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https://www.readbyqxmd.com/read/28449092/genome-wide-dna-methylomes-from-discrete-developmental-stages-reveal-the-predominance-of-non-cpg-methylation-in-tribolium-castaneum
#1
Xiaowen Song, Fei Huang, Juanjuan Liu, Chengjun Li, Shanshan Gao, Wei Wu, Mengfan Zhai, Xiaojuan Yu, Wenfeng Xiong, Jia Xie, Bin Li
Cytosine DNA methylation is a vital epigenetic regulator of eukaryotic development. Whether this epigenetic modification occurs in Tribolium castaneum has been controversial, its distribution pattern and functions have not been established. Here, using bisulphite sequencing (BS-Seq), we confirmed the existence of DNA methylation and described the methylation profiles of the four life stages of T. castaneum. In the T. castaneum genome, both symmetrical CpG and non-CpG methylcytosines were observed. Symmetrical CpG methylation, which was catalysed by DNMT1 and occupied a small part in T...
April 25, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28449087/methyl-cpg-binding-domain-protein-1-regulates-localization-and-activity-of-tet1-in-a-cxxc3-domain-dependent-manner
#2
Peng Zhang, Cathia Rausch, Florian D Hastert, Boyana Boneva, Alina Filatova, Sujit J Patil, Ulrike A Nuber, Yu Gao, Xinyu Zhao, M Cristina Cardoso
Cytosine modifications diversify and structure the genome thereby controlling proper development and differentiation. Here, we focus on the interplay of the 5-methylcytosine reader Mbd1 and modifier Tet1 by analyzing their dynamic subcellular localization and the formation of the Tet oxidation product 5-hydroxymethylcytosine in mammalian cells. Our results demonstrate that Mbd1 enhances Tet1-mediated 5-methylcytosine oxidation. We show that this is due to enhancing the localization of Tet1, but not of Tet2 and Tet3 at heterochromatic DNA...
April 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448896/differentially-methylated-embryonal-fyn-associated-substrate-efs-gene-as-a-blood-specific-epigenetic-marker-and-its-potential-application-in-forensic-casework
#3
Athina Vidaki, Cecilia Johansson, Federica Giangasparo
DNA methylation patterns have the ability to reveal the activities of genes within a certain tissue at a particular time point. Tissue-specific DNA methylation patterns have been previously investigated for their applicability in the identification of forensically relevant body fluids, however there is still a lack in robust markers. While following a genome-wide scale investigation has a great potential to reveal useful tissue-specific changes, a gene-targeted approach can also lead to significant outcomes, especially in genomic locations not included in the genome-wide experiments...
April 19, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28448740/sequencing-on-the-solid-5500xl-system-in-depth-characterization-of-the-gc-bias
#4
Simone Roeh, Peter Weber, Monika Rex-Haffner, Jan M Deussing, Elisabeth B Binder, Mira Jakovcevski
Different types of sequencing biases have been described and subsequently improved for a variety of sequencing systems, mostly focusing on the widely used Illumina systems. Similar studies are missing for the SOLiD 5500xl system, a sequencer which produced many data sets available to researchers today. Describing and understanding the bias is important to accurately interpret and integrate these published data in various ongoing research projects. We report a particularly strong GC bias for this sequencing system when analyzing a defined gDNA mix of five microbes with a wide range of different GC contents (20-72%) when comparing to the expected distribution and Illumina MiSeq data from the same DNA pool...
April 27, 2017: Nucleus
https://www.readbyqxmd.com/read/28448736/orphan-cpg-islands-define-a-novel-class-of-highly-active-enhancers
#5
Joshua S K Bell, Paula M Vertino
CpG islands (CGI) are critical genomic regulatory elements that support transcriptional initiation and are associated with the promoters of most human genes. CGI are distinguished from the bulk genome by their high CpG density, lack of DNA methylation, and euchromatic features. While CGI are canonically known as strong promoters, thousands of 'orphan' CGI lie far from any known transcript, leaving their function an open question. We undertook a comprehensive analysis of the epigenetic state of orphan CGI across over 100 cell types...
April 27, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28448718/cannabis-use-by-women-during-pregnancy-does-not-influence-infant-dna-methylation-of-the-dopamine-receptor-drd4
#6
Peter D Fransquet, Delyse Hutchinson, Craig A Olsson, Steve Allsop, Elizabeth J Elliott, Lucinda Burns, Richard Mattick, Richard Saffery, Joanne Ryan
BACKGROUND: Maternal cannabis use in pregnancy is linked with long-term adverse behavioral outcomes in offspring. Epigenetic processes established in utero that affect dopaminergic (reward) signaling may mediate risks. Associations between cannabis use and offspring DNA methylation have not been investigated; however, maternal tobacco smoking in pregnancy is associated with distinct patterns of DNA methylation at birth and beyond. OBJECTIVES: To determine whether maternal cannabis use is associated with methylation of the dopamine receptor gene DRD4 promoter in infants...
April 27, 2017: American Journal of Drug and Alcohol Abuse
https://www.readbyqxmd.com/read/28447857/cpg-specific-methylation-at-rheumatoid-arthritis-diagnosis-as-a-marker-of-treatment-response
#7
Steven Horsburgh, Marzena Ciechomska, Steven O'Reilly
No abstract text is available yet for this article.
April 27, 2017: Epigenomics
https://www.readbyqxmd.com/read/28444219/dna-methylation-of-a-novel-pak4-locus-influences-ototoxicity-susceptibility-following-cisplatin-and-radiation-therapy-for-pediatric-embryonal-tumors
#8
Austin L Brown, Kayla L Foster, Philip J Lupo, Erin C Peckham-Gregory, Jeffrey C Murray, M Fatih Okcu, Ching C Lau, Surya P Rednam, Murali Chintagumpala, Michael E Scheurer
Background: Ototoxicity is a common adverse side effect of platinum chemotherapy and cranial radiation therapy; however, individual susceptibility is highly variable. Therefore, the objective of this study was to conduct an epigenome-wide association study to identify differentially methylated CpG sites associated with ototoxicity susceptibility among cisplatin-treated pediatric patients with embryonal tumors. Methods: Samples were collected for a discovery (n=62) and a replication cohort (n=18) of medulloblastoma and primitive neuroectodermal tumor patients...
April 24, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28444195/dna-methylome-analysis-reveals-distinct-epigenetic-patterns-of-ascending-aortic-dissection-and-bicuspid-aortic-valve
#9
Sun Pan, Hao Lai, Yiru Shen, Charles Breeze, Stephan Beck, Tao Hong, Chunsheng Wang, Andrew E Teschendorff
Epigenetics may mediate the effects of environmental risk factors on disease, including heart disease. Thus, measuring the DNA methylome offers the opportunity to identify novel disease biomarkers and novel insights into disease mechanisms. The DNA methylation landscape of ascending aortic dissection (AD) and bicuspid aortic valve (BAV) with aortic aneurysmal dilatation remain uncharacterized. The present study aimed to explore the genome-wide DNA methylation landscape underpinning these two diseases. Methods and results: We used Illumina 450k DNA methylation beadarrays to analyze 21 ascending aorta samples, including 10 cases with AD, 5 with BAV and 6 healthy controls...
April 19, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28443478/role-of-oxidative-stress-in-epigenetic-modification-in-endometriosis
#10
Fuminori Ito, Yuki Yamada, Aiko Shigemitsu, Mika Akinishi, Hiroko Kaniwa, Ryuta Miyake, Shoichiro Yamanaka, Hiroshi Kobayashi
Aberrant DNA methylation and histone modification are associated with an increased risk of reproductive disorders such as endometriosis. However, a cause-effect relationship between epigenetic mechanisms and endometriosis development has not been fully determined. This review provides current information based on oxidative stress in epigenetic modification in endometriosis. This article reviews the English-language literature on epigenetics, DNA methylation, histone modification, and oxidative stress associated with endometriosis in an effort to identify epigenetic modification that causes a predisposition to endometriosis...
January 1, 2017: Reproductive Sciences
https://www.readbyqxmd.com/read/28443051/social-behavior-of-pet-dogs-is-associated-with-peripheral-oxtr-methylation
#11
Giulia Cimarelli, Zsófia Virányi, Borbála Turcsán, Zsolt Rónai, Mária Sasvári-Székely, Zsófia Bánlaki
Oxytocin is a key modulator of emotional processing and social cognitive function. In line with this, polymorphisms of genes involved in oxytocin signaling, like the oxytocin receptor (OXTR) gene, are known to influence social behavior in various species. However, to date, no study has investigated environmental factors possibly influencing the epigenetic variation of the OXTR gene and its behavioral effects in dogs. Pet dogs form individualized and strong relationships with their owners who are central figures in the social environment of their dogs and therefore might influence the methylation levels of their OXTR gene...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28442560/obesity-and-menopause-modify-the-epigenomic-profile-of-breast-cancer
#12
Ana B Crujeiras, Angel Díaz-Lagares, Olafur A Stefansson, Manuel Macias, Juan Sandoval, Juan Cueva, Rafael López-López, Sebastian Moran, Jon G Jonasson, Laufey Tryggvadottir, Elinborg Olafsdottir, Francisco J Tinahones, Marcos C Carreira, Felipe F Casanueva, Manel Esteller
Obesity is a high risk factor for breast cancer. This relationship could be marked by a specific methylome. The current work was aimed to explore the impact of obesity and menopausal status on variation in breast cancer methylomes. Data from Infinium 450K array-based methylomes of 64 breast tumor were coupled with information on BMI and menopausal status. Additionally, DNA methylation results were validated in 18 non-tumor and 81 tumor breast samples. Breast tumors arising in either pre- or postmenopausal women stratified by BMI or menopausal status alone were not associated with a specific DNA methylation pattern...
April 25, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28441648/the-epigenetic-regulation-of-gata4-dependent-brain-natriuretic-peptide-expression-during-alcohol-withdrawal
#13
Alexander Glahn, Mathias Rhein, Annemarie Heberlein, Marc Muschler, Johannes Kornhuber, Helge Frieling, Stefan Bleich, Thomas Hillemacher
OBJECTIVE: Natriuretic peptides participate in the collection of metabolic effects during alcohol withdrawal. Having witnessed modulation of other natriuretic peptides in alcohol-dependent patients during alcohol withdrawal, we were interested in the relation of brain natriuretic peptide (BNP) methylation with protein expression and craving in this longitudinal study. METHODS: Ninety-nine male patients were compared to 101 healthy controls concerning epigenetic regulation and protein expression during detoxification treatment...
April 26, 2017: Neuropsychobiology
https://www.readbyqxmd.com/read/28440505/detection-of-fetal-epigenetic-biomarkers-through-genome-wide-dna-methylation-study-for-non-invasive-prenatal-diagnosis
#14
Hong-Dan Wang, Lin Liu, Hui-Ru Zhao, Qiao-Fang Hou, Jing-Bin Yan, Wei-Li Shi, Qian-Nan Guo, Li Wang, Shi-Xiu Liao, Bo-Feng Zhu
The discovery of cell-free DNA fetal (cff DNA) in maternal plasma during pregnancy provides a novel perspective for the development of non‑invasive prenatal diagnosis (NIPD). Against the background of maternal DNA, the use of the relatively low concentration of cff DNA is limited in NIPD. Therefore, in order to overcome the complication of the background of maternal DNA and expand the scope of cff DNA application in clinical practice, it is necessary to identify novel universal fetal‑specific DNA markers...
April 25, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28440489/genome-wide-dna-methylation-sequencing-reveals-mir-663a-is-a-novel-epimutation-candidate-in-cimp-high-endometrial-cancer
#15
Megumi Yanokura, Kouji Banno, Masataka Adachi, Daisuke Aoki, Kuniya Abe
Aberrant DNA methylation is widely observed in many cancers. Concurrent DNA methylation of multiple genes occurs in endometrial cancer and is referred to as the CpG island methylator phenotype (CIMP). However, the features and causes of CIMP-positive endometrial cancer are not well understood. To investigate DNA methylation features characteristic to CIMP-positive endometrial cancer, we first classified samples from 25 patients with endometrial cancer based on the methylation status of three genes, i.e. MLH1, CDH1 (E-cadherin) and APC: CIMP-high (CIMP-H, 2/25, 8...
April 19, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28440441/preliminary-analysis-of-the-association-between-methylation-of-the-ace2-promoter-and-essential-hypertension
#16
Rui Fan, Shu-Qi Mao, Tian-Lun Gu, Fa-De Zhong, Min-Li Gong, Ling-Mei Hao, Feng-Ying Yin, Chang-Zheng Dong, Li-Na Zhang
The aim of the present study was to investigate whether methylation of the angiotensin I converting enzyme 2 (ACE2) promoter increases the risk of essential hypertension (EH). A total of 96 patients with EH were recruited and 96 sex‑ and age‑matched healthy controls. Methylation of 5 CpG dinucleotides in the ACE2 promoter was quantified using bisulfite pyrosequencing. Logistic regression and multiple linear regression were used to adjust for confounding factors and the generalized multifactor dimensionality reduction (GMDR) method was applied to investigate high‑order interactions...
April 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28439875/epigenetic-repression-of-mir-375-is-the-dominant-mechanism-for-constitutive-activation-of-the-pdpk1-rps6ka3-signalling-axis-in-multiple-myeloma
#17
Shotaro Tatekawa, Yoshiaki Chinen, Masaki Ri, Tomoko Narita, Yuji Shimura, Yayoi Matsumura-Kimoto, Taku Tsukamoto, Tsutomu Kobayashi, Eri Kawata, Nobuhiko Uoshima, Tomohiko Taki, Masafumi Taniwaki, Hiroshi Handa, Shinsuke Iida, Junya Kuroda
Cytogenetic/molecular heterogeneity is the hallmark of multiple myeloma (MM). However, we recently showed that the serine/threonine kinase PDPK1 and its substrate RPS6KA3 (also termed RSK2) are universally active in MM, and play pivotal roles in myeloma pathophysiology. In this study, we assessed involvement of aberrant miR-375 repression in PDPK1 overexpression in MM. An analysis of plasma cells from 30 pre-malignant monoclonal gammopathies of undetermined significance and 73 MM patients showed a significant decrease in miR-375 expression in patient-derived plasma cells regardless of the clinical stage, compared to normal plasma cells...
April 25, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28439102/mecp2-regulated-mirnas-control-early-human-neurogenesis-through-differential-effects-on-erk-and-akt-signaling
#18
N Mellios, D A Feldman, S D Sheridan, J P K Ip, S Kwok, S K Amoah, B Rosen, B A Rodriguez, B Crawford, R Swaminathan, S Chou, Y Li, M Ziats, C Ernst, R Jaenisch, S J Haggarty, M Sur
Rett syndrome (RTT) is an X-linked, neurodevelopmental disorder caused primarily by mutations in the methyl-CpG-binding protein 2 (MECP2) gene, which encodes a multifunctional epigenetic regulator with known links to a wide spectrum of neuropsychiatric disorders. Although postnatal functions of MeCP2 have been thoroughly investigated, its role in prenatal brain development remains poorly understood. Given the well-established importance of microRNAs (miRNAs) in neurogenesis, we employed isogenic human RTT patient-derived induced pluripotent stem cell (iPSC) and MeCP2 short hairpin RNA knockdown approaches to identify novel MeCP2-regulated miRNAs enriched during early human neuronal development...
April 25, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28438695/wnt-inhibitory-factor-1-promoter-hypermethylation-is-an-early-event-during-gallbladder-cancer-tumorigenesis-that-predicts-poor-survival
#19
Bin Lin, HaiJie Hong, XiaoJie Jiang, ChengZong Li, SiYuan Zhu, NanHong Tang, XiaoQian Wang, FeiFei She, YanLing Chen
Gallbladder cancer (GBC) is the most common malignant tumor in the human biliary tract, but the lack of a marker for timely diagnosis leads to an extremely poor prognosis. In this study, we assessed CpG sites in the WIF-1 promoter using bisulfite sequencing PCR and methylation-specific PCR to detect methylation in gallbladder cancer and cholecystitis tissues. WIF-1 promoter methylation was present in 36 of 50 (72.0%) gallbladder cancers but only 5 of 20 (25.0%) cholecystitis tissues (P=0.000<0.05), suggesting that WIF-1 promoter methylation might participate in the malignant transformation of cholecystitis into gallbladder cancer...
April 21, 2017: Gene
https://www.readbyqxmd.com/read/28438683/identification-and-expression-of-piwil2-in-turbot-scophthalmus-maximus-with-implications-of-the-involvement-in-embryonic-and-gonadal-development
#20
Huizhen Wang, Bo Wang, Xiaobing Liu, Yuezhong Liu, Xinxin Du, Quanqi Zhang, XuBo Wang
Piwil2, a member of the Argonaute family, is involved in the biogenesis of PIWI-interacting RNAs (piRNAs) and plays an important role in regulating gametogenesis. In the present study, we identified turbot Scophthalmus maximus piwil2 gene, named Smpiwil2, which contained a PAZ domain and a PIWI domain. Sequence comparison, genomic structure and phylogenetic analyses showed that Smpiwil2 is homologous to that of teleosts and tetrapods. The Smpiwil2 transcript showed higher expression in ovary than in testis, demonstrating a sexually dimorphic gene expression pattern...
April 21, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
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