expression-and-dna-hydroxymethylation-are-affected-by-physical-exercise-in-aged-mice
#4
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/29718457/the-phage-t4-mota-transcription-factor-contains-a-novel-dna-binding-motif-that-specifically-recognizes-modified-dna
#5
Maxime G Cuypers, Rosanna M Robertson, Leslie Knipling, M Brett Waddell, Kyung Moon, Deborah M Hinton, Stephen W White
During infection, bacteriophage T4 produces the MotA transcription factor that redirects the host RNA polymerase to the expression of T4 middle genes. The C-terminal 'double-wing' domain of MotA binds specifically to the MotA box motif of middle T4 promoters. We report the crystal structure of this complex, which reveals a new mode of protein-DNA interaction. The domain binds DNA mostly via interactions with the DNA backbone, but the binding is enhanced in the specific cognate structure by additional interactions with the MotA box motif in both the major and minor grooves...
April 30, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29698767/regulation-of-neural-differentiation-synaptic-scaling-and-animal-behavior-by-mecp2-phophorylation
#6
Xiaofen Zhong, Hongda Li, Jason Kim, Qiang Chang
Highly expressed in the mammalian brain and widely distributed across the genome, MeCP2 is a key player in recognizing modified DNA and interpreting the epigenetic information encoded in different DNA methylation/hydroxymethylation patterns. Alterations in sequence or copy number of the X-linked human MECP2 gene cause either Rett syndrome (RTT) or MECP2 duplication syndrome. Alterations in MECP2 levels have also been identified in patients with autism. To fully understand the significant role of MECP2 in regulating the development and function of the nervous system, it is important to study all aspects of MeCP2 function...
April 23, 2018: Neurobiology of Learning and Memory
https://www.readbyqxmd.com/read/29696733/quantification-of-dna-methylation-and-hydroxymethylation-in-alzheimer-s-disease-mouse-model-using-lc-ms-ms
#7
Qionglin Huang, Simin Xu, Mingming Mo, Qingjin Yang, Jian Li, Yu Zhong, Junjie Zhang, Lijian Zhang, Xiaoxiao Ye, Zhou Liu, Chun Cai
Ambiguous alteration patterns of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) involved in Alzheimer's disease (AD) obstructed the mechanism investigation of this neurological disorder from epigenetic view. Here, we applied a fully quantitative and validated LC-MS/MS method to determine genomic 5mC and 5hmC in the brain cortex of three month-aged (12, 15 and 18 month) AD model mouse, and found significant increases of 5mC and 5hmC levels in different months of AD mouse when compared with age-matched wild-type control and exhibited rising trend from 12-month to 18-month AD mouse, thereby supporting genomic DNA methylation and hydroxymethylation was positively correlated with developing AD...
April 25, 2018: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/29682093/dna-methylation-in-osteoarthritis-current-status-and-therapeutic-implications
#8
REVIEW
Antonio Miranda-Duarte
Background: Primary Osteoarthritis (OA) is a multifactorial disease in which genetic factors are strongly associated with its development; however, recently it has been observed that epigenetic modifications are also involved in the pathogenesis of OA. DNA methylation is related to gene silencing, and several studies have investigated its role in the loci of different pathways or molecules associated to OA. Objective: This review is focused on the current status of DNA methylation studies related to OA pathogenesis...
2018: Open Rheumatology Journal
https://www.readbyqxmd.com/read/29602950/arsenic-containing-hydrocarbons-effects-on-gene-expression-epigenetics-and-biotransformation-in-hepg2-cells
#9
S M Müller, H Finke, F Ebert, J F Kopp, F Schumacher, B Kleuser, K A Francesconi, G Raber, T Schwerdtle
Arsenic-containing hydrocarbons (AsHCs), a subgroup of arsenolipids found in fish and algae, elicit substantial toxic effects in various human cell lines and have a considerable impact on cellular energy levels. The underlying mode of action, however, is still unknown. The present study analyzes the effects of two AsHCs (AsHC 332 and AsHC 360) on the expression of 44 genes covering DNA repair, stress response, cell death, autophagy, and epigenetics via RT-qPCR in human liver (HepG2) cells. Both AsHCs affected the gene expression, but to different extents...
March 30, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29556496/tet-enzymes-variants-and-differential-effects-on-function
#10
REVIEW
Philippa Melamed, Yahav Yosefzon, Cfir David, Anna Tsukerman, Lilach Pnueli
Discovery of the ten-eleven translocation 1 (TET) methylcytosine dioxygenase family of enzymes, nearly 10 years ago, heralded a major breakthrough in understanding the epigenetic modifications of DNA. Initially described as catalyzing the oxidation of methyl cytosine (5mC) to hydroxymethyl cytosine (5hmC), it is now clear that these enzymes can also catalyze additional reactions leading to active DNA demethylation. The association of TET enzymes, as well as the 5hmC, with active regulatory regions of the genome has been studied extensively in embryonic stem cells, although these enzymes are expressed widely also in differentiated tissues...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29555775/identification-and-biosynthesis-of-thymidine-hypermodifications-in-the-genomic-dna-of-widespread-bacterial-viruses
#11
Yan-Jiun Lee, Nan Dai, Shannon E Walsh, Stephanie Müller, Morgan E Fraser, Kathryn M Kauffman, Chudi Guan, Ivan R Corrêa, Peter R Weigele
Certain viruses of bacteria (bacteriophages) enzymatically hypermodify their DNA to protect their genetic material from host restriction endonuclease-mediated cleavage. Historically, it has been known that virion DNAs from the Delftia phage ΦW-14 and the Bacillus phage SP10 contain the hypermodified pyrimidines α-putrescinylthymidine and α-glutamylthymidine, respectively. These bases derive from the modification of 5-hydroxymethyl-2'-deoxyuridine (5-hmdU) in newly replicated phage DNA via a pyrophosphorylated intermediate...
March 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29542811/ten-eleven-translocation-2-regulates-dna-hydroxymethylation-status-and-psoriasiform-dermatitis-progression-in-mice
#12
Xin Wang, Xinxin Liu, Xiaoru Duan, Ke Zhu, Song Zhang, Lu Gan, Nian Liu, Himanshu Jaypaul, Johanna T Makamure, Zhangyin Ming, Hongxiang Chen
Epigenetics plays an important role in the development and progression of many diseases. There is increasing evidence for the importance of epigenetic modifications in the progression of psoriasis. The aim of this study was to examine the role and potential mechanism of action of 5-hydroxymethylcytosine (5-hmC) and ten-eleven translocation-2 (TET2) in psoriasiform dermatitis in mice. Immunohistochemical staining was performed on psoriasis patients and healthy controls. Topical application of imiquimod cream to the dorsal skin of mice was used to induce psoriasiform dermatitis...
March 15, 2018: Acta Dermato-venereologica
https://www.readbyqxmd.com/read/29529342/dna-hydroxymethylation-of-colorectal-primary-carcinoma-and-its-association-with-survival
#13
Anjing Zhong, Yiping Tian, Honghe Zhang, Maode Lai
METHODS: A total of 71 cases of colorectal carcinoma with hepatic metastasis were enrolled from the Department of Pathology of SIR RUN RUN SHAW Hospital. Paired primary tumors, hepatic metastases, and normal mucosa samples were collected from formalin-fixed paraffin-embedded tissues by manual macrodissection. And global levels of DNA methylation and hydroxymethylation in these tissues, measured by an ELISA-like microplate-based colorimetric methods. The immunohistochemical expression of 5-methylcytosine and 5-hydroxymethylcytosine were analyzed also...
March 12, 2018: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29524144/whole-genome-bisulfite-sequencing-for-the-analysis-of-genome-wide-dna-methylation-and-hydroxymethylation-patterns-at-single-nucleotide-resolution
#14
Magali Kernaleguen, Christian Daviaud, Yimin Shen, Eric Bonnet, Victor Renault, Jean-François Deleuze, Florence Mauger, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29514210/new-insights-into-the-methylation-status-of-virulent-diuraphis-noxia-hemiptera-aphididae-biotypes
#15
Kelly Breeds, N Francois V Burger, Anna-Maria Botha
Epigenetic modifications provide a means for aphid biotype development that a lack of genetic variation, owing to an anholocyclic reproduction lifecycle, fails to do. Here we present data on the DNA methylation status in four South African Russian wheat aphids (RWA), Diuraphis noxia (Kurdjomov) (Hemiptera: Aphididae) biotypes expressing different levels of virulence against its host, Triticum aestivum L. (Poales: Poaceae, Triticeae). The DNA methylation status of these biotypes was determined through the use of methylation-sensitive amplification polymorphism analysis, restriction site-specific fluorescence labeling-a novel technique, and measuring relative global DNA methylation and hydroxymethylation...
March 5, 2018: Journal of Economic Entomology
https://www.readbyqxmd.com/read/29507648/integrated-analyses-of-multi-omics-reveal-global-patterns-of-methylation-and-hydroxymethylation-and-screen-the-tumor-suppressive-roles-of-hadhb-in-colorectal-cancer
#16
Yimin Zhu, Hanlin Lu, Dandan Zhang, Meiyan Li, Xiaohui Sun, Ledong Wan, Dan Yu, Yiping Tian, Hongchuan Jin, Aifen Lin, Fei Gao, Maode Lai
Background: DNA methylation is an important epigenetic modification, associated with gene expression. 5-Methylcytosine and 5-hydroxymethylcytosine are two epigenetic hallmarks that maintain the equilibrium of epigenetic reprogramming. Disequilibrium in genomic methylation leads to carcinogenesis. The purpose of this study was to elucidate the epigenetic mechanisms of DNA methylation and hydroxymethylation in the carcinogenesis of colorectal cancer. Methods: Genome-wide patterns of DNA methylation and hydroxymethylation in six paired colorectal tumor tissues and corresponding normal tissues were determined using immunoprecipitation and sequencing...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29506131/comparative-biochemical-analysis-of-uhrf-proteins-reveals-molecular-mechanisms-that-uncouple-uhrf2-from-dna-methylation-maintenance
#17
Robert M Vaughan, Bradley M Dickson, Evan M Cornett, Joseph S Harrison, Brian Kuhlman, Scott B Rothbart
UHRF1 is a histone- and DNA-binding E3 ubiquitin ligase that functions with DNMT1 to maintain mammalian DNA methylation. UHRF1 facilitates DNMT1 recruitment to replicating chromatin through a coordinated mechanism involving histone and DNA recognition and histone ubiquitination. UHRF2 shares structural homology with UHRF1, but surprisingly lacks functional redundancy to facilitate DNA methylation maintenance. Molecular mechanisms uncoupling UHRF2 from DNA methylation maintenance are poorly defined. Through comprehensive and comparative biochemical analysis of recombinant human UHRF1 and UHRF2 reader and writer activities, we reveal conserved modes of histone PTM recognition but divergent DNA binding properties...
February 28, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29492310/dna-methylation-alterations-in-alzheimer-s-disease
#18
REVIEW
Amy S Yokoyama, John C Rutledge, Valentina Medici
The observation that Alzheimer's disease (AD) patients with similar and even identical genetic backgrounds often present with heterogeneous pathologies has prompted the hypothesis that epigenetics may contribute to AD. While the study of epigenetics encompasses a variety of modifications including histone modifications and non-coding RNAs, much of the research on how epigenetics might impact AD pathology has been focused on DNA methylation. To this end, several studies have characterized DNA methylation alterations in various brain regions of individuals with AD, with conflicting results...
May 2017: Environmental Epigenetics
https://www.readbyqxmd.com/read/29491831/species-specific-5-mc-and-5-hmc-genomic-landscapes-indicate-epigenetic-contribution-to-human-brain-evolution
#19
Andy Madrid, Pankaj Chopra, Reid S Alisch
Human evolution from non-human primates has seen substantial change in the central nervous system, with the molecular mechanisms underlying human brain evolution remaining largely unknown. Methylation of cytosine at the fifth carbon (5-methylcytosine; 5 mC) is an essential epigenetic mark linked to neurodevelopment, as well as neurological disease. The emergence of another modified form of cytosine (5-hydroxymethylcytosine; 5 hmC) that is enriched in the brain further substantiates a role for these epigenetic marks in neurodevelopment, yet little is known about the evolutionary importance of these marks in brain development...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29482634/individual-retrotransposon-integrants-are-differentially-controlled-by-kzfp-kap1-dependent-histone-methylation-dna-methylation-and-tet-mediated-hydroxymethylation-in-na%C3%A3-ve-embryonic-stem-cells
#20
Andrea Coluccio, Gabriela Ecco, Julien Duc, Sandra Offner, Priscilla Turelli, Didier Trono
BACKGROUND: The KZFP/KAP1 (KRAB zinc finger proteins/KRAB-associated protein 1) system plays a central role in repressing transposable elements (TEs) and maintaining parent-of-origin DNA methylation at imprinting control regions (ICRs) during the wave of genome-wide reprogramming that precedes implantation. In naïve murine embryonic stem cells (mESCs), the genome is maintained highly hypomethylated by a combination of TET-mediated active demethylation and lack of de novo methylation, yet KAP1 is tethered by sequence-specific KZFPs to ICRs and TEs where it recruits histone and DNA methyltransferases to impose heterochromatin formation and DNA methylation...
February 26, 2018: Epigenetics & Chromatin
keyword
keyword
20466
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"