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Dna hydroxymethylation

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https://www.readbyqxmd.com/read/28649282/asymmetric-dna-methylation-of-cpg-dyads-is-a-feature-of-secondary-dmrs-associated-with-the-dlk1-gtl2-imprinting-cluster-in-mouse
#1
Megan Guntrum, Ekaterina Vlasova, Tamara L Davis
BACKGROUND: Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28648900/tet-catalyzed-5-hydroxymethylation-precedes-hnf4a-promoter-choice-during-differentiation-of-bipotent-liver-progenitors
#2
Pierre-Benoit Ancey, Szilvia Ecsedi, Marie-Pierre Lambert, Fazlur Rahman Talukdar, Marie-Pierre Cros, Denise Glaise, Diana Maria Narvaez, Veronique Chauvet, Zdenko Herceg, Anne Corlu, Hector Hernandez-Vargas
Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity...
June 19, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28647531/a-rapid-mass-spectrometric-method-for-the-measurement-of-catalytic-activity-of-ten-eleven-translocation-enzymes
#3
Babu Sudhamalla, Debasis Dey, Megan Breski, Kabirul Islam
Enzymatic methylation at carbon five on cytosine (5mC) in DNA is a hallmark of mammalian epigenetic programming and is critical to gene regulation during early embryonic development. It has recently been shown that dynamic erasure of 5mC by three members of the ten-eleven translocation (TET) family plays a key role in cellular differentiation. TET enzymes belong to Fe (II)- and 2-ketoglutarate (2KG) dependent dioxygenases that successively oxidize 5mC to 5-hydroxymethyl cytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5CaC), thus providing a chemical basis for the removal of 5mC which once was thought to be a permanent mark in mammalian genome...
June 21, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28642138/molecular-cloning-of-chicken-tet-family-genes-and-role-of-chicken-tet1-in-erythropoiesis
#4
Yuya Okuzaki, Hidenori Kaneoka, Ken-Ichi Nishijima, Seitaro Murakami, Yuki Ozawa, Shinji Iijima
Ten-eleven translocation (TET) methylcytosine dioxygenase has potential as an active eraser to regulate the genomic DNA methylation status. We herein cloned chicken TET (cTET) family genes, and confirmed their functions. Quantitative reverse-transcription PCR showed that cTET1 was strongly expressed in erythrocytes throughout development. This cTET1 expression pattern, together with the results of methylated or hydroxymethylated DNA immunoprecipitation, suggests that cTET1 contributes to demethylation around the promoter region of the definitive-type β-globin gene βΑ in erythroid cells...
June 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28621264/dna-methylation-hydroxymethylation-in-melanoma
#5
REVIEW
Siqi Fu, Haijing Wu, Huiming Zhang, Christine G Lian, Qianjin Lu
Melanoma is a malignant tumor of melanocytes and is considered to be the most aggressive cancer among all skin diseases. The pathogenesis of melanoma has not been well documented, which may restrict the research and development of biomarkers and therapies. To date, several genetic and epigenetic factors have been identified as contributing to the development and progression of melanoma. Besides the findings on genetic susceptibilities, the recent progress in epigenetic studies has revealed that loss of the DNA hydroxymethylation mark, 5-hydroxymethylcytosine (5-hmC), along with high levels of DNA methylation at promoter regions of several tumor suppressor genes in melanoma, may serve as biomarkers for melanoma...
May 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28617821/supplementation-with-small-extracellular-vesicles-from-ovarian-follicular-fluid-during-in-vitro-production-modulates-bovine-embryo-development
#6
Juliano C da Silveira, Gabriella M Andrade, Maite Del Collado, Rafael V Sampaio, Juliano R Sangalli, Luciano A Silva, Fábio V L Pinaffi, Izabelle B Jardim, Marcelo C Cesar, Marcelo F G Nogueira, Aline S M Cesar, Luiz L Coutinho, Rinaldo W Pereira, Felipe Perecin, Flávio V Meirelles
Pregnancy success results from the interaction of multiple factors, among them are folliculogenesis and early embryonic development. Failure during these different processes can lead to difficulties in conception. Alternatives to overcome these problems are based on assisted reproductive techniques. Extracellular vesicles are cell-secreted vesicles present in different body fluids and contain bioactive materials, such as messenger RNA, microRNAs (miRNAs), and proteins. Thus, our hypothesis is that extracellular vesicles from follicular fluid from 3-6 mm ovarian follicles can modulate bovine embryo development in vitro...
2017: PloS One
https://www.readbyqxmd.com/read/28613929/dna-methylation-and-hydroxymethylation-profile-of-cd34-enriched-cell-products-intended-for-autologous-cd34-cell-transplantation
#7
Jasmina-Ziva Rozman, Maja Pohar Perme, Mojca Jez, Elvira Malicev, Metka Krasna, Bojan Vrtovec, Primoz Rozman
Epigenetic dysregulation has been shown to limit functional capacity of aging hematopoietic stem cells, which may contribute to impaired outcome of hematopoietic stem cell-based therapies. The aim of our study was to gain better insight into the epigenetic profile of CD34(+)-enriched cell products intended for autologous CD34(+) cell transplantation in patients with cardiomyopathy. We found global DNA methylation content significantly higher in immunoselected CD34(+) cells compared to leukocytes in leukapheresis products (2...
June 14, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28611311/genome-wide-5-hydroxymethylcytosine-patterns-in-human-spermatogenesis-are-associated-with-semen-quality
#8
Olga A Efimova, Anna A Pendina, Andrei V Tikhonov, Sergey E Parfenyev, Irina D Mekina, Evgeniia M Komarova, Mariia A Mazilina, Eugene V Daev, Olga G Chiryaeva, Ilona A Galembo, Mikhail I Krapivin, Oleg S Glotov, Irina S Stepanova, Svetlana A Shlykova, Igor Yu. Kogan, Alexander M Gzgzyan, Tatyana V Kuznetzova, Vladislav S Baranov
We performed immunofluorescent analysis of DNA hydroxymethylation and methylation in human testicular spermatogenic cells from azoospermic patients and ejaculated spermatozoa from sperm donors and patients from infertile couples. In contrast to methylation which was present throughout spermatogenesis, hydroxymethylation was either high or almost undetectable in both spermatogenic cells and ejaculated spermatozoa. On testicular cytogenetic preparations, 5-hydroxymethylcytosine was undetectable in mitotic and meiotic chromosomes, and was present exclusively in interphase spermatogonia Ad and in a minor spermatid population...
June 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28601635/silencing-hif-1%C3%AE-induces-tet2-expression-and-augments-ascorbic-acid-induced-5-hydroxymethylation-of-dna-in-human-metastatic-melanoma-cells
#9
Adam P Fischer, Sarah L Miles
Expression and function of Ten-eleven translocation (TET) enzymes, which initiate DNA demethylation by catalyzing the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine (5 hmC) on methylated DNA, are frequently lost in malignant tissue. This ultimately results in lost expression of methylated tumor suppressor genes. Many malignancies, including melanoma, also aberrantly overexpress the oncogenic hypoxia inducible factor-1α (HIF-1α) transcription factor, however the association between HIF-1α and TET enzyme expression is largely uninvestigated...
June 7, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28590037/epigenetic-effects-of-an-adenosine-derivative-in-a-wistar-rat-model-of-liver-cirrhosis
#10
Jesús Rafael Rodríguez-Aguilera, Carlos Guerrero-Hernández, Rosario Pérez-Molina, Carla Elizabeth Cadena-Del-Castillo, Rebeca Pérez-Cabeza de Vaca, Nuria Guerrero-Celis, Mariana Domínguez-López, Adrián Rafael Murillo-de-Ozores, Rodrigo Arzate-Mejía, Félix Recillas-Targa, Victoria Chagoya de Sánchez
The pathological characteristic of cirrhosis is scarring which results in a structurally distorted and dysfunctional liver. Previously, we demonstrated that Col1a1 and Pparg genes are deregulated in CCl4 -induced cirrhosis but their normal expression levels are recovered upon treatment with IFC-305, an adenosine derivative. We observed that adenosine was able to modulate S-adenosylmethionine-dependent trans-methylation reactions, and recently, we found that IFC-305 modulates HDAC3 expression. Here, we investigated whether epigenetic mechanisms, involving DNA methylation processes and histone acetylation, could explain the re-establishment of gene expression mediated by IFC-305 in cirrhosis...
June 7, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28582417/genome-wide-alteration-in-dna-hydroxymethylation-in-the-sperm-from-bisphenol-a-exposed-men
#11
Huajun Zheng, Xiaoyu Zhou, De-Kun Li, Fen Yang, Hongjie Pan, Tianqi Li, Maohua Miao, Runsheng Li, Wei Yuan
Environmental BPA exposure has been shown to impact human sperm concentration and motility, as well as rodent spermatogenesis. However, it is unclear whether BPA exposure is associated with alteration in DNA hydroxymethylation, a marker for epigenetic modification, in human sperm. A genome-wide DNA hydroxymethylation study was performed using sperm samples of men who were occupationally exposed to BPA. Compared with controls who had no occupational BPA exposure, the total levels of 5-hydroxymethylcytosine (5hmc) increased significantly (19...
2017: PloS One
https://www.readbyqxmd.com/read/28537228/-current-methods-of-extracellular-dna-methylation-analysis
#12
O E Bryzgunova, P P Laktionov
The discovery of the enormous role methylated cytosine plays in regulating gene expression has led to the development of a variety of techniques for detecting cytosine modification. A majority of these techniques are geared towards analyzing genomic DNA, which is typically available in large quantities. The concentration of cell-free DNAs (cfDNA) extracted from biological fluids including plasma, saliva, tears, or urine is relatively low and their degree of the fragmentation is high. Moreover, for noninvasive diagnostics of cancer, methylation patterns must be studied in minor cancer-specific fractions of DNA molecules substantially diluted by excess unmethylated molecules...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28523538/mecp2-a-modulator-of-neuronal-chromatin-organization-involved-in-rett-syndrome
#13
Alexia Martínez de Paz, Juan Ausió
From an epigenetic perspective, the genomic chromatin organization of neurons exhibits unique features when compared to somatic cells. Methyl CpG binding protein 2 (MeCP2), through its ability to bind to methylated DNA, seems to be a major player in regulating such unusual organization. An important contribution to this uniqueness stems from the intrinsically disordered nature of this highly abundant chromosomal protein in neurons. Upon its binding to methylated/hydroxymethylated DNA, MeCP2 is able to recruit a plethora of interacting protein and RNA partners...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28505334/direction-a-machine-learning-framework-for-predicting-and-characterizing-dna-methylation-and-hydroxymethylation-in-mammalian-genomes
#14
Milos Pavlovic, Pradipta Ray, Kristina Pavlovic, Aaron Kotamarti, Min Chen, Michael Q Zhang
Motivation: 5-Methylcytosine and 5-Hydroxymethylcytosine in DNA are major epigenetic modifications known to significantly alter mammalian gene expression. High-throughput assays to detect these modifications are expensive, labor-intensive, unfeasible in some contexts, and leave a portion of the genome unqueried. Hence, we devised a novel, supervised, integrative learning framework to perform whole-genome methylation and hydroxymethylation predictions in CpG dinucleotides. Our framework can also perform imputation of missing or low quality data in existing sequencing datasets...
May 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28504700/lineage-specific-functions-of-tet1-in-the-postimplantation-mouse-embryo
#15
Rita Khoueiry, Abhishek Sohni, Bernard Thienpont, Xinlong Luo, Joris Vande Velde, Michela Bartoccetti, Bram Boeckx, An Zwijsen, Anjana Rao, Diether Lambrechts, Kian Peng Koh
The mammalian TET enzymes catalyze DNA demethylation. While they have been intensely studied as major epigenetic regulators, little is known about their physiological roles and the extent of functional redundancy following embryo implantation. Here we define non-redundant roles for TET1 at an early postimplantation stage of the mouse embryo, when its paralogs Tet2 and Tet3 are not detectably expressed. TET1 regulates numerous genes defining differentiation programs in the epiblast and extraembryonic ectoderm...
May 15, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28501209/a-sensitive-signal-off-electrogenerated-chemiluminescence-biosensing-method-for-the-discrimination-of-dna-hydroxymethylation-based-on-glycosylation-modification-and-signal-quenching-from-ferroceneboronic-acid
#16
Yuling Zhang, Yan Li, Yingying Wei, Huiping Sun, Huan Wang
In this study, a new and sensitive signal-off electrogenerated chemiluminescence (ECL) biosensing method for the quantification of 5-hydroxymethylcytosine in DNA (5-hmC-DNA) was developed. The method achieved simple and sensitive detection of 5-hmC-DNA based on the glycosylation of 5-hmC, combining both the amplification function of gold nanoparticles (AuNPs) and the high quenching efficiency of the tris(2, 2'-ripyridine) dichlororuthenium(II) (Ru(bpy)3(2+))-ferrocene (Fc) system. First, the electrode modified with a mixture of Nafion and AuNPs was utilized as the platform for electrostatically adsorbing Ru(bpy)3(2+)(an ECL-emitting species) and assembling 5-hmC-DNA...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28497329/effect-of-cadmium-on-cytosine-hydroxymethylation-in-gastropod-hepatopancreas
#17
Dragos Nica, Cristina Popescu, George Draghici, Ionela Privistirescu, Maria Suciu, Reinhard Stöger
5-Hydroxymethylcytosine (5hmC) is an important, yet poorly understood epigenetic DNA modification, especially in invertebrates. Aberrant genome-wide 5hmC levels have been associated with cadmium (Cd) exposure in humans, but such information is lacking for invertebrate bioindicators. Here, we aimed to determine whether this epigenetic mark is present in DNA of the hepatopancreas of the land snail Cantareus aspersus and is responsive to Cd exposure. Adult snails were reared under laboratory conditions and exposed to graded amounts of dietary cadmium for 14 days...
June 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28489894/analysis-of-global-dna-methylation-changes-in-primary-human-fibroblasts-in-the-early-phase-following-x-ray-irradiation
#18
Anna Maierhofer, Julia Flunkert, Marcus Dittrich, Tobias Müller, Detlev Schindler, Indrajit Nanda, Thomas Haaf
Epigenetic alterations may contribute to the generation of cancer cells in a multi-step process of tumorigenesis following irradiation of normal body cells. Primary human fibroblasts with intact cell cycle checkpoints were used as a model to test whether X-ray irradiation with 2 and 4 Gray induces direct epigenetic effects (within the first cell cycle) in the exposed cells. ELISA-based fluorometric assays were consistent with slightly reduced global DNA methylation and hydroxymethylation, however the observed between-group differences were usually not significant...
2017: PloS One
https://www.readbyqxmd.com/read/28477115/zn-ii-phos-tag-sds-page-for-separation-and-detection-of-a-dna-damage-related-signaling-large-phosphoprotein
#19
Eiji Kinoshita, Emiko Kinoshita-Kikuta, Tohru Koike
In this chapter, we provide a standard protocol for phosphate-affinity sodium dodecyl sulfate-polyacrylamide gel electrophoresis (Zn(2+)-Phos-tag SDS-PAGE). This technique uses a dizinc(II) complex of the phosphate-binding molecule Phos-tag in conjunction with a neutral-pH gel system, Tris [tris(hydroxymethyl)aminomethane], and acetic acid (Tris-AcOH), to detect shifts in the mobility of phosphorylated ataxia telangiectasia-mutated (ATM) kinase. This protocol, which employs a 3% (w/v) polyacrylamide gel strengthened with 0...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28453518/lc-ms-ms-quantitative-analysis-reveals-the-association-between-fto-and-dna-methylation
#20
Yuting Zhu, Guangyu Zhou, Xuebin Yu, Qiang Xu, Kai Wang, Dan Xie, Qingkai Yang, Lina Wang
Fat mass and obesity-associated protein (FTO) is α-ketoglutarate-dependent dioxygenase and responsible for demethylating N6-methyladenosine (m6A) in mRNA, 3-methylthymine (m3T) in single-stranded DNA (ssDNA) and 3-methyluracil (m3U) in single-stranded RNA (ssRNA). Its other function remains unknown but thousands of mammalian DNA show 5-methyl-2'-deoxycytidine (5mdC) modification and 5mdC demethylases are required for mammalian energy homeostasis and fertility. Here, we aimed to confirm whether FTO proteins can demethylate 5mdC in DNA...
2017: PloS One
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