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Methylation of sites CpG in promoter

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https://www.readbyqxmd.com/read/27905995/cdkn2b-methylation-is-associated-with-carotid-artery-calcification-in-ischemic-stroke-patients
#1
Shuyu Zhou, Yumeng Zhang, Li Wang, Zhizhong Zhang, Biyang Cai, Keting Liu, Hao Zhang, Minhui Dai, Lingli Sun, Xiaomeng Xu, Huan Cai, Xinfeng Liu, Guangming Lu, Gelin Xu
BACKGROUND: Cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/2B) near chromosome 9p21 have been associated with both atherosclerosis and artery calcification, but the underlying mechanisms remained largely unknown. Considering that CDKN2A/2B is a frequently reported site for DNA methylation, this study aimed to evaluate whether carotid artery calcification (CarAC) is related to methylation levels of CDKN2A/2B in patients with ischemic stroke. METHODS: DNA methylation levels of CDKN2A/2B were measured in 322 ischemic stroke patients using peripheral blood leukocytes...
December 1, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27902763/temperature-shift-alters-dna-methylation-and-histone-modification-patterns-in-gonadal-aromatase-cyp19a1-gene-in-species-with-temperature-dependent-sex-determination
#2
Yuiko Matsumoto, Brette Hannigan, David Crews
The environment surrounding the embryos has a profound impact on the developmental process and phenotypic outcomes of the organism. In species with temperature-dependent sex determination, gonadal sex is determined by the incubation temperature of the eggs. A mechanistic link between temperature and transcriptional regulation of developmental genes, however, remains elusive. In this study, we examine the changes in DNA methylation and histone modification patterns of the aromatase (cyp19a1) gene in embryonic gonads of red-eared slider turtles (Trachemys scripta) subjected to a temperature shift during development...
2016: PloS One
https://www.readbyqxmd.com/read/27893715/tgf%C3%AE-promotes-mesenchymal-phenotype-of-pancreatic-cancer-cells-in-part-through-epigenetic-activation-of-vav1
#3
P-H Huang, P-J Lu, L-Y Ding, P-C Chu, W-Y Hsu, C-S Chen, C-C Tsao, B-H Chen, C-T Lee, Y-S Shan, C-S Chen
The highly homeostasis-resistant nature of cancer cells leads to their escape from treatment and to liver metastasis, which in turn makes pancreatic ductal adenocarcinoma (PDAC) difficult to treat, especially the squamous/epithelial-to-mesenchymal transition (EMT)-like subtype. As the molecular mechanisms underlying tumour heterogeneity remain elusive, we investigated whether epigenetic regulation might explain inter-individual differences in the progression of specific subtypes. DNA methylation profiling performed on cancer tissues prior to chemo/radiotherapy identified one hypermethylated CpG site (CpG6882469) in the VAV1 gene body that was correlated with demethylation of two promoter CpGs (CpG6772370/CpG6772811) in both PDAC and peripheral blood...
November 28, 2016: Oncogene
https://www.readbyqxmd.com/read/27893424/accumulated-promoter-methylation-as-a-potential-biomarker-for-esophageal-cancer
#4
Xianzhen Peng, Hengchuan Xue, Lingshuang Lü, Peiyi Shi, Jianping Wang, Jianming Wang
We performed a two-stage molecular epidemiological study to explore DNA methylation profiles for potential biomarkers of esophageal squamous cell carcinoma (ESCC) in a Chinese population. Infinium Methylation 450K BeadChip was used to identify genes with differentially methylated CpG sites. Sixteen candidate genes were validated by sequencing 1160 CpG sites in their promoter regions using the Illumina MiSeq platform. When excluding sites with negative changes, 10 genes (BNIP3, BRCA1, CCND1, CDKN2A, HTATIP2, ITGAV, NFKB1, PIK3R1, PRDM16 and PTX3) showed significantly different methylation levels among cancer lesions, remote normal-appearing tissues, and healthy controls...
November 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27886370/epigenetic-alterations-of-the-bdnf-gene-in-combat-related-post-traumatic-stress-disorder
#5
T Y Kim, S J Kim, H G Chung, J H Choi, S H Kim, J I Kang
OBJECTIVE: Brain-derived neurotrophic factor (BDNF) plays a crucial role in modulating resilience and vulnerability to stress. The aim of this study was to investigate whether epigenetic regulation of the BDNF gene is a biomarker of post-traumatic stress disorder (PTSD) development among veterans exposed to combat in the Vietnam War. METHODS: Using the Clinician-Administered PTSD Scale, combat veterans were grouped into those with (n = 126) and without (n = 122) PTSD...
November 25, 2016: Acta Psychiatrica Scandinavica
https://www.readbyqxmd.com/read/27881847/epigenetic-regulation-of-l-type-voltage-gated-ca-2-channels-in-mesenteric-arteries-of-aging-hypertensive-rats
#6
Jingwen Liao, Yanyan Zhang, Fang Ye, Lin Zhang, Yu Chen, Fanxing Zeng, Lijun Shi
Accumulating evidence has shown that epigenetic regulation is involved in hypertension and aging. L-type voltage-gated Ca(2+) channels (LTCCs), the dominant channels in vascular myocytes, greatly contribute to arteriole contraction and blood pressure (BP) control. We investigated the dynamic changes and epigenetic regulation of LTCC in the mesenteric arteries of aging hypertensive rats. LTCC function was evaluated by using microvascular rings and whole-cell patch-clamp in the mesenteric arteries of male Wistar-Kyoto rats and spontaneously hypertensive rats at established hypertension (3 month old) and an aging stage (16 month old), respectively...
November 24, 2016: Hypertension Research: Official Journal of the Japanese Society of Hypertension
https://www.readbyqxmd.com/read/27873492/aberrant-hypomethylation-of-solute-carrier-family-6-member-12-promoter-induces-metastasis-of-ovarian-cancer
#7
Hye Youn Sung, San Duk Yang, Ae Kyung Park, Woong Ju, Jung Hyuck Ahn
PURPOSE: Ovarian cancer (OC) is the most fatal of gynecological malignancies with a high rate of recurrence. We aimed to evaluate the expression of solute carrier family 6, member 12 (SLC6A12) and methylation of its promoter CpG sites in a xenograft mouse model of metastatic OC, and to investigate the regulatory mechanisms that promote aggressive properties during OC progression. MATERIALS AND METHODS: Expression of SLC6A12 mRNA was determined by reverse-transcription quantitative polymerase chain reaction (RT-qPCR), and DNA methylation status of its promoter CpGs was detected by quantitative methylation-specific PCR...
January 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/27861356/a-childhood-acute-lymphoblastic-leukemia-genome-wide-association-study-identifies-novel-sex-specific-risk-variants
#8
Sandeep K Singh, Philip J Lupo, Michael E Scheurer, Anshul Saxena, Amy E Kennedy, Boubakari Ibrahimou, Manuel Alejandro Barbieri, Ken I Mills, Jacob L McCauley, Mehmet Fatih Okcu, Mehmet Tevfik Dorak
Childhood acute lymphoblastic leukemia (ALL) occurs more frequently in males. Reasons behind sex differences in childhood ALL risk are unknown. In the present genome-wide association study (GWAS), we explored the genetic basis of sex differences by comparing genotype frequencies between male and female cases in a case-only study to assess effect-modification by sex.The case-only design included 236 incident cases of childhood ALL consecutively recruited at the Texas Children's Cancer Center in Houston, Texas from 2007 to 2012...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27848899/computational-modeling-approach-in-probing-effects-of-cytosine-methylation-on-the-transcription-factor-binding-to-dna
#9
John Tenayuca, Kimberley Cousins, Shumei Yang, Lubo Zhang
Cytosine methylation at CpG dinucleotides is a chief mechanism in epigenetic modification of gene expression patterns. Previous studies demonstrated that increased CpG methylation of Sp1 sites at -268 and -346 of protein kinase C  promoter repressed the gene expression. The present study investigated the impact of CpG methylation on the Sp1 binding via molecular modeling and electrophoretic mobility shift assay. Each of the Sp1 sites contain two CpGs. Methylation of either CpG lowered the binding affinity of Sp1, whereas methylation of both CpGs produced a greater decrease in the binding affinity...
November 16, 2016: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/27845898/transcription-factor-lsf-dnmt1-complex-dissociation-by-fqi1-leads-to-aberrant-dna-methylation-and-gene-expression
#10
Hang Gyeong Chin, V K Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, Scott E Schaus, Ulla Hansen, Sriharsa Pradhan
The transcription factor LSF is highly expressed in hepatocellular carcinoma (HCC) and promotes oncogenesis. Factor quinolinone inhibitor 1 (FQI1), inhibits LSF DNA-binding activity and exerts anti-proliferative activity. Here, we show that LSF binds directly to the maintenance DNA (cytosine-5) methyltransferase 1 (DNMT1) and its accessory protein UHRF1 both in vivo and in vitro. Binding of LSF to DNMT1 stimulated DNMT1 activity and FQI1 negated the methyltransferase activation. Addition of FQI1 to the cell culture disrupted LSF bound DNMT1 and UHRF1 complexes, resulting in global aberrant CpG methylation...
November 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27835705/dna-methylation-mediated-downregulation-of-defb1-in-prostate-cancer-cells
#11
Jaehyouk Lee, Jun Hyun Han, Ara Jang, Jin Wook Kim, Soon Auck Hong, Soon Chul Myung
Epigenetic aberrations play crucial roles in prostate cancer (PCa) development and progression. The DEFB1 gene, which encodes human ß-defensin-1 (HBD-1), contributes to innate immune responses and functions as a potential tumor suppressor in urological cancers. We investigated whether differential DNA methylation at the low CpG-content promoter (LCP) of DEFB1 was associated with transcriptional regulation of DEFB1 in PCa cells. To identify distinct CpG loci within the DEFB1 LCP related to the epigenetic regulation of DEFB1, we performed an in vitro methylated reporter assay followed by bisulfite sequencing of the DEFB1 promoter fragment...
2016: PloS One
https://www.readbyqxmd.com/read/27832427/dna-methylation-changes-in-response-to-active-smoking-exposure-are-associated-with-leukocyte-telomere-length-among-older-adults
#12
Xu Gao, Ute Mons, Yan Zhang, Lutz Philipp Breitling, Hermann Brenner
Telomere length (TL) is associated with an increased risk of aging-related diseases. As a preventable environmental hazard of morbidity and mortality, smoking has been reported to promote TL attrition by producing a variety of oxidants and free radicals. Since DNA methylation has been demonstrated to play an important role in the pathways of smoking and smoking-induced diseases, this study aimed to address whether the smoking-associated DNA methylation changes could be associated with accelerated TL shortening...
November 10, 2016: European Journal of Epidemiology
https://www.readbyqxmd.com/read/27814638/new-insights-on-the-role-of-dna-methylation-from-a-global-view
#13
Karin Meier, Félix Recillas-Targa
In mammals, DNA methylation is a crucial epigenetic modification with key functions during development. Cellular processes that are regulated by DNA methylation comprise X chromosome inactivation, gene imprinting, genomic stability and transcriptional regulation. Generally, the methylation status of the majority of target sites is reliably propagated during mitosis. However, advances in genome-wide DNA methylation analysis at base-resolution have discovered a substantial amount of differential DNA methylation between normal cells of different tissue-origin...
January 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/27813113/promoter-cpg-site-methylation-of-the-kai1-metastasis-suppressor-gene-contributes-to-its-epigenetic-repression-in-prostate-cancer
#14
Jaeseob Lee, Moon-Sung Lee, Doo-Il Jeoung, Young-Myeong Kim, Hansoo Lee
BACKGROUND: Repression of the KAI1 metastasis suppressor gene is closely associated with malignancy and poor prognosis in many human cancer types including prostate cancer. Since gene repression in human cancers frequently results from epigenetic alterations by DNA methylation and histone modifications, we examined whether the KAI1 gene becomes silenced through these epigenetic mechanisms in prostate cancer. METHODS: KAI1 mRNA and protein levels were determined by RT-PCR and immunoblotting analyses, respectively...
November 3, 2016: Prostate
https://www.readbyqxmd.com/read/27788248/dna-methylation-patterns-in-the-hypothalamus-of-female-pubertal-goats
#15
Chen Yang, Jing Ye, Xiumei Li, Xiaoxiao Gao, Kaifa Zhang, Lei Luo, Jianping Ding, Yunhai Zhang, Yunsheng Li, Hongguo Cao, Yinghui Ling, Xiaorong Zhang, Ya Liu, Fugui Fang
Female pubertal development is tightly controlled by complex mechanisms, including neuroendocrine and epigenetic regulatory pathways. Specific gene expression patterns can be influenced by DNA methylation changes in the hypothalamus, which can in turn regulate timing of puberty onset. In order to understand the relationship between DNA methylation changes and gene expression patterns in the hypothalamus of pubertal goats, whole-genome bisulfite sequencing and RNA-sequencing analyses were carried out. There was a decline in DNA methylation levels in the hypothalamus during puberty and 268 differentially methylated regions (DMR) in the genome, with differential patterns in different gene regions...
2016: PloS One
https://www.readbyqxmd.com/read/27776265/epigenetic-regulation-of-estrogen-receptor-%C3%AE-contributes-to-age-related-differences-in-transcription-across-the-hippocampal-regions-ca1-and-ca3
#16
Lara Ianov, Ashok Kumar, Thomas C Foster
The expression of estrogen receptor alpha (ERα) varies across brain regions and changes with age and according to the previous history of estradiol exposure. ERα is regulated by a number of mechanisms including the level of mRNA (Esr1) expression. For this study, we took advantage of regional differences in hippocampal ERα expression to investigate DNA ERα promoter methylation at CpG dinucleotide sites as a potential epigenetic mechanism for regulating gene expression. Young and aged female Fischer 344 rats were ovariectomized, and Esr1 expression and ERα promoter methylation were examined in hippocampal regions CA1 and CA3, either 3 or 14 weeks following surgery...
September 28, 2016: Neurobiology of Aging
https://www.readbyqxmd.com/read/27773886/cdkn2b-methylation-and-aortic-arch-calcification-in-patients-with-ischemic-stroke
#17
Shuyu Zhou, Biyang Cai, Zhizhong Zhang, Yumeng Zhang, Li Wang, Keting Liu, Hao Zhang, Lingli Sun, Huan Cai, Guangming Lu, Xinfeng Liu, Gelin Xu
AIM: CDKN2A/2B near chromosome 9p21 has been proposed as a potential genetic etiology for both atherosclerosis and arterial calcification. DNA methylation, which can change the expression of CDKN2A/2B, may be an underlying mechanism for this association. This study aimed to evaluate whether CDKN2A/2B methylation is related to aortic arch calcification (AAC) in patients with ischemic stroke. METHODS: DNA methylation levels of CDKN2A/2B was measured using venous blood samples in 322 patients with ischemic stroke...
October 21, 2016: Journal of Atherosclerosis and Thrombosis
https://www.readbyqxmd.com/read/27760737/genome-wide-dna-methylation-analysis-identifies-candidate-epigenetic-markers-and-drivers-of-hepatocellular-carcinoma
#18
Yongchang Zheng, Qianqian Huang, Zijian Ding, Tingting Liu, Chenghai Xue, Xinting Sang, Jin Gu
The alteration of DNA methylation landscape is a key epigenetic event in cancer. As the accumulation of large-scale genome-wide DNA methylation data from clinical samples, we are able to characterize the patterns of DNA methylation alterations for identifying candidate epigenetic markers and drivers. In this survey, we take hepatocellular carcinoma (HCC) as an example to show the basic steps of analyzing the DNA methylation patterns in cancer across multiple data sets. We collected three genome-wide DNA methylation data sets with ∼800 clinical samples and the corresponding gene expression data sets...
October 19, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27754252/os-36-03-e-box-cpg-hypomethylation-of-nmn-producing-enzyme-nampt-in-proximal-tubules-enables-constant-supply-of-nmn-from-tubules-to-glomeruli-which-is-disrupted-in-diabetic-nephropathy
#19
Hirokazu Muraoka, Kazuhiro Hasegawa, Shu Wakino
OBJECTIVE: Nicotinamide phosphoribosyltransferase (Nampt) cooperates with a longevity gene, Sirt1, to exert the potentiation of stress resistance. We have reported that the high expression level of Nampt in PTs contributes to the sufficient supply of NMN to glomeruli. We also showed that downregulation of Nampt and NMN in PT in DN leads to glomerular damages (Nature Medicine 2013). However, the regulation mechanisms of Nampt expression remain unknown. DESIGN AND METHOD: We investigated how Nampt expression is consistently retained at high levels in PTs under normal conditions and how Nampt levels are decreased in DN...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27716309/correlation-of-an-epigenetic-mitotic-clock-with-cancer-risk
#20
Zhen Yang, Andrew Wong, Diana Kuh, Dirk S Paul, Vardhman K Rakyan, R David Leslie, Shijie C Zheng, Martin Widschwendter, Stephan Beck, Andrew E Teschendorff
BACKGROUND: Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk. RESULTS: Here, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue...
October 3, 2016: Genome Biology
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