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Andrey Golubov, Igor Kovalchuk
Hydroxymethylcytosine (hmC or 5-hmC) is a nitrogen base occurring as a result of cytosine methylation followed by replacing a methyl group with a hydroxyl group through active oxidation. 5-hmC is considered to be one of the forms of epigenetic modification and is suggested as an intermediate step in a semi-active loss of DNA methylation mark. 5-hmC plays an important role in the epigenetic regulation of gene expression in animals, although its role in plants remains controversial. Here, we present a colorimetric method of quantification of 5-hmC using Brassica rapa DNA...
2017: Methods in Molecular Biology
Gerald Saldanha, Kushal Joshi, Kathryn Lawes, Mark Bamford, Farhaan Moosa, Kah Wee Teo, J Howard Pringle
Outcomes for melanoma patients vary within cancer stage. Prognostic biomarkers are potential adjuncts to provide more precise prognostic information. Simple, low-cost biomarker assays, such as those based on immunohistochemistry, have strong translational potential. 5-hydroxymethylcytosine (5 hmC) shows prognostic potential in melanoma but prior studies were small. We, therefore, analysed 5 hmC in a retrospective cohort to provide external validation of its prognostic value. Two hundred primary melanomas were evaluated for 5 hmC expression using immunohistochemistry...
October 7, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Shangxian Ma, Huiping Sun, Yan Li, Honglan Qi, Jianbin Zheng
DNA methylation is used to dynamically reprogram cells in the course of early embryonic development in mammals. 5-Hydroxymethylcytosine in DNA (5-hmC-DNA) plays essential roles in the demethylation processes. 5-Methylcytosine in DNA (5-mC-DNA) is oxidized to 5-hmC-DNA by 10-11 translocation proteins, which are relatively high abundance in embryonic stem cells and neurons. A new method was developed herein to quantify 5-hmC-DNA based on selective electrogenerated chemiluminescence (ECL) labeling with the specific oxidation of 5-hmC to 5-fC by KRuO4...
October 18, 2016: Analytical Chemistry
Amit Ganguly, Marlin Touma, Shanthie Thamotharan, Darryl C De Vivo, Sherin U Devaskar
We examined the effect of mild (Mi; ∼25%) and moderate (Mo; ∼50%) maternal calorie restriction (MCR) vs ad libitum-fed controls on placental glucose and leucine transport impacting fetal growth potential. We observed in MiMCR a compensatory increase in transplacental (TP) glucose transport due to increased placental glucose transporter isoform (GLUT)-3 but no change in GLUT1 protein concentrations. This change was paralleled by increased glut3 mRNA and 5-hydroxymethylated cytosines with enhanced recruitment of histone 3 lysine demethylase to the glut3 gene locus...
October 2016: Endocrinology
Carolina M Greco, Paolo Kunderfranco, Marcello Rubino, Veronica Larcher, Pierluigi Carullo, Achille Anselmo, Kerstin Kurz, Thomas Carell, Andrea Angius, Michael V G Latronico, Roberto Papait, Gianluigi Condorelli
Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC)-5-mC's oxidation product-in cardiac biology and disease is unknown. Here we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks during heart development and failure. DNA hydroxymethylation marks the body of highly expressed genes as well as distal regulatory regions with enhanced activity...
August 4, 2016: Nature Communications
Olesya Pavlova, Sylvie Fraitag, Daniel Hohl
Differentiation of proliferative nodules in giant congenital nevi from melanoma arising within such nevi is an important diagnostic challenge. DNA methylation is a well-established epigenetic modification already observed in the earliest stages of carcinogenesis, which increases during melanoma progression. The Ten-eleven translocation (TET) enzymes catalyze the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC), which recently has been reported as an epigenetic hallmark associated with tumor aggressiveness and poor prognosis in a wide variety of cancers...
July 22, 2016: Journal of Investigative Dermatology
Osama K Zahid, Boxuan Simen Zhao, Chuan He, Adam R Hall
5-hydroxymethylcytosine (5 hmC), the oxidized form of 5-methylcytosine (5 mC), is a base modification with emerging importance in biology and disease. However, like most epigenetic elements, it is transparent to many conventional genetic techniques and is thus challenging to probe. Here, we report a rapid solid-state nanopore assay that is capable of resolving 5 hmC with high specificity and sensitivity and demonstrate its utility in assessing global modification abundance in genomic DNA.
2016: Scientific Reports
Samrat Roy Choudhury, Yi Cui, Katarzyna Lubecka, Barbara Stefanska, Joseph Irudayaraj
DNA hypermethylation at the promoter of tumour-suppressor genes is tightly correlated with their transcriptional repression and recognized as the hallmark of majority of cancers. Epigenetic silencing of tumour suppressor genes impairs their cellular functions and activates a cascade of events driving cell transformation and cancer progression. Here, we examine site-specific and spatiotemporal alteration in DNA methylation at a target region in BRCA1 gene promoter, a model tumour suppressor gene. We have developed a programmable CRISPR-Cas9 based demethylase tool containing the deactivated Cas9 (dCas9) fused to the catalytic domain (CD) of Ten-Eleven Translocation (TET) dioxygenase1 (TET1CD)...
June 23, 2016: Oncotarget
Alina P S Pang, Christopher Sugai, Alika K Maunakea
Chemical modifications of DNA comprise epigenetic mechanisms that contribute to the maintenance of cellular activities and memory. Although the function of 5-methylcytosine (5-mC) has been extensively studied, little is known about the function(s) of relatively rarer and underappreciated cytosine modifications including 5-hydroxymethylcytosine (5-hmC). The discovery that ten-eleven translocation (Tet) proteins mediate conversion of 5-mC to 5-hmC, and other oxidation derivatives, sparked renewed interest to understand the biological role of 5-hmC...
June 1, 2016: Biomolecular Concepts
Yunfei Liao, Jie Gu, Yongbing Wu, Xiang Long, D I Ge, Jianjun Xu, Jianyong Ding
The loss of 5-hydroxymethylcytosine (5-hmC) has previously been demonstrated to be implicated in the initiation and progression of various tumors. However, its role in non-small cell lung cancer (NSCLC) remains unknown. The present study aimed to determine the level of 5-hmC in NSCLC and their adjacent normal lung tissues by immunohistochemistry and dot-blot analysis; then the relationship between 5-hmC level and the clinicopathological features of NSCLC and the prognostic significance of 5-hmC level in NSCLC patients were analyzed...
June 2016: Oncology Letters
Yanfang Zhang, Kexia Wu, Yuan Shao, Fang Sui, Qi Yang, Bingyin Shi, Peng Hou, Meiju Ji
Accumulating evidences suggest that large-scale loss of 5-hydroxymethylcytosine (5-hmC) is an epigenetic hallmark in different cancers. However, the levels of 5-hmC in laryngeal squamous cell carcinoma (LSCC) and its prognostic value in this cancer remain largely unknown. Using dot-blot and quantitative RT-PCR assays, we investigate 5-hmC levels and expression of TET-1, -2 and -3 in LSCCs and explore the association of 5-hmC levels with clinicopathological characteristics and clinical outcome of LSCC patients...
2016: American Journal of Cancer Research
Emna Mahfoudhi, Ibtissam Talhaoui, Xenia Cabagnols, Véronique Della Valle, Lise Secardin, Philippe Rameau, Olivier A Bernard, Alexander A Ishchenko, Salem Abbes, William Vainchenker, Murat Saparbaev, Isabelle Plo
The family of Ten-Eleven Translocation (TET) proteins is implicated in the process of active DNA demethylation and thus in epigenetic regulation. TET 1, 2 and 3 proteins are oxygenases that can hydroxylate 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) and further oxidize 5-hmC into 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). The base excision repair (BER) pathway removes the resulting 5-fC and 5-caC bases paired with a guanine and replaces them with regular cytosine. The question arises whether active modification of 5-mC residues and their subsequent elimination could affect the genomic DNA stability...
July 2016: DNA Repair
Lili Li, Chen Li, Haitao Mao, Zhenfang Du, Wai Yee Chan, Paul Murray, Bing Luo, Anthony Tc Chan, Tony Sk Mok, Francis Kl Chan, Richard F Ambinder, Qian Tao
Promoter CpG methylation is a fundamental regulatory process of gene expression. TET proteins are active CpG demethylases converting 5-methylcytosine to 5-hydroxymethylcytosine, with loss of 5 hmC as an epigenetic hallmark of cancers, indicating critical roles of TET proteins in epigenetic tumorigenesis. Through analysis of tumor methylomes, we discovered TET1 as a methylated target, and further confirmed its frequent downregulation/methylation in cell lines and primary tumors of multiple carcinomas and lymphomas, including nasopharyngeal, esophageal, gastric, colorectal, renal, breast and cervical carcinomas, as well as non-Hodgkin, Hodgkin and nasal natural killer/T-cell lymphomas, although all three TET family genes are ubiquitously expressed in normal tissues...
2016: Scientific Reports
Chao Ye, Ran Tao, Qingyi Cao, Danhua Zhu, Yini Wang, Jie Wang, Juan Lu, Ermei Chen, Lanjuan Li
Hepatocellular carcinoma (HCC) is a common solid tumor worldwide with a poor prognosis. Accumulating evidence has implicated important regulatory roles of epigenetic modifications in the occurrence and progression of HCC. In the present study, we analyzed 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels in the tumor tissues and paired adjacent peritumor tissues (APTs) from four individual HCC patients using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing [(h)MeDIP-Seq]...
August 2016: International Journal of Oncology
Kai Ni, Temuujin Dansranjavin, Nina Rogenhofer, Nihan Oeztuerk, Johanna Deuker, Martin Bergmann, Hans-Christian Schuppe, Florian Wagenlehner, Wolfgang Weidner, Klaus Steger, Undraga Schagdarsurengin
STUDY QUESTION: Are ten-eleven-translocation (TET) 1-3 family enzymes involved in human spermatogenesis and do they impact male fertility? SUMMARY ANSWER: TET1, TET2 and TET3 are successively expressed at different stages of human spermatogenesis, and their expression levels associate with male fertility. WHAT IS KNOWN ALREADY: Spermatogenesis is a complex cell differentiation process accompanied by a drastic epigenetic remodeling. TET1-3 dioxygenases are essential for active DNA demethylation in the paternal pronucleus and in embryonic stem cells...
July 2016: Human Reproduction
Yao-Fei Pei, Ran Tao, Jian-Fang Li, Li-Ping Su, Bei-Qin Yu, Xiong-Yan Wu, Min Yan, Qin-Long Gu, Zheng-Gang Zhu, Bing-Ya Liu
Ten-Eleven Translocation 1 (TET1) is a member of ten eleven translocation enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC). TET1 can promote CpG islands demethylation in specific genes and often absent in various cancers. Herein, we found that TET1 expression and 5-hmC content were low in gastric tumors compared to its adjacent non-tumor tissues. Cell proliferation, migration and invasion were enhanced upon TET1 knockdown in gastric cancer cells in vitro. This phenomenon was confirmed by an animal xeongraft model...
May 24, 2016: Oncotarget
Camilla B F Gomes, Karina G Zechin, Shuyun Xu, Rafael F Stelini, Ines N Nishimoto, Qian Zhan, Ting Xu, Gungwei Qin, Nathaniel S Treister, George F Murphy, Christine G Lian
Although melanoma is an aggressive cancer, the understanding of the virulence-conferring pathways involved remains incomplete. We have demonstrated that loss of ten-eleven translocation methylcytosine dioxygenase (TET2)-mediated 5-hydroxymethylcytosine (5-hmC) is an epigenetic driver of melanoma growth and a biomarker of clinical virulence. We also have determined that the intermediate filament protein nestin correlates with tumorigenic and invasive melanoma growth. Here we examine the relationships between these two biomarkers...
June 2016: American Journal of Pathology
Xuejiao Shi, Yue Yu, Mei Luo, Zhirong Zhang, Susheng Shi, Xiaoli Feng, Zhaoli Chen, Jie He
Ten-eleven translocation (TET) enzymes catalyze the oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine and 5-carboxylcytosine, which result in genomic DNA demethylation. It was reported that 5-hmC levels were decreased in a variety of cancers and could be regarded as an epigenetic hallmark of cancer. In the present study, 5-hmC levels were detected by immunohistochemistry (IHC) in 173 esophageal squamous cell carcinoma (ESCC) tissues and 91 corresponding adjacent non-tumor tissues; DNA dot blot assays were used to detect the 5-hmC level in another 50 pairs of ESCC tissues and adjacent non-tumor tissues...
2016: PloS One
Ming Zhao, Jing Wang, Wei Liao, Duo Li, Mengying Li, Haijing Wu, Yiqun Zhang, M Eric Gershwin, Qianjin Lu
One of the major disappointments in autoimmunity has been the relative lack of informative data when genomewide associations (GWAS) have been applied to patients with systemic lupus erythematosus (SLE). Indeed, there is increasing evidence that SLE is characterized by widespread epigenetic changes. 5-Hydroxymethylcytosine (5-hmC) is a newly discovered modified form of cytosine suspected to be an important epigenetic modification in embryonic development, cell differentiation and cancer. DNA methylation dynamics have already been implicated in the pathogenesis of SLE, while little is known about hydroxymethylation in this process...
May 2016: Journal of Autoimmunity
Renata Scopim-Ribeiro, João Agostinho Machado-Neto, Paula de Melo Campos, Fernanda Soares Niemann, Irene Lorand-Metze, Fernando Ferreira Costa, Sara Teresinha Olalla Saad, Fabiola Traina
BACKGROUND: New sequencing technologies have enabled the identification of mutations in Ten-eleven-translocation 2 (TET2), an enzyme that catalyzes the conversion of 5-methylcytosine into 5-hydroxymethylcytosine (5-hmC) in myeloid neoplasms. We have recently identified reduced TET2 mRNA expression in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), which is associated with a poor overall survival in MDS. We herein aimed to investigate TET2 mutations and their impact on TET2 expression in a cohort of patients with myeloid neoplasms, including MDS and AML patients...
2016: Diagnostic Pathology
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