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https://www.readbyqxmd.com/read/29445086/the-oncogene-etv5-promotes-met-in-somatic-reprogramming-and-orchestrates-epiblast-primitive-endoderm-specification-during-mescs-differentiation
#1
Jinglong Zhang, Hongxia Cao, Jing Xie, Chen Fan, Youlong Xie, Xin He, Mingzhi Liao, Shiqiang Zhang, Huayan Wang
Unipotent spermatogonial stem cells (SSCs) can be efficiently reprogrammed into pluripotent stem cells only by manipulating the culture condition, without introducing exogenous reprogramming factors. This phenotype raises the hypothesis that the endogenous transcription factors (TFs) in SSCs may facilitate reprogramming to acquire pluripotency. In this study, we screened a pool of SSCs TFs (Bcl6b, Lhx1, Foxo1, Plzf, Id4, Taf4b, and Etv5), and found that oncogene Etv5 could dramatically increase the efficiency of induced pluripotent stem cells (iPSCs) generation when combined with Yamanaka factors...
February 14, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29432895/a-cross-omics-approach-to-investigate-temporal-gene-expression-regulation-by-5-hydroxymethylcytosine-via-tbh-derived-oxidative-stress-showed-involvement-of-different-regulatory-kinases
#2
Jacob J Briedé, Lize Deferme, Jarno E J Wolters, Sandra M H Claessen, Twan van den Beucken, J Richard Wagner, Simone G van Breda, Jos C S Kleinjans
Regulation of DNA methylation plays a crucial role in biological processes and carcinogenesis. The formation of 5-hydroxymethylcytosine (5hmC) by oxidation of 5-methylcytosine (5mC) has been proposed as an intermediate of active demethylation. However, whether and how active demethylation is regulated by oxidative stress-related processes is not well understood. Here we investigated whether free oxygen radicals are capable of directly forming 5hmC and how this enhanced whole genome gene expression. We applied LC-MS/MS technology for the analysis of 5mC, 5hmC, 5-formylcytosine (5fC) and 5-hydroxymethyluracyl (5hmU) in HepG2 cells exposed to hydroxyl- and methyl radicals, formed by tert-butyl hydroperoxide (TBH) at multiple time points...
February 9, 2018: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/29430663/dna-hydroxymethylation-rate-in-the-ache-and-hoxc4-promoter-associated-with-human-sperm-quality
#3
Y Li, Y H Li, X Zhou, B Wu, J P Chen, Z K Wang, X Wang, H J Shi, R S Li
The relationship of altered DNA 5'-hydroxymethylation in human spermatozoa with seminal parameters remains unclear. The aim of the study was to investigate the association between the 5'-hydroxymethylcytosine (5hmC) rate in the promoters of acetylcholinesterase (AChE) and homeobox C4 (HoxC4) genes and human sperm concentration/motility. The study population consisted of three groups: asthenozoospermia (AZ), oligoasthenozoospermia (OAZ) and normozoospermia (NZ). The 5hmC rate in the promoter was measured by CCGG loci-dependent MspI/HpaII restriction mapping of glycosylation-modified sperm DNA combined with a hydroxymethylation-specific real-time polymerase chain reaction assay...
February 11, 2018: Andrologia
https://www.readbyqxmd.com/read/29428975/5-hydroxymethylcytosine-preferentially-targets-genes-upregulated-in-isocitrate-dehydrogenase-1-mutant-high-grade-glioma
#4
Wioletta K Glowacka, Harshika Jain, Makiko Okura, Abulizi Maimaitiming, Yasin Mamatjan, Romina Nejad, Hamza Farooq, Michael D Taylor, Kenneth Aldape, Paul Kongkham
Gliomas demonstrate epigenetic dysregulation exemplified by the Glioma CpG Island Methylator Phenotype (G-CIMP) seen in IDH1 mutant tumors. 5-Hydroxymethylcytosine (5hmC) is implicated in glioma pathogenesis; however, its role in IDH1 mutant gliomas is incompletely understood. To characterize 5hmC in IDH1 mutant gliomas further, we examine 5hmC in a cohort of IDH1 mutant and wild-type high-grade gliomas (HGG) using a quantitative locus-specific approach. Regions demonstrating high 5hmC abundance and differentially hydroxymethylated regions (DHMR) enrich for enhancers implicated in glioma pathogenesis...
February 10, 2018: Acta Neuropathologica
https://www.readbyqxmd.com/read/29422991/preeclampsia-is-associated-with-hypermethylation-of-igf-1-promoter-mediated-by-dnmt1
#5
Min Ma, Qiong-Jie Zhou, Yu Xiong, Bin Li, Xiao-Tian Li
Previous studies have demonstrated a dynamic epigenetic regulation of genes expression in placenta trophoblasts and a dynamic imbalance of DNA methylation and hydroxymethylation. Reduced IGF-1 has been observed in preeclampsia. This study was to investigate the interactive roles between IGF-1 and the global DNA methylation/hydroxymethylation, and the status of DNA methylation/hydroxymethylation and associated enzymes such as DNMTs and TETs in peeeclamptic placentas and hypoxic trophoblasts. It was found that IGF-1 was decreased in preeclamptic placentas and hypoxic trophoblasts when compared to the control group using immunohistochemisty, western blot, qRT-PCR and ELISA...
2018: American Journal of Translational Research
https://www.readbyqxmd.com/read/29411480/genome-re-sequencing-and-simple-sequence-repeat-markers-reveal-the-existence-of-divergent-lineages-in-the-canadian-puccinia-striiformis-f-sp-tritici-population-with-extensive-dna-methylation
#6
Gurcharn S Brar, Sajid Ali, Dinah Qutob, Stephen Ambrose, Kun Lou, Ron Maclachlan, Curtis J Pozniak, Yong-Bi Fu, Andrew G Sharpe, Hadley R Kutcher
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is an important disease in Canada. The worldwide genetic structure of Pst populations have been characterized, excluding Canada. Here, we elucidated the genetic structure of the western Canadian Pst population using molecular markers, revealing the presence of four divergent lineages with predominantly clonal structure. In the worldwide context, two previously reported lineages were identified: PstS0 (22%), representing an old northwestern-European, and PstS1 (35%), an invasive warm-temperature adapted...
February 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29394393/decoding-the-dynamic-dna-methylation-and-hydroxymethylation-landscapes-in-endodermal-lineage-intermediates-during-pancreatic-differentiation-of-hesc
#7
Jia Li, Xinwei Wu, Yubin Zhou, Minjung Lee, Lei Guo, Wei Han, William Mo, Wen-Ming Cao, Deqiang Sun, Ruiyu Xie, Yun Huang
Dynamic changes in DNA methylation and demethylation reprogram transcriptional outputs to instruct lineage specification during development. Here, we applied an integrative epigenomic approach to unveil DNA (hydroxy)methylation dynamics representing major endodermal lineage intermediates during pancreatic differentiation of human embryonic stem cells (hESCs). We found that 5-hydroxymethylcytosine (5hmC) marks genomic regions to be demethylated in the descendent lineage, thus reshaping the DNA methylation landscapes during pancreatic lineage progression...
January 31, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29357837/detecting-tf-mirna-gene-network-based-modules-for-5hmc-and-5mc-brain-samples-a-intra-and-inter-species-case-study-between-human-and-rhesus
#8
Ujjwal Maulik, Sagnik Sen, Saurav Mallik, Sanghamitra Bandyopadhyay
BACKGROUND: Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on brain tissue between human and rhesus on two methylation cytosine variants based data-profiles (viz., 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) samples) through TF-miRNA-gene network based module detection. RESULTS: First of all, we determine differentially 5hmC methylated genes for human as well as rhesus for intra-species analysis, and differentially multi-stage methylated genes for inter-species analysis...
January 22, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29356143/alterations-in-glucose-concentrations-affect-dna-methylation-at-lrg1-in-an-ex-vivo-rat-cortical-slice-model-of-preterm-brain-injury
#9
Jessy Cartier, Chinthika Piyasena, Sarah A Sparrow, James P Boardman, Amanda J Drake
Preterm birth affects 5-18% of all babies and is associated with neurodevelopmental impairment and increased neuropsychiatric disease risk. Although preterm birth associates with differential DNA methylation at neurodevelopmental genes in buccal DNA, including Leucine-rich alpha-2-glycoprotein 1 (LRG1), it is not known whether these differences also occur in the brain, or if they persist. Thus, there is a need for animal models or in vitro systems in which to undertake longitudinal and mechanistic studies. We used a combination of in vivo rat studies and ex vivo experiments in rat cortical slices to explore their utility in modelling the human preterm brain...
January 22, 2018: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29286410/an-engineered-split-tet2-enzyme-for-chemical-inducible-dna-hydroxymethylation-and-epigenetic-remodeling
#10
Minjung Lee, Yubin Zhou, Yun Huang
DNA methylation is a stable and heritable epigenetic modification in the mammalian genome and is involved in regulating gene expression to control cellular functions. The reversal of DNA methylation, or DNA demethylation, is mediated by the ten-eleven translocation (TET) protein family of dioxygenases. Although it has been widely reported that aberrant DNA methylation and demethylation are associated with developmental defects and cancer, how these epigenetic changes directly contribute to the subsequent alteration in gene expression or disease progression remains unclear, largely owing to the lack of reliable tools to accurately add or remove DNA modifications in the genome at defined temporal and spatial resolution...
December 18, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29285192/ten-eleven-translocation-1-dysfunction-reduces-5-hydroxymethylcytosine-expression-levels-in-gastric-cancer-cells
#11
Kuo-Chiang Wang, Chi-Hsiang Kang, Chung-Yu Tsai, Nan-Hua Chou, Ya-Ting Tu, Guan-Cheng Li, Hing-Chung Lam, Shiuh-Inn Liu, Po-Min Chang, Yan-Hwai Lin, Kuo-Wang Tsai
A sixth base, 5-hydroxymethylcytosine (5hmC), is formed by the oxidation of 5-methylcytosine (5mC) via the catalysis of the ten-eleven translocation (TET) protein family in cells. Expression levels of 5hmC are frequently depleted during carcinogenesis. However, the detailed mechanisms underlying the depletion of 5hmC expression in gastric cancer cells remains unclear, and further research is required. The present study examined the expression levels of 5mC and 5hmC and the expression levels of TET1 and TET2 in gastric cancer tissues using immunohistochemistry...
January 2018: Oncology Letters
https://www.readbyqxmd.com/read/29277934/fam20c-could-be-targeted-by-tet1-to-promote-odontoblastic-differentiation-potential-of-human-dental-pulp-cells
#12
Qimeng Li, Baicheng Yi, Zhihui Feng, Runsha Meng, Cheng Tian, Qiong Xu
OBJECTIVES: Ten-eleven translocation 1 (TET1) is a DNA methylcytosine (mC) dioxygenase discovered recently that can convert 5-mC into 5-hydroxymethylcytosine (5hmC). We previously reported that TET1 promotes odontoblastic differentiation of human dental pulp cells (hDPCs). The gene encoding the family with sequence similarity 20, member C (FAM20C) protein, is a potential TET1 target and showed demethylation during odontoblastic differentiation of hDPCs in our previous study. This study aimed to explore whether TET1-mediated hydroxymethylation could activate the FAM20C gene, thereby regulating hDPC differentiation...
December 25, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/29258984/research-progress-on-5hmc-and-tet-dioxygenases-in-neurodevelopment-and-neurological-diseases
#13
Jian Wang, Kai Xiang Zhang, Guo Zhen Lu, Xiang Hui Zhao
The development of the nervous system is coordinately regulated by multiple interacting factors. If a certain factor is altered or mutated, the coordinated developmental processes could be disrupted, resulting in neurological diseases. The 5-hydroxymethylcytosine (5hmC) is an intermediate product of the DNA demethylation processes. 5hmC and its metabolic enzymes, the ten-eleven translocation protein-TET family of dioxygenases, have recently been identified as new epigenetic players important in the regulation of the nervous system development, as well as in cognition, memory and other neurological functions...
December 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29239726/camp-signaling-regulates-dna-hydroxymethylation-by-augmenting-the-intracellular-labile-ferrous-iron-pool
#14
Vladimir Camarena, David W Sant, Tyler C Huff, Sushmita Mustafi, Ryan K Muir, Allegra T Aron, Christopher J Chang, Adam R Renslo, Paula V Monje, Gaofeng Wang
It is widely accepted that cAMP regulates gene transcription principally by activating the protein kinase A (PKA)-targeted transcription factors. Here, we show that cAMP enhances the generation of 5-hydroxymethylcytosine (5hmC) in multiple cell types. 5hmC is converted from 5-methylcytosine (5mC) by Tet methylcytosine dioxygenases, for which Fe(II) is an essential cofactor. The promotion of 5hmC was mediated by a prompt increase of the intracellular labile Fe(II) pool (LIP). cAMP enhanced the acidification of endosomes for Fe(II) release to the LIP likely through RapGEF2...
December 14, 2017: ELife
https://www.readbyqxmd.com/read/29235481/targeted-inhibition-of-stat-tet1-axis-as-a-therapeutic-strategy-for-acute-myeloid-leukemia
#15
Xi Jiang, Chao Hu, Kyle Ferchen, Ji Nie, Xiaolong Cui, Chih-Hong Chen, Liting Cheng, Zhixiang Zuo, William Seibel, Chunjiang He, Yixuan Tang, Jennifer R Skibbe, Mark Wunderlich, William C Reinhold, Lei Dong, Chao Shen, Stephen Arnovitz, Bryan Ulrich, Jiuwei Lu, Hengyou Weng, Rui Su, Huilin Huang, Yungui Wang, Chenying Li, Xi Qin, James Mulloy, Yi Zheng, Jiajie Diao, Jie Jin, Chong Li, Paul P Liu, Chuan He, Yuan Chen, Jianjun Chen
Effective therapy of acute myeloid leukemia (AML) remains an unmet need. DNA methylcytosine dioxygenase Ten-eleven translocation 1 (TET1) is a critical oncoprotein in AML. Through a series of data analysis and drug screening, we identified two compounds (i.e., NSC-311068 and NSC-370284) that selectively suppress TET1 transcription and 5-hydroxymethylcytosine (5hmC) modification, and effectively inhibit cell viability in AML with high expression of TET1 (i.e., TET1-high AML), including AML carrying t(11q23)/MLL-rearrangements and t(8;21) AML...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233176/uncoordinated-expression-of-dna-methylation-related-enzymes-in-human-cancer
#16
Jiao Liu, Xiuliang Cui, Jinhua Jiang, Dan Cao, Yufei He, Hongyang Wang
BACKGROUND: In addition to the important roles played by 5-methylcytosine (5mC), emerging evidence suggests that 5mC derivatives, such as 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), also exhibit regulatory functions in physiological and pathological processes. Four cytosine modifications (5mC, 5hmC, 5fC and 5caC) are produced and erased by a cyclic enzymatic cascade mediated by DNA methyltransferases (DNMTs), ten-eleven translocation (TET) family enzymes and thymine DNA glycosylase (TDG)...
December 12, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29224170/affinity-based-enrichment-techniques-for-the-genome-wide-analysis-of-5-hydroxymethylcytosine
#17
John P Thomson, Richard R Meehan
Since its initial characterization in 2009 there has been a great degree of interest in comparative profiling of 5-hydroxymethylcytosine (5hmC) nucleotides in vertebrate DNA. Through a host of genome-wide studies the distribution of 5hmC has been mapped in a range of cell lines, tissue types and organisms; the majority of which have been generated through affinity-based methods for 5hmC enrichment. Although recent advances in the field have resulted in the ability to investigate the levels of both methylated and hydroxymethylated cytosines at single base resolution, such studies are still relatively cost-prohibitive as well as technically challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224169/multiplexing-for-oxidative-bisulfite-sequencing-oxbs-seq
#18
Kristina Kirschner, Felix Krueger, Anthony R Green, Tamir Chandra
DNA modifications, especially methylation, are known to play a crucial part in many regulatory processes in the cell. Recently, 5-hydroxymethylcytosine (5hmC) was discovered, a DNA modification derived as an intermediate of 5-methylcytosine (5mC) oxidation. Efforts to gain insights into function of this DNA modification are underway and several methods were recently described to assess 5hmC levels using sequencing approaches. Here we integrate adaptation based multiplexing and high-efficiency library prep into the oxidative Bisulfite Sequencing (oxBS-seq) workflow reducing the starting amount and cost per sample to identify 5hmC levels genome-wide...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224168/tet-assisted-bisulfite-sequencing-tab-seq
#19
Miao Yu, Dali Han, Gary C Hon, Chuan He
5-Hydroxymethylcytosine (5hmC) is a modified form of cytosine, which has recently been found in mammalian cells and tissues. 5hmC is derived from 5-methylcytosine (5mC) by Ten-eleven translocation (TET) family protein-mediated oxidation and may regulate gene expression. Numerous affinity-based profiling methods have been developed to help understand the exact function of 5hmC in the genome. However, these methods have a relatively low resolution (~100 bp) without quantitative information of the modification percentage on each site...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224139/antibody-based-detection-of-global-nuclear-dna-methylation-in-cells-tissue-sections-and-mammalian-embryos
#20
Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, Sari Pennings
Immunostaining is widely used in cell biology for the in situ detection of proteins in fixed cells. The method is based on the specificity of antibodies for recognizing and binding to a selected target, combined with immunolabeling techniques for microscopic imaging. Antibodies with high specificities for modified nucleotides have also been widely developed, and among those, antibodies that recognize modified cytosine: 5-methylcytosine (5mC), and more recently, its derivates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)...
2018: Methods in Molecular Biology
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