keyword
MENU ▼
Read by QxMD icon Read
search

Dna hydroxymethylation

keyword
https://www.readbyqxmd.com/read/28428825/comprehensive-evaluation-of-genome-wide-5-hydroxymethylcytosine-profiling-approaches-in-human-dna
#1
Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M Gould, Shalima S Nair, Susan J Clark, Clare Stirzaker
BACKGROUND: The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28422379/increased-5-hydroxymethylation-levels-in-the-hippocampus-of-rat-extinguished-from-cocaine-self-administration
#2
Anna Sadakierska-Chudy, Małgorzata Frankowska, Karolina Wydra, Joanna Jastrzębska, Joanna Miszkiel, Małgorzata Filip
Drug craving and relapse risk during abstinence from cocaine are thought to be caused by persistent changes in transcription and chromatin regulation. Although several brain regions are involved in these processes, the hippocampus seems to play an important role in context-evoked craving and drug-seeking behavior. Only a few studies have examined epigenetic alterations during a period of cocaine abstinence. To investigate the effects of cocaine abstinence on DNA methylation and gene expression, rats that self-administered the drug underwent cocaine abstinence in two time points with extinction training...
April 19, 2017: Hippocampus
https://www.readbyqxmd.com/read/28418776/7-glutathione-pyrrole-and-7-cysteine-pyrrole-are-potential-carcinogenic-metabolites-of-pyrrolizidine-alkaloids
#3
Xiaobo He, Qingsu Xia, Peter P Fu
Many pyrrolizidine alkaloids (PAs) are hepatotoxic, genotoxic, and carcinogenic phytochemicals. Metabolism of PAs in vivo generates four (±)-6,7-dihydro-7-hydroxy-1-hydroxymethyl-5H-pyrrolizine (DHP)-DNA adducts that have been proposed to be responsible for PA-induced liver tumor formation in rats. In this present study, we determined that the same set of DHP-DNA adducts was formed upon the incubation of 7-glutathione-DHP and 7-cysteine-DHP with cultured human hepatocarcinoma HepG2 cells. These results suggest that 7-glutathione-DHP and 7-cysteine-DHP are reactive metabolites of PAs that can bind to cellular DNA to form DHP-DNA adducts in HepG2 cells, and can potentially initiate liver tumor formation...
March 1, 2017: Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews
https://www.readbyqxmd.com/read/28411382/interaction-between-maternal-and-paternal-shmt1-c1420t-predisposes-to-neural-tube-defects-in-the-fetus-evidence-from-case-control-and-family-based-triad-approaches
#4
Prasoona K Rebekah, Sunitha Tella, Srinadh Buragadda, Muni Kumari Tiruvatturu, Jyothy Akka
BACKGROUND: Neural tube defects (NTDs) are caused by the failure of neural tube formation which occurs during early embryonic development. NTDs are the most severe and leading cause of fetal mortality. Serine hydroxymethyl transferase (SHMT1) provides one-carbon units necessary for embryogenesis and defects in one-carbon production result in specific pathological conditions during pregnancy. The present study is aimed to evaluate the association of SHMT1 C1420T with NTD risk in the fetus using fetal, maternal and paternal groups by applying both case-control and family-based triad approaches...
April 14, 2017: Birth Defects Res
https://www.readbyqxmd.com/read/28393704/epigenetic-regulation-of-memory-therapeutic-potential-for-disorders
#5
Padmanabh Singh, Sweta Srivas, M K Thakur
Memory is a vital function which declines in different physiological and pathological conditions such as aging and neurodegenerative diseases. Research in the past has reported that memory formation and consolidation require the precise expression of synaptic plasticity genes. However, little is known about the regulation of these genes. Epigenetic modification is now a well established mechanism that regulates synaptic plasticity genes and neuronal functions including memory. Such modification includes mainly DNA methylation and hydroxymethylation, histone acetylation and methylation which involve chromatin modifying enzymes...
April 4, 2017: Current Neuropharmacology
https://www.readbyqxmd.com/read/28388873/changes-in-the-dna-methylation-and-hydroxymethylation-status-of-the-intercellular-adhesion-molecule-1-gene-promoter-in-thyrocytes-from-autoimmune-thyroiditis-patients
#6
Tingting Liu, Jie Sun, Zhaojun Wang, Wenqing Yang, Hao Zhang, Chenling Fan, Zhongyan Shan, Weiping Teng
BACKGROUND: The intercellular adhesion molecule 1 (ICAM1) gene is not expressed in normal thyroid tissue but was shown to be expressed in the thyroid tissue of autoimmune thyroiditis (AIT) patients. METHODS: This study aimed to explore whether the DNA methylation and hydroxymethylation status of the ICAM1 promoter are aberrantly altered in the thyroid cells of AIT patients and whether this change is associated with dysfunctional expression of ICAM1. A total of 35 AIT patients and 35 sex- and age-matched controls were studied...
April 7, 2017: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/28387726/rethinking-the-epigenetic-framework-to-unravel-the-molecular-pathology-of-schizophrenia
#7
REVIEW
Ariel Cariaga-Martinez, Raúl Alelú Paz
Schizophrenia is a complex mental disorder whose causes are still far from being known. Although researchers have focused on genetic or environmental contributions to the disease, we still lack a scientific framework that joins molecular and clinical findings. Epigenetic can explain how environmental variables may affect gene expression without modifying the DNA sequence. In fact, neuroepigenomics represents an effort to unify the research available on the molecular pathology of mental diseases, which has been carried out through several approaches ranging from interrogating single DNA methylation events and hydroxymethylation patterns, to epigenome-wide association studies, as well as studying post-translational modifications of histones, or nucleosomal positioning...
April 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28371147/quantitative-lc-ms-provides-no-evidence-for-m-6-da-or-m-4-dc-in-the-genome-of-mouse-embryonic-stem-cells-and-tissues
#8
Sarah Schiffers, Charlotte Ebert, René Rahimoff, Olesea Kosmatchev, Jessica Steinbacher, Alexandra-Viola Bohne, Fabio Spada, Stylianos Michalakis, Jörg Nickelsen, Markus Müller, Thomas Carell
Until recently, it was believed that the genomes of higher organisms contain, in addition to the four canonical DNA bases, only 5-methyl-dC (m(5) dC) as a modified base to control epigenetic processes. In recent years, this view has changed dramatically with the discovery of 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC) in DNA from stem cells and brain tissue. N(6) -methyldeoxyadenosine (m(6) dA) is the most recent base reported to be present in the genome of various eukaryotic organisms...
March 30, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28369586/uracil-dna-glycosylase-udg-activities-in-bradyrhizobium-diazoefficiens-characterization-of-a-new-class-of-udg-with-broad-substrate-specificity
#9
Ullas Valiya Chembazhi, Vinod Vikas Patil, Shivjee Sah, Wayne Reeve, Ravi P Tiwari, Euijeon Woo, Umesh Varshney
Repair of uracils in DNA is initiated by racil NA lycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 ( Bdi Ung) from Bradyrhizobium diazoefficiens . Although Bdi Ung contains the motif A (GQDPA), it has low sequence identity to known UDGs. Bdi Ung prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it...
March 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28359242/small-molecule-inhibitors-of-epigenetic-mutations-as-compelling-drug-targets-for-myelodysplastic-syndromes
#10
Bani Bandana Ganguly
BACKGROUND: Involvement of mutations in epigenetic mechanism in development of heterogeneous MDS and its evolution to AML has been understood with at least one mutation and median of 2-3 mutations of the landscapes of driver mutations in ~40 genes described >90% MDS patients. Exclusivity and cooperating effects of mutations have directed therapeutic implementation with hypomethylating agents and identified a number of first-in-class small molecules as inhibitors of mutational expression...
March 30, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28341638/tet1-exerts-its-tumor-suppressor-function-by-regulating-autophagy-in-glioma-cells
#11
Rui Fu, Yan Ding, Jie Luo, Li Yu, Cheng Lin Li, Dong Sheng Li, Shi Wen Wen Guo
BACKGROUND: DNA methylation and demethylation play a critical role in the regulation of the molecular pathogenesis of gliomas. TET1 catalyzes the sequential oxidation of 5-methylcytosine to 5-hydroxymethyl-cytosine, leading to eventual DNA demethylation. It has reported that TET1 is a tumor suppressor in several cancers. However, whether TET1 play a role in glioma development is largely unclear. METHODS: Different glioma specimens and corresponding normal contols were collected to analysis the expression of TET1...
March 24, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28331549/dynamics-of-5-methylcytosine-and-5-hydroxymethylcytosine-during-pronuclear-development-in-equine-zygotes-produced-by-icsi
#12
Sonia Heras, Katrien Smits, Catharina De Schauwer, Ann Van Soom
BACKGROUND: Global epigenetic reprogramming is considered to be essential during embryo development to establish totipotency. In the classic model first described in the mouse, the genome-wide DNA demethylation is asymmetric between the paternal and the maternal genome. The paternal genome undergoes ten-eleven translocation (TET)-mediated active DNA demethylation, which is completed before the end of the first cell cycle. Since TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, the latter is postulated to be an intermediate stage toward DNA demethylation...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28298607/human-herpesvirus-6b-induces-hypomethylation-on-chromosome-17p13-3-correlating-with-increased-gene-expression-and-virus-integration
#13
Elin Engdahl, Nicky Dunn, Pitt Niehusmann, Sarah Wideman, Peter Wipfler, Albert J Becker, Tomas J Ekström, Malin Almgren, Anna Fogdell-Hahn
Human herpesvirus 6B (HHV-6B) is a neurotropic beta-herpesvirus that achieves latency by integrating its genome into host cell chromosomes. Several viruses can induce epigenetic modifications in their host cells, but no study has investigated the epigenetic modifications induced by HHV-6B. This study analyzed methylation with Illumina 450K array comparing HHV-6B infected and uninfected Molt-3 T cells three days post infection. Bisulfite pyrosequencing was used to validate Illumina results and investigate methylation over time in vitro Expression of genes was investigated using qPCR, and virus integration was investigated with PCR...
March 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28294608/engineered-split-tet2-enzyme-for-inducible-epigenetic-remodeling
#14
Minjung Lee, Jia Li, Yi Liang, Guolin Ma, Jixiang Zhang, Lian He, Yuliang Liu, Qian Li, Minyong Li, Deqiang Sun, Yubin Zhou, Yun Huang
The Ten-eleven translocation (TET) family of 5-methylcytosine (5mC) dioxygenases catalyze the conversion of 5mC into 5-hydroxymethylcytosine (5hmC) and further oxidized species to promote active DNA demethylation. Here we engineered a split-TET2 enzyme to enable temporal control of 5mC oxidation and subsequent remodeling of epigenetic states in mammalian cells. We further demonstrate the use of this chemically inducible system to dissect the correlation between DNA hydroxymethylation and chromatin accessibility in the mammalian genome...
April 5, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28293326/line-1-is-preferentially-hypomethylated-within-adenomatous-polyps-in-the-presence-of-synchronous-colorectal-cancer
#15
Alice Chu Jiang, Lela Buckingham, William Barbanera, Amoah Yeboah Korang, Faraz Bishesari, Joshua Melson
BACKGROUND: Conventional tubular adenomas are frequently detected in patients undergoing average risk screening colonoscopy and are over-represented in patients who will develop colorectal cancer (CRC). Whether features of adenomas could serve as predictors of synchronous CRC is not known. Here, we investigate whether global methylation markers, including LINE-1, differ within adenomas in patients with and without synchronous CRC. METHODS: Colorectal tubular/tubulovillous adenomatous polyps in the absence (P group, n = 45) and in the presence of synchronous CRC (PC group, n = 32) were identified...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28282966/experimental-mitochondria-targeted-dna-methylation-identifies-gpc-methylation-not-cpg-methylation-as-potential-regulator-of-mitochondrial-gene-expression
#16
Monique G P van der Wijst, Amanda Y van Tilburg, Marcel H J Ruiters, Marianne G Rots
Like the nucleus, mitochondria contain their own DNA and recent reports provide accumulating evidence that also the mitochondrial DNA (mtDNA) is subjective to DNA methylation. This evidence includes the demonstration of mitochondria-localised DNA methyltransferases and demethylases, and the detection of mtDNA methylation as well as hydroxymethylation. Importantly, differential mtDNA methylation has been linked to aging and diseases, including cancer and diabetes. However, functionality of mtDNA methylation has not been demonstrated...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28272510/apolipoprotein-e4-and-insulin-resistance-interact-to-impair-cognition-and-alter-the-epigenome-and-metabolome
#17
Lance A Johnson, Eileen Ruth S Torres, Soren Impey, Jan F Stevens, Jacob Raber
Apolipoprotein E4 (E4) and type 2 diabetes are major risk factors for cognitive decline and late onset Alzheimer's disease (AD). E4-associated phenotypes and insulin resistance (IR) share several features and appear to interact in driving cognitive dysfunction. However, shared mechanisms that could explain their overlapping pathophysiology have yet to be found. We hypothesized that, compared to E3 mice, E4 mice would be more susceptible to the harmful cognitive effects of high fat diet (HFD)-induced IR due to apoE isoform-specific differences in brain metabolism...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28260562/the-effect-of-paternal-methyl-group-donor-intake-on-offspring-dna-methylation-and-birth-weight
#18
S Pauwels, I Truijen, M Ghosh, R C Duca, S A S Langie, B Bekaert, K Freson, I Huybrechts, G Koppen, R Devlieger, L Godderis
Most nutritional studies on the development of children focus on mother-infant interactions. Maternal nutrition is critically involved in the growth and development of the fetus, but what about the father? The aim is to investigate the effects of paternal methyl-group donor intake (methionine, folate, betaine, choline) on paternal and offspring global DNA (hydroxy)methylation, offspring IGF2 DMR DNA methylation, and birth weight. Questionnaires, 7-day estimated dietary records, whole blood samples, and anthropometric measurements from 74 fathers were obtained...
March 6, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28250235/methylation-dynamics-during-folliculogenesis-and-early-embryo-development-in-sheep
#19
Laura Masala, Giovanni Pietro Burrai, Emanuela Bellu, Federica Ariu, Luisa Bogliolo, Sergio Ledda, Daniela Bebbere
Genome-wide DNA methylation reprogramming occurs during mammalian gametogenesis and early embryogenesis. Post-fertilization demethylation of paternal and maternal genomes is considered to occur by an active and passive mechanism, respectively, in most mammals but sheep; in this species no loss of methylation was observed in either pronucleus. Post-fertilization reprogramming relies on methylating and de-methylating enzymes and co-factors that are stored during oocyte growth, concurrently with the re-methylation of the oocyte itself...
March 1, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28230192/an-endoparasitoid-wasp-influences-host-dna-methylation
#20
Sunil Kumar, Yonggyun Kim
Parasitism by endoparasitoid wasps changes the expression of various host genes, and alters host immune and developmental processes. However, it is not clearly understood how parasitism changes host gene expression in a whole genome scale. This study focused on an epigenetic control of Cotesia plutellae, an endoparasitoid wasp, against its host, Plutella xylostella. Two DNA methyltransferases (DNMT-1 and DNMT-2) are encoded in the genome of P. xylostella. In addition, methyl-binding domain proteins (MBDs) and DNA demethylation factor, ten-eleven translation protein (TET) are encoded...
February 23, 2017: Scientific Reports
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"