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https://www.readbyqxmd.com/read/28205556/hrgfish-a-database-of-hypoxia-responsive-genes-in-fishes
#1
Iliyas Rashid, Naresh Sahebrao Nagpure, Prachi Srivastava, Ravindra Kumar, Ajey Kumar Pathak, Mahender Singh, Basdeo Kushwaha
Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28193856/contribution-of-epigenetic-mechanisms-to-variation-in-cancer-risk-among-tissues
#2
Michael Klutstein, Joshua Moss, Tommy Kaplan, Howard Cedar
Recently, it was suggested that tissue variation in cancer risk originates from differences in the number of stem-cell divisions underlying each tissue, leading to different mutation loads. We show that this variation is also correlated with the degree of aberrant CpG island DNA methylation in normal cells. Methylation accumulates during aging in a subset of molecules, suggesting that the epigenetic landscape within a founder-cell population may contribute to tumor formation.
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28188826/convenient-expression-purification-and-quantitative-liquid-chromatography-tandem-mass-spectrometry-based-analysis-of-tet2-5-methylcytosine-demethylase
#3
Mohit Jaiswal, Subhradeep Bhar, Harika Vemula, Swami Prakash, V K Chaithanya Ponnaluri, William G Gutheil, Mridul Mukherji
5-Methylcytosine within CpG islands in DNA plays a crucial role in epigenetic transcriptional regulation during metazoan development. Recently, it has been established that the Ten-Eleven Translocation (TET) family, Fe(II)- and 2-oxoglutarate (2OG/αKG)-dependent oxygenases initiate 5-methylcytosine demethylation by iterative oxidation reactions. Mutations in the TET2 gene are frequently detected in patients with myeloid malignancies. Here, we describe the cloning of untagged human TET2 demethylase using Gateway technology and its efficient expression in E...
February 8, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28187703/ihms-a-database-integrating-human-histone-modification-data-across-developmental-stages-and-tissues
#4
Yanglan Gan, Han Tao, Jihong Guan, Shuigeng Zhou
BACKGROUND: Differences in chromatin states are critical to the multiplicity of cell states. Recently genome-wide histone modification maps of diverse human developmental stages and tissues have been charted. DESCRIPTION: To facilitate the investigation of epigenetic dynamics and regulatory mechanisms in cellular differentiation processes, we developed iHMS, an integrated human histone modification database that incorporates massive histone modification maps spanning different developmental stages, lineages and tissues ( http://www...
February 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28181048/evolutionary-mechanism-and-biological-functions-of-8-mers-containing-cg-dinucleotide-in-yeast
#5
Yan Zheng, Hong Li, Yue Wang, Hu Meng, Qiang Zhang, Xiaoqing Zhao
The rules of k-mer non-random usage and the biological functions are worthy of special attention. Firstly, the article studied human 8-mer spectra and found that only the spectra of cytosine-guanine (CG) dinucleotide classification formed independent unimodal distributions when the 8-mers were classified into three subsets under 16 dinucleotide classifications. Secondly, the distribution rules were reproduced by other seven species including yeast, which showed that the evolution phenomenon had species universality...
February 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28176663/gsk3%C3%AE-5-flanking-dna-methylation-and-expression-in-alzheimer-s-disease-patients
#6
Vincenzina Nicolia, Viviana Ciraci, Rosaria A Cavallaro, Isidre Ferrer, Sigfrido Scarpa, Andrea Fuso
BACKGROUND: The GSK3β has been associated to pathological functions in neurodegenerative diseases. This kinase is involved in hyperphosphorylation of microtubule-associated tau protein, leading to aggregation andformation of NFTs.It has clearly been shown that GSK3β is regulated at post-translational level: phosphorylation at Tyr216 activates kinase while phosphorylation at Ser9 is essential to inhibit its activity. OBJECTIVES: At present, there are contradictory findings about the possibility that GSK3β may be regulated at gene level...
February 3, 2017: Current Alzheimer Research
https://www.readbyqxmd.com/read/28176656/outlook-on-epigenetic-therapeutic-approaches-for-treatment-of-gastric-cancer
#7
Petra Hudler
The incidence of gastric cancer has been declining globally in the last decades. Despite the improvements in the diagnostic procedures, most cases are still detected at advanced stages due to lack of specific symptoms associated with early phases of tumour development. Consequently, gastric cancer poses a major health burden worldwide due to high mortality rates. Continuing advances in high-throughput technologies are revealing an intricate network of genetic and epigenetic changes associated with carcinogenesis...
February 3, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28174608/genome-wide-dna-methylation-profile-identified-a-unique-set-of-differentially-methylated-immune-genes-in-oral-squamous-cell-carcinoma-patients-in-india
#8
Baidehi Basu, Joyeeta Chakraborty, Aditi Chandra, Atul Katarkar, Jadav Ritesh Kumar Baldevbhai, Debjit Dhar Chowdhury, Jay Gopal Ray, Keya Chaudhuri, Raghunath Chatterjee
BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and validated in an additional 53 well-differentiated OSCC and adjacent normal samples...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28169463/relationship-between-epigenetic-regulation-dietary-habits-and-the-developmental-origins-of-health-and-disease-theory
#9
REVIEW
Kazuki Mochizuki, Natsuyo Hariya, Kazue Honma, Toshinao Goda
Environmental stressors during developmental stages are hypothesized to increase the risk of developing metabolic diseases such as obesity, type 2 diabetes, hypertension, and psychiatric diseases during later life. This theory is known as the Developmental Origins of Health and Disease (DOHaD). Recent studies suggest that accumulation of environmental stress, including during developmental stages, is internalized as acquired information designated as "epigenetic memory." This epigenetic memory is generally indicated as DNA methylation and histone modifications in the chromatin...
February 7, 2017: Congenital Anomalies
https://www.readbyqxmd.com/read/28167288/impact-of-tet2-deficiency-on-iron-metabolism-in-erythroblasts
#10
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/28167242/epigenome-wide-dna-methylation-profiling-identifies-differential-methylation-biomarkers-in-high-grade-bladder-cancer
#11
Ekaterina Olkhov-Mitsel, Andrea J Savio, Ken J Kron, Vaijayanti V Pethe, Thomas Hermanns, Neil E Fleshner, Bas W van Rhijn, Theodorus H van der Kwast, Alexandre R Zlotta, Bharati Bapat
Epigenetic changes, including CpG island hypermethylation, occur frequently in bladder cancer (BC) and may be exploited for BC detection and distinction between high-grade (HG) and low-grade (LG) disease. Genome-wide methylation analysis was performed using Agilent Human CpG Island Microarrays to determine epigenetic differences between LG and HG cases. Pathway enrichment analysis and functional annotation determined that the most frequently methylated pathways in HG BC were enriched for anterior/posterior pattern specification, embryonic skeletal system development, neuron fate commitment, DNA binding, and transcription factor activity...
February 3, 2017: Translational Oncology
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
#12
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/28158250/potential-roles-of-dna-methylation-in-the-initiation-and-establishment-of-replicative-senescence-revealed-by-array-based-methylome-and-transcriptome-analyses
#13
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/28155687/subtype-specific-cpg-island-shore-methylation-and-mutation-patterns-in-30-breast-cancer-cell-lines
#14
Heejoon Chae, Sangseon Lee, Kenneth P Nephew, Sun Kim
BACKGROUND: Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from normal and benign tissues, as well as molecular subtypes of breast cancer, can be distinguished based on their distinct genomic, transcriptomic, and epigenomic profiles. In this study, we used affinity-based methylation sequencing data in 30 breast cancer cell lines representing functionally distinct cancer subtypes to investigate methylation and mutation patterns at the whole genome level...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28152499/contributions-of-polyunsaturated-fatty-acids-pufa-on-cerebral-neurobiology-an-integrated-omics-approach-with-epigenomic-focus
#15
Nabarun Chakraborty, Seid Muhie, Raina Kumar, Aarti Gautam, Seshamalini Srinivasan, Bintu Sowe, George Dimitrov, Stacy-Ann Miller, Marti Jett, Rasha Hammamieh
The epigenetic landscape is vulnerable to diets. Here, we investigated the influence of different polyunsaturated fatty acids (PUFA) dietary supplements on rodents' nervous system development and functions and potential consequences to neurodegenerative disorders. Our previous nutrigenomics study showed significant impact of high n-3 PUFA-enriched diet (ERD) on synaptogenesis and various neuromodulators. The present study introduced a second equicaloric diet with n-6 PUFA balanced by n-3 PUFA (BLD). The typical lab diet with high n-6 PUFA was the baseline...
January 5, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28151741/associations-between-genome-wide-gene-expression-and-ambient-nitrogen-oxides-nox
#16
Nahid Mostafavi, Jelle Vlaanderen, Lutzen Portengen, Marc Chadeau-Hyam, Lars Modig, Domenico Palli, Ingvar A Bergdahl, Bert Brunekreef, Paolo Vineis, Dennie G A J Hebels, Jos C S Kleinjans, Vittorio Krogh, Gerard Hoek, Panagiotis Georgiadis, Soterios A Kyrtopoulos, Roel Vermeulen
BACKGROUND: We hypothesize that biological perturbations due to exposure to ambient air pollution are reflected in gene-expression levels in peripheral blood mononuclear cells. METHODS: We assessed the association between exposure to ambient air pollution and genome-wide gene-expression levels in peripheral blood mononuclear cells collected from 550 healthy subjects participating in cohorts from Italy and Sweden. Annual air pollution estimates of nitrogen oxides (NOx) at time of blood collection (1990 to 2006) were available from the ESCAPE study...
January 30, 2017: Epidemiology
https://www.readbyqxmd.com/read/28149334/epigenome-wide-association-study-of-dna-methylation-in-panic-disorder
#17
Mihoko Shimada-Sugimoto, Takeshi Otowa, Taku Miyagawa, Tadashi Umekage, Yoshiya Kawamura, Miki Bundo, Kazuya Iwamoto, Mamoru Tochigi, Kiyoto Kasai, Hisanobu Kaiya, Hisashi Tanii, Yuji Okazaki, Katsushi Tokunaga, Tsukasa Sasaki
BACKGROUND: Panic disorder (PD) is considered to be a multifactorial disorder emerging from interactions among multiple genetic and environmental factors. To date, although genetic studies reported several susceptibility genes with PD, few of them were replicated and the pathogenesis of PD remains to be clarified. Epigenetics is considered to play an important role in etiology of complex traits and diseases, and DNA methylation is one of the major forms of epigenetic modifications. In this study, we performed an epigenome-wide association study of PD using DNA methylation arrays so as to investigate the possibility that different levels of DNA methylation might be associated with PD...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28149327/in-utero-exposure-to-maternal-smoking-is-associated-with-dna-methylation-alterations-and-reduced-neuronal-content-in-the-developing-fetal-brain
#18
Zac Chatterton, Brigham J Hartley, Man-Ho Seok, Natalia Mendelev, Sean Chen, Maria Milekic, Gorazd Rosoklija, Aleksandar Stankov, Iskra Trencevsja-Ivanovska, Kristen Brennand, Yongchao Ge, Andrew J Dwork, Fatemeh Haghighi
BACKGROUND: Intrauterine exposure to maternal smoking is linked to impaired executive function and behavioral problems in the offspring. Maternal smoking is associated with reduced fetal brain growth and smaller volume of cortical gray matter in childhood, indicating that prenatal exposure to tobacco may impact cortical development and manifest as behavioral problems. Cellular development is mediated by changes in epigenetic modifications such as DNA methylation, which can be affected by exposure to tobacco...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28145864/epigenetic-regulation-of-lateralized-fetal-spinal-gene-expression-underlies-hemispheric-asymmetries
#19
Sebastian Ocklenburg, Judith Schmitz, Zahra Moinfar, Dirk Moser, Rena Klose, Stephanie Lor, Georg Kunz, Martin Tegenthoff, Pedro Faustmann, Clyde Francks, Jörg T Epplen, Robert Kumsta, Onur Güntürkün
Lateralization is a fundamental principle of nervous system organization but its molecular determinants are mostly unknown. In humans, asymmetric gene expression in the fetal cortex has been suggested as the molecular basis of handedness. However, human fetuses already show considerable asymmetries in arm movements before the motor cortex is functionally linked to the spinal cord, making it more likely that spinal gene expression asymmetries form the molecular basis of handedness. We analyzed genome-wide mRNA expression and DNA methylation in cervical and anterior thoracal spinal cord segments of five human fetuses and show development-dependent gene expression asymmetries...
February 1, 2017: ELife
https://www.readbyqxmd.com/read/28143871/role-of-host-microrna-hsa-mir-139-3p-in-hpv-16-induced-carcinomas
#20
Malay Kr Sannigrahi, Rajni Sharma, Varinder Singh, Naresh K Panda, Vidya Rattan, Madhu Khullar
PURPOSE: Human papillomavirus 16 (HPV-16) is important risk factor in Head and Neck Cancer (HNC). Studies suggest that microRNAs play an important role in cancer, however, their role in HPV mediated oncogenesis remains largely unknown. We investigated the role of microRNAs with HPV-16 as putative target in HPV-16 mediated cancers. EXPERIMENTAL DESIGN: Using in-silico tools, we identified microRNAs with putative binding sequences on HPV-16 mRNAs. Hsa-miR-139-3p was identified as best candidate miRNA by luciferase reporter assay and was found to be significantly down-regulated in HPV-16 positive tissues and cell lines...
January 31, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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