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Methylation of sites CpG in promoter

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https://www.readbyqxmd.com/read/28222527/gene-expression-and-methylation-analysis-of-abca7-in-patients-with-alzheimer-s-disease
#1
Kiyohiro Yamazaki, Yuta Yoshino, Takaaki Mori, Taku Yoshida, Yuki Ozaki, Tomoko Sao, Yoko Mori, Shinichiro Ochi, Jun-Ichi Iga, Shu-Ichi Ueno
BACKGROUND/OBJECTIVE: The aim of this study was to examine the blood gene expression and methylation of ATP-binding cassette sub-family A member 7 gene (ABCA7) as a biological marker of AD. METHODS: AD subjects (n = 50; 11 males, 77.7±6.05 years old) and age- and sex-matched healthy controls (n = 50) were recruited. A single nucleotide polymorphism in ABCA7 (rs3764650), methylation rates of CpG sites in the ABCA7 promoter region, and ABCA7 mRNA expression levels in peripheral blood were examined...
February 10, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28219444/a-functional-snp-associated-with-atopic-dermatitis-controls-cell-type-specific-methylation-of-the-vstm1-gene-locus
#2
Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H A Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun, Astrid Irwanto, Benjamin P Fairfax, Vivek Naranbhai, John E A Common, Mark Tang, Chin Keh Chuang, Marjo-Riitta Jarvelin, Julian C Knight, Xuejun Zhang, Fook Tim Chew, Shyam Prabhakar, Liu Jianjun, De Yun Wang, Francesca Zolezzi, Michael Poidinger, E Birgitte Lane, Linde Meyaard, Olaf Rötzschke
BACKGROUND: Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1) as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals...
February 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28213474/a-bayesian-approach-for-analysis-of-whole-genome-bisulphite-sequencing-data-identifies-disease-associated-changes-in-dna-methylation
#3
Owen J L Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28194813/microrna-191-acts-as-a-tumor-promoter-by-modulating-the-tet1-p53-pathway-in-intrahepatic-cholangiocarcinoma
#4
Hao Li, Zun-Qiang Zhou, Zhang-Ru Yang, Da-Nian Tong, Jiao Guan, Bao-Jie Shi, Jia Nie, Xian-Ting Ding, Bin Li, Guang-Wen Zhou, Zheng-Yun Zhang
: Current treatment of intrahepatic cholangiocarcinoma (ICC) remains ineffective because knowledge of ICC carcinogenesis is unclear. Increasing evidence suggests that microRNAs (miRNAs), including miRNA-191, play an important role in tumorigenesis, but expression and biological functions of miRNA-191 in ICC remain to be established. This study aimed to investigate the functions and underlying mechanisms of miRNA-191 in ICC. ICC miRNA profiles were generated in 5 pairs of ICC and matched to normal bile duct tissues by next-generation sequencing technology; ICC miRNA profiles were verified in 18 pairs of ICC tissues and normal bile duct tissues by quantitative reverse transcription PCR (qRT-PCR)...
February 14, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28193703/methylation-in-the-matrix-metalloproteinase-2-gene-is-associated-with-cerebral-ischemic-stroke
#5
Hsiu-Fen Lin, Edward Hsi, Ling-Chun Huang, Yi-Chu Liao, Suh-Hang H Juo, Ruey-Tay Lin
Matrix metalloproteinase-2 (MMP-2) is involved in the pathophysiology of stroke. Previous studies have shown that MMP-2 activity is increased in stroke; however, evidence of epigenetic regulation of the MMP-2 in stroke is still limited. We examined methylation of the MMP-2 promoter in patients with ischemic stroke. This study included 298 patients with ischemic stroke and 258 age-matched and sex-matched controls. MMP-2 promoter methylation levels were measured by pyrosequencing at eight potential cytosine-guanine (CpG) sites...
February 13, 2017: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/28185533/mapping-the-methylation-status-of-the-mir-145-promoter-in-saphenous-vein-smooth-muscle-cells-from-individuals-with-type-2-diabetes
#6
Kirsten Riches, John Huntriss, Claire Keeble, Ian C Wood, David J O'Regan, Neil A Turner, Karen E Porter
Type 2 diabetes mellitus prevalence is growing globally, and the leading cause of mortality in these patients is cardiovascular disease. Epigenetic mechanisms such as microRNAs (miRs) and DNA methylation may contribute to complications of type 2 diabetes mellitus. We discovered an aberrant type 2 diabetes mellitus-smooth muscle cell phenotype driven by persistent up-regulation of miR-145. This study aimed to determine whether elevated expression was due to changes in methylation at the miR-145 promoter. Smooth muscle cells were cultured from saphenous veins of 22 non-diabetic and 22 type 2 diabetes mellitus donors...
March 2017: Diabetes & Vascular Disease Research
https://www.readbyqxmd.com/read/28178989/individualized-analysis-reveals-cpg-sites-with-methylation-aberrations-in-almost-all-lung-adenocarcinoma-tissues
#7
Haidan Yan, Qingzhou Guan, Jun He, Yunqing Lin, Juan Zhang, Hongdong Li, Huaping Liu, Yunyan Gu, Zheng Guo, Fei He
BACKGROUND: Due to the heterogeneity of cancer, identifying differentially methylated (DM) CpG sites between a set of cancer samples and a set of normal samples cannot tell us which patients have methylation aberrations in a particular DM CpG site. METHODS: We firstly showed that the relative methylation-level orderings (RMOs) of CpG sites within individual normal lung tissues are highly stable but widely disrupted in lung adenocarcinoma tissues. This finding provides the basis of using the RankComp algorithm, previously developed for differential gene expression analysis at the individual level, to identify DM CpG sites in each cancer tissue compared with its own normal state...
February 8, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28178655/chl1-hypermethylation-as-a-potential-biomarker-of-poor-prognosis-in-breast-cancer
#8
Esperanza Martín-Sánchez, Saioa Mendaza, Ane Ulazia-Garmendia, Iñaki Monreal-Santesteban, Idoia Blanco-Luquin, Alicia Córdoba, Francisco Vicente-García, Noemí Pérez-Janices, David Escors, Diego Megías, Paula López-Serra, Manel Esteller, José Juan Illarramendi, David Guerrero-Setas
The CHL1 gene encodes a cell-adhesion molecule proposed as being a putative tumour-suppressor gene in breast cancer (BC). However, neither the underlying molecular mechanisms nor the clinical value of CHL1 downregulation in BC has been explored. The methylation status of three CpG sites in the CHL1 promoter was analysed by pyrosequencing in neoplastic biopsies from 142 patients with invasive BC and compared with that of non-neoplastic tissues. We found higher CHL1 methylation levels in breast tumours than in non-neoplastic tissues, either from mammoplasties or adjacent-to-tumour, which correlated with lower levels of protein expression in tumours measured by immunohistochemistry...
February 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28167288/impact-of-tet2-deficiency-on-iron-metabolism-in-erythroblasts
#9
Kyoko Inokura, Tohru Fujiwara, Kei Saito, Tatsuya Iino, Shunsuke Hatta, Yoko Okitsu, Noriko Fukuhara, Yasushi Onishi, Kenichi Ishizawa, Kazuya Shimoda, Hideo Harigae
Sideroblastic anemia is characterized by the presence of ring sideroblasts, which are caused by iron accumulation in the mitochondria of erythroblasts and are present in both acquired and congenital forms of sideroblastic anemia. However, the mechanism leading to ring sideroblast formation remains elusive. Acquired sideroblastic anemia is usually observed in myelodysplastic syndrome. Because a subset of myelodysplastic syndrome harbors a somatic mutation of TET2, it may be involved in iron metabolism and/or heme biosynthesis in erythroblasts...
February 3, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28163185/genomic-characterization-and-dynamic-methylation-of-promoter-facilitates-transcriptional-regulation-of-h2a-variants-h2a-1-and-h2a-2-in-various-pathophysiological-states-of-hepatocyte
#10
Monica Tyagi, Divya Reddy, Sanjay Gupta
Differential expression of homomorphous variants of H2A family of histone H2A.1 and H2A.2 have been associated with hepatocellular carcinoma and maintenance of undifferentiated state of hepatocyte. However, not much is known about the transcriptional regulation of these H2A variants. The current study revealed the presence of 43bp 5'-regulatory region upstream of translation start site and a 26bp 3' stem loop conserved region for both the H2A.1 and H2A.2 variants. However, alignment of both H2A.1 and H2A.2 5'-untranslated region (UTR) sequences revealed no significant degree of homology between them despite the coding exon being very similar amongst the variants...
February 3, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28161997/patterns-of-dna-methylation-across-the-leptin-core-promoter-in-four-diverse-asian-and-north-american-populations
#11
M J Mosher, P E Melton, P Stapleton, M S Schanfield, M H Crawford
DNA methylation is the most widely studied of epigenetic mechanisms, with environmental effects recorded through patterned attachments of methyl groups along the DNA that are capable of modifying gene expression without altering the DNA sequencing. The degree to which these patterns of DNA methylation are heritable, the expected range of normality across populations, and the phenotypic relevance of pattern variation remain unclear. Genes regulating metabolic pathways appear to be vulnerable to ongoing nutritional programming over the life course, as dietary nutrients are significant environmental determinants of DNA methylation, supplying both the methyl groups and energy to generate the methylation process...
April 2016: Human Biology
https://www.readbyqxmd.com/read/28158250/potential-roles-of-dna-methylation-in-the-initiation-and-establishment-of-replicative-senescence-revealed-by-array-based-methylome-and-transcriptome-analyses
#12
Mizuho Sakaki, Yukiko Ebihara, Kohji Okamura, Kazuhiko Nakabayashi, Arisa Igarashi, Kenji Matsumoto, Kenichiro Hata, Yoshiro Kobayashi, Kayoko Maehara
Cellular senescence is classified into two groups: replicative and premature senescence. Gene expression and epigenetic changes are reported to differ between these two groups and cell types. Normal human diploid fibroblast TIG-3 cells have often been used in cellular senescence research; however, their epigenetic profiles are still not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed the gene expression and DNA methylation profiles of three types of senescent cells, namely, replicatively senescent, ras-induced senescent (RIS), and non-permissive temperature-induced senescent SVts8 cells, using gene expression and DNA methylation microarrays...
2017: PloS One
https://www.readbyqxmd.com/read/28143725/methylation-at-3-lcr-of-hpv16-can-be-affected-by-patient-age-and-disruption-of-e1-or-e2-genes
#13
Sérgio Menezes Amaro Filho, Neilane Bertoni, Ayslan Castro Brant, João Paulo Castello Branco Vidal, Shayany Pinto Felix, Silvia Maria Baeta Cavalcanti, Fernanda N Carestiato, Luís Felipe Leite Martins, Liz Maria de Almeida, Miguel Angelo Martins Moreira
CpG methylation at early promoter of HPV16 DNA, in the 3' end of the Long Control Region (3'LCR), has been associated to the presence of episomal forms of viral genome and, consequently, intact E1 and E2 ORFs. The DNA methylation would block the access of E2 viral protein to the E2 binding sites at early-promoter. However, is still unclear if methylation at 3'LCR of HPV16 DNA can also vary depending of other tumor characteristics in addition to viral DNA physical state. In this study, we evaluate whether the methylation level at the five CpG located at 3'LCR of HPV16 is associated to patient age and E1 and/or E2 ORFs integrity...
January 29, 2017: Virus Research
https://www.readbyqxmd.com/read/28131957/the-role-of-methylation-dna-polymorphisms-and-micrornas-on-hla-g-expression-in-human-embryonic-stem-cells
#14
A Verloes, C Spits, M Vercammen, M Geens, J LeMaoult, K Sermon, W Coucke, H Van de Velde
The human leukocyte antigen (HLA)-G gene seems to play a pivotal role in maternal tolerance to the fetus. Little is known about HLA-G expression and its molecular control during in vivo human embryogenesis. Human embryonic stem cells (hESC) provide an interesting in vitro model to study early human development. Different studies reported discrepant findings on whether HLA-G mRNA and protein are present or absent in hESC. Several lines of evidence indicate that promoter CpG methylation and 3' untranslated region (3'UTR) polymorphisms may influence HLA-G expression...
January 9, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28130569/histone-demethylase-utx-counteracts-glucocorticoid-deregulation-of-osteogenesis-by-modulating-histone-dependent-and-independent-pathways
#15
Feng-Sheng Wang, Wei-Shiung Lian, Mel S Lee, Wen-Tsan Weng, Ying-Hsien Huang, Yu-Shan Chen, Yi-Chih Sun, Shing-Long Wu, Pei-Chin Chuang, Jih-Yang Ko
: Excess glucocorticoid administration impairs osteogenic activities, which raises the risk of osteoporotic disorders. Epigenetic methylation of DNA and histone regulates the lineage commitment of progenitor cells. This study was undertaken to delineate the actions of histone lysine demethylase 6a (UTX) with regard to the glucocorticoid impediment of osteogenic differentiation. Osteogenic progenitor cells responded to supraphysiological glucocorticoid by elevating CpG dinucleotide methylation proximal to transcription start sites within Runx2 and osterix promoters and Wnt inhibitor Dickkopf-1 (Dkk1) expression concomitant with low UTX expression...
January 27, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28130259/prenatal-exposure-to-tobacco-smoke-sex-dependently-influences-methylation-and-mrna-levels-of-the-igf-axis-in-lungs-of-mouse-offspring
#16
Karolin F Meyer, Susanne Krauss-Etschmann, Wierd Kooistra, Marjan Reinders-Luinge, Wim Timens, Lester Kobzik, Torsten Plösch, Machteld N Hylkema
BACKGROUND: Prenatal smoke exposure is a risk factor for abnormal lung development and increased sex-dependent susceptibility for asthma and COPD. Birth cohort studies show genome wide DNA methylation changes in children from smoking mothers, but evidence for sex-dependent smoke-induced effects is limited. The insulin-like growth factor (IGF) system plays an important role in lung development. We hypothesized that prenatal exposure to smoke induces lasting changes in promoter methylation patterns of Igf1 and Igf1r, thus influencing transcriptional activity, and contributing to abnormal lung development...
January 27, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28122909/prospective-study-of-crmp4-promoter-methylation-in-prostate-biopsies-as-a-predictor-for-lymph-node-metastases
#17
Xin Gao, Liao-Yuan Li, Jörg Rassler, Jun Pang, Ming-Kun Chen, Wei-Peng Liu, Zheng Chen, Shan-Cheng Ren, Fang-Jian Zhou, Ke-Ji Xie, Xing Zhou, Hui-Jun Qian, Xian-Zhong Bai, Jiu-Min Liu, Jiang-Gen Yang, Dan He, Chun-Kui Shao, Zu-Lan Su, Jing Wang, Jian-Guang Qiu, Li Ling
BACKGROUND: For patients with prostate cancer (PCa), the presence of pelvic lymph node metastasis (LNM) is a strong predictor of poor outcome. However, the approaches with promising sensitivity and specificity to detect LNM are still lacking. We investigated the value of collapsin response mediator protein 4 (CRMP4) promoter methylation in biopsies as a predictor for LNM. METHODS: CRMP4 promoter methylation at two previously identified CpG sites was determined in 80 case-matched biopsy samples (the training set) using bisulfite pyrosequencing...
January 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28116812/genome-wide-measures-of-peripheral-blood-dna-methylation-and-prostate-cancer-risk-in-a-prospective-nested-case-control-study
#18
Liesel M FitzGerald, Haroon Naeem, Enes Makalic, Daniel F Schmidt, James G Dowty, Jihoon E Joo, Chol-Hee Jung, Julie K Bassett, Pierre-Antoine Dugue, Jessica Chung, Andrew Lonie, Roger L Milne, Ee Ming Wong, John L Hopper, Dallas R English, Gianluca Severi, Laura Baglietto, John Pedersen, Graham G Giles, Melissa C Southey
BACKGROUND: Global measures of peripheral blood DNA methylation have been associated with risk of some malignancies, including breast, bladder, and gastric cancer. Here, we examined genome-wide measures of peripheral blood DNA methylation in prostate cancer and its non-aggressive and aggressive disease forms. METHODS: We used a matched, case-control study of 687 incident prostate cancer samples, nested within a larger prospective cohort study. DNA methylation was measured in pre-diagnostic, peripheral blood samples using the Illumina Infinium HM450K BeadChip...
January 24, 2017: Prostate
https://www.readbyqxmd.com/read/28108228/a-preliminary-study-of-endocannabinoid-system-regulation-in-psychosis-distinct-alterations-of-cnr1-promoter-dna-methylation-in-patients-with-schizophrenia
#19
Claudio D'Addario, Vincenzo Micale, Martina Di Bartolomeo, Tibor Stark, Mariangela Pucci, Alexandra Sulcova, Mariacarlotta Palazzo, Zuzana Babinska, Laura Cremaschi, Filippo Drago, A Carlo Altamura, Mauro Maccarrone, Bernardo Dell'Osso
Compelling evidence supports the involvement of the endocannabinoid system (ECS) in psychosis vulnerability. We here evaluated the transcriptional regulation of ECS components in human peripheral blood mononuclear cells (PBMCs) obtained from subjects suffering from bipolar disorder, major depressive disorder and schizophrenia, focusing in particular on the effects of DNA methylation. We observed selective alterations of DNA methylation at the promoter of CNR1, the gene coding for the type-1 cannabinoid receptor, in schizophrenic patients (N=25) with no changes in any other disorder...
January 17, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28105934/charm-discovery-of-combinatorial-chromatin-modification-patterns-in-hepatitis-b-virus-x-transformed-mouse-liver-cancer-using-association-rule-mining
#20
Sung Hee Park, Sun-Min Lee, Young-Joon Kim, Sangsoo Kim
BACKGROUND: Various chromatin modifications, identified in large-scale epigenomic analyses, are associated with distinct phenotypes of different cells and disease phases. To improve our understanding of these variations, many computational methods have been developed to discover novel sites and cell-specific chromatin modifications. Despite the availability of existing methods, there is still room for further improvement when they are applied to resolve the histone code hypothesis. Hence, we aim to investigate the development of a computational method to provide new insights into de novo combinatorial pattern discovery of chromatin modifications to characterize epigenetic variations in distinct phenotypes of different cells...
December 13, 2016: BMC Bioinformatics
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