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Methylation of sites CpG in promoter

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https://www.readbyqxmd.com/read/29235098/hepcidin-and-dna-promoter-methylation-in-hepatocellular-carcinoma
#1
Silvia Udali, Annalisa Castagna, Michela Corbella, Andrea Ruzzenente, Sara Moruzzi, Filippo Mazzi, Tommaso Campagnaro, Domenica De Santis, Antonia Franceschi, Patrizia Pattini, Rossella Gottardo, Oliviero Olivieri, Luigi Perbellini, Alfredo Guglielmi, Sang-Woon Choi, Domenico Girelli, Simonetta Friso
BACKGROUND: The liver hormone hepcidin regulates iron homeostasis that is often altered in hepatocellular carcinoma (HCC). Epigenetic phenomena control gene expression through a dynamic fashion, therefore, considering the plasticity of both iron homeostasis and epigenetic mechanisms and their role in liver carcinogenesis, we investigated whether hepcidin gene (HAMP) expression is modulated by DNA methylation thus affecting iron status in human HCC. MATERIALS AND METHODS: Thirty-two patients affected by non-viral HCC were enrolled and their main clinical and biochemical characteristics obtained...
December 13, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29233090/dna-methylation-regulates-discrimination-of-enhancers-from-promoters-through-a-h3k4me1-h3k4me3-seesaw-mechanism
#2
Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J Taft, Hans R Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J Araúzo-Bravo
BACKGROUND: DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. RESULTS: We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci...
December 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29230669/p21waf1-cip1-and-p27kip1-are-correlated-with-the-development-and-invasion-of-prolactinoma
#3
Wei Dong, Jianhua Li, Qian Liu, Chunhui Liu, Chuzhong Li, Guidong Song, Haibo Zhu, Hua Gao, Yazhuo Zhang
Cell cycle control can prevent excessive proliferative response in the pituitary homeostasis. Cyclin dependent kinases (Cdks) are modulated by cyclins or Cdk inhibitors, such as p21 and p27, which can regulate cell cycle progression from the G1 to S phases. This study was conducted to evaluate the levels and the promoter region methylation status of p21 and p27 in prolactinomas (PRL) and analyze their association with clinicopathologic features. We found high-p21 level cases were featured by 5/23 and H-scores 142...
December 11, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29229679/epigenetic-and-posttranscriptional-regulation-of-cd16-expression-during-human-nk-cell-development
#4
Aaron R Victor, Christoph Weigel, Steven D Scoville, Wing Keung Chan, Kelsey Chatman, Mary M Nemer, Charlene Mao, Karen A Young, Jianying Zhang, Jianhua Yu, Aharon G Freud, Christopher C Oakes, Michael A Caligiuri
The surface receptor FcγRIIIA (CD16a) is encoded by the FCGR3A gene and is acquired by human NK cells during maturation. NK cells bind the Fc portion of IgG via CD16a and execute Ab-dependent cell-mediated cytotoxicity, which is critical for the effectiveness of several antitumor mAb therapies. The role of epigenetic regulatory mechanisms controlling transcriptional and posttranscriptional CD16 expression in NK cells is unknown. In this study, we compared specific patterns of DNA methylation and expression of FCGR3A with FCGR3B, which differ in cell type-specific expression despite displaying nearly identical genomic sequences...
December 11, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29224162/methylation-specific-multiplex-ligation-dependent-probe-amplification-ms-mlpa
#5
Cathy B Moelans, Lilit Atanesyan, Suvi P Savola, Paul J van Diest
This chapter describes a method for the rapid assessment of promoter hypermethylation levels or methylation of imprinted regions in human genomic DNA extracted from various sources using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Multiplex ligation-dependent probe amplification (MLPA) is a powerful and easy-to-perform PCR-based technique that can identify gains, amplifications, losses, deletions, methylation and mutations of up to 55 targets in a single reaction, while requiring only minute quantities of DNA (about 50 ng) extracted from blood, fresh frozen or formalin-fixed paraffin-embedded materials...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223680/dysregulation-of-c-x-c-motif-ligand-10-during-aging-and-association-with-cognitive-performance
#6
Steven Bradburn, Jamie McPhee, Liam Bagley, Michael Carroll, Mark Slevin, Nasser Al-Shanti, Yoann Barnouin, Jean-Yves Hogrel, Mati Pääsuke, Helena Gapeyeva, Andrea Maier, Sarianna Sipilä, Marco Narici, Andrew Robinson, David Mann, Antony Payton, Neil Pendleton, Gillian Butler-Browne, Chris Murgatroyd
Chronic low-grade inflammation during aging (inflammaging) is associated with cognitive decline and neurodegeneration; however, the mechanisms underlying inflammaging are unclear. We studied a population (n = 361) of healthy young and old adults from the MyoAge cohort. Peripheral levels of C-X-C motif chemokine ligand 10 (CXCL10) was found to be higher in older adults, compared with young, and negatively associated with working memory performance. This coincided with an age-related reduction in blood DNA methylation at specific CpGs within the CXCL10 gene promoter...
November 23, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29221193/steroidogenic-factor-1-hypermethylation-in-maternal-rat-blood-could-serve-as-a-biomarker-for-intrauterine-growth-retardation
#7
Dong-Mei Wu, Liang-Peng Ma, Gui-Li Song, Yong Long, Han-Xiao Liu, Yang Liu, Jie Ping
Intrauterine growth retardation (IUGR) is a common obstetric complication lacking an optimal method for prenatal screening. DNA methylation profile in maternal blood holds significant promise for prenatal screening. Here, we aimed to screen out potential IUGR biomarkers in maternal blood from the perspective of DNA methylation. The IUGR rat model was established by prenatal maternal undernutrition. High-throughput bisulfite sequencing of genomic DNA methylation followed by functional clustering analysis for differentially methylated region (DMR)-associated genes demonstrated that genes regulating transcription had the most significantly changed DNA methylation status in maternal blood with IUGR...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29208029/tissue-source-determines-the-differentiation-potentials-of-mesenchymal-stem-cells-a-comparative-study-of-human-mesenchymal-stem-cells-from-bone-marrow-and-adipose-tissue
#8
Liangliang Xu, Yamei Liu, Yuxin Sun, Bin Wang, Yunpu Xiong, Weiping Lin, Qiushi Wei, Haibin Wang, Wei He, Bin Wang, Gang Li
BACKGROUND: Mesenchymal stem cells (MSCs) possess intrinsic regeneration capacity as part of the repair process in response to injury, such as fracture or other tissue injury. Bone marrow and adipose tissue are the major sources of MSCs. However, which cell type is more effective and suitable for cell therapy remains to be answered. The intrinsic molecular mechanism supporting the assertion has also been lacking. METHODS: Human bone marrow-derived MSCs (BMSCs) and adipose tissue-derived MSCs (ATSCs) were isolated from bone marrow and adipose tissue obtained after total hip arthroplasty...
December 6, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29191063/changes-in-dna-methylation-induced-by-multi-walled-carbon-nanotube-exposure-in-the-workplace
#9
Manosij Ghosh, Deniz Öner, Katrien Poels, Ali M Tabish, Jelle Vlaanderen, Anjoeka Pronk, Eelco Kuijpers, Qing Lan, Roel Vermeulen, Bram Bekaert, Peter Hm Hoet, Lode Godderis
This study was designed to assess the epigenetic alterations in blood cells, induced by occupational exposure to multi-wall carbon nanotubes (MWCNT). The study population comprised of MWCNT-exposed workers (n=24) and unexposed controls (n=43) from the same workplace. We measured global DNA methylation/hydroxymethylation levels on the 5th cytosine residues using a validated liquid chromatography tandem-mass spectrometry (LC-MS/MS) method. Sequence-specific methylation of LINE1 retrotransposable element 1 (L1RE1) elements, and promoter regions of functionally important genes associated with epigenetic regulation [DNA methyltransferase-1 (DNMT1) and histone deacetylase 4 (HDAC4)], DNA damage/repair and cell cycle pathways [nuclear protein, coactivator of histone transcription/ATM serine/threonine kinase (NPAT/ATM)], and a potential transforming growth factor beta (TGF-β) repressor [SKI proto-oncogene (SKI)] were studied using bisulfite pyrosequencing...
November 30, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/29187436/identification-of-cpg-sites-of-serpina5-promoter-with-opposite-methylation-patterns-in-benign-and-malignant-prostate-cells
#10
Albert Hagelgans, Carsten Jandeck, Markus Friedemann, Anastasia Donchin, Susan Richter, Mario Menschikowski
BACKGROUND/AIM: To date there has been no investigation into the epigenetic regulation of the serine protease inhibitor SERPINA5 in prostate cancer, where lack of this gene was considered to facilitate invasive growth patterns. MATERIALS AND METHODS: Methylation degrees of eight CpG sites of SERPINA5 were analyzed in normal and malignant prostate cells using nucleotide sequencing, methylation-specific high resolution melting and digital droplet PCR techniques. RESULTS: The methylation degree of five CpG sites significantly correlated with lower SERPINA5 expression levels...
December 2017: Anticancer Research
https://www.readbyqxmd.com/read/29181058/value-of-cnrip1-promoter-methylation-in-colorectal-cancer-screening-and-prognosis-assessment-and-its-influence-on-the-activity-of-cancer-cells
#11
Ting Zhang, Ge Cui, Yun-Liang Yao, Qi-Chun Wang, Hong-Guang Gu, Xi-Ning Li, Hui Zhang, Wen-Ming Feng, Qi-Lin Shi, Weiwei Cui
Introduction: The aim of the study was to investigate the effect of CNRIP1 promoter methylation on the proliferative, invasive and migration potential of colorectal cancer cells, including its potential use for the early detection and prognostic assessment of colorectal cancer. Material and methods: Quantitative methylation-specific PCR (qMSP) was used to detect the methylation status of the CNRIP1 promoter region in peripheral blood samples drawn from patients with colorectal adenocarcinoma, benign colorectal adenoma, and matched healthy controls...
October 2017: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/29161408/landscape-of-dna-methylation-on-the-marsupial-x
#12
Shafagh A Waters, Alexandra M Livernois, Hardip Patel, Denis O'Meally, Jeff M Craig, Jennifer A Marshall Graves, Catherine M Suter, Paul D Waters
DNA methylation plays a key role in maintaining transcriptional silence on the inactive X chromosome of eutherian mammals. Beyond eutherians, there are limited genome wide data on DNA methylation from other vertebrates. Previous studies of X borne genes in various marsupial models revealed no differential DNA methylation of promoters between the sexes, leading to the conclusion that CpG methylation plays no role in marsupial X-inactivation. Using reduced representation bisulfite sequencing, we generated male and female CpG methylation profiles in four representative vertebrates (mouse, gray short-tailed opossum, platypus and chicken)...
November 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29160127/the-fetal-programming-effect-of-prenatal-smoking-on-igf1r-and-igf1-methylation-is-organ-and-sex-specific
#13
Karolin F Meyer, Rikst Nynke Verkaik-Schakel, Wim Timens, Lester Kobzik, Torsten Plösch, Machteld N Hylkema
The impact of prenatal smoke exposure (PSE) on DNA methylation has been demonstrated in blood samples from children of smoking mothers, but evidence for sex-dependent smoke-induced effects is limited. As the identified differentially methylated genes can be associated with developmental processes, and insulin-like growth factors (IGFs) play a critical role in prenatal tissue growth, we hypothesized that PSE induces fetal programming of Igf1r and Igf1. Using a mouse model of smoking during pregnancy, we show that PSE alters promoter methylation of Igf1r and Igf1 and deregulates their gene expression in lung and liver of fetal (E17...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29155330/expression-pattern-and-functional-analysis-of-r-spondin1-in-tongue-sole-cynoglossus-semilaevis
#14
Jinxiang Liu, Tiantian Liu, Jingjing Niu, Xiaolong Wu, Jieming Zhai, Quanqi Zhang, Jie Qi
R-spondin 1 (Rspo1) is a potential female-determining gene in mammals that could regulate the Wnt/β-catenin signaling pathway. The deletion of Rspo1 causes sex reversal in females. To investigate sexual determination and differentiation, we cloned and analyzed the Rspo1 gene in Cynoglossus semilaevis. Phylogenetic and gene structure analyses revealed that Rspo1 gene exhibited high sequence conservation and contained an N-terminal signal peptide, two furin-like cysteine-rich domains (FU1 and FU2), a thrombospondin type 1 repeat, and a C-terminal region enriched with basic charged amino acids...
November 16, 2017: Gene
https://www.readbyqxmd.com/read/29146936/hypomethylation-of-hoxa4-promoter-is-common-in-silver-russell-syndrome-and-growth-restriction-and-associates-with-stature-in-healthy-children
#15
Mari Muurinen, Katariina Hannula-Jouppi, Lovisa E Reinius, Cilla Söderhäll, Simon Kebede Merid, Anna Bergström, Erik Melén, Göran Pershagen, Marita Lipsanen-Nyman, Dario Greco, Juha Kere
Silver-Russell syndrome (SRS) is a growth retardation syndrome in which loss of methylation on chromosome 11p15 (11p15 LOM) and maternal uniparental disomy for chromosome 7 [UPD(7)mat] explain 20-60% and 10% of the syndrome, respectively. To search for a molecular cause for the remaining SRS cases, and to find a possible common epigenetic change, we studied DNA methylation pattern of more than 450 000 CpG sites in 44 SRS patients. Common to all three SRS subgroups, we found a hypomethylated region at the promoter region of HOXA4 in 55% of the patients...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29143365/epigenetic-down-regulation-of-sox2-is-an-independent-poor-prognostic-factor-for-hypopharyngeal-cancers
#16
Mehmet Ozgur Avincsal, Naoe Jimbo, Kohei Fujikura, Hirotaka Shinomiya, Naoki Otsuki, Koichi Morimoto, Tatsuya Furukawa, Naruhiko Morita, Ritsuko Maehara, Tomoo Itoh, Ken-Ichi Nibu, Yoh Zen
AIMS: We recently reported that a small subset (7%) of oesophageal squamous cell carcinomas completely lacking SOX2 expression had unique clinicopathological features and a dismal prognosis. The present study aimed to elucidate whether the findings obtained in oesophageal cancers are applicable to hypopharyngeal or oropharyngeal squamous cell carcinomas (HPSCCs or OPSCCs, respectively). METHODS AND RESULTS: The study cohort consisted of consecutive patients with HPSCC (n=130) and OPSCC (n=65) who underwent surgery without preoperative therapy...
November 15, 2017: Histopathology
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#17
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29135282/genome-wide-dna-methylation-drives-human-embryonic-stem-cell-erythropoiesis-by-remodeling-gene-expression-dynamics
#18
Zhijing Liu, Qiang Feng, Pengpeng Sun, Yan Lu, Minlan Yang, Xiaowei Zhang, Xiangshu Jin, Yulin Li, Shi-Jiang Lu, Chengshi Quan
AIM: To investigate the role of DNA methylation during erythrocyte production by human embryonic stem cells (hESCs). METHODS: We employed an erythroid differentiation model from hESCs, and then tracked the genome-wide DNA methylation maps and gene expression patterns through an Infinium HumanMethylation450K BeadChip and an Ilumina Human HT-12 v4 Expression Beadchip, respectively. RESULTS: A negative correlation between DNA methylation and gene expression was substantially enriched during the later differentiation stage and was present in both the promoter and the gene body...
November 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/29129997/trichloroethylene-induced-alterations-in-dna-methylation-were-enriched-in-polycomb-protein-binding-sites-in-effector-memory-cd4-t-cells
#19
Kathleen M Gilbert, Sarah J Blossom, Brad Reisfeld, Stephen W Erickson, Kanan Vyas, Mary Maher, Brannon Broadfoot, Kirk West, Shasha Bai, Craig A Cooney, Sudeepa Bhattacharyya
Exposure to industrial solvent and water pollutant trichloroethylene (TCE) can promote autoimmunity, and expand effector/memory (CD62L) CD4(+) T cells. In order to better understand etiology reduced representation bisulfite sequencing was used to study how a 40-week exposure to TCE in drinking water altered methylation of ∼337 770 CpG sites across the entire genome of effector/memory CD4(+) T cells from MRL+/+ mice. Regardless of TCE exposure, 62% of CpG sites in autosomal chromosomes were hypomethylated (0-15% methylation), and 25% were hypermethylated (85-100% methylation)...
July 2017: Environmental Epigenetics
https://www.readbyqxmd.com/read/29103775/cyclin-d1-promoter-56-and-54bp-cpg-un-methylation-predicts-invasive-progression-in-arsenic-induced-bowen-s-disease
#20
Wei-Ting Liao, Huey-Ling You, Chee-Yin Chai, Chih-Hung Lee, Cheng-Che E Lan, Shun-Jen Chang, Chu-Ling Yu, Hsin-Su Yu
BACKGROUND: Patients with arsenic-induced Bowen's disease (As-BD) are at risk of developing invasive cancers in the skin, lung, and urinary bladder. However, a longitudinal follow-up study on the association between As-BD and invasive cancers is still lacking. OBJECTIVES: This study aims to investigate the underlying molecular mechanisms of this malignant progression in the skin and internal organs. METHODS: This is a biopsy-based follow-up study...
October 31, 2017: Journal of Dermatological Science
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