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CpG methylation

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https://www.readbyqxmd.com/read/30341178/fabp3-in-the-anterior-cingulate-cortex-modulates-the-methylation-status-of-the-glutamic-acid-decarboxylase-67-promoter-region
#1
Yui Yamamoto, Hiroyuki Kida, Yoshiteru Kagawa, Yuki Yasumoto, Hirofumi Miyazaki, Ariful Islam, Masaki Ogata, Yuchio Yanagawa, Dai Mitsushima, Kohji Fukunaga, Yuji Owada
Polyunsaturated fatty acids (PUFAs) are essential for brain development and function. Increasing evidence has shown that an imbalance of PUFAs is associated with various human psychiatric disorders, including autism and schizophrenia. Fatty acid-binding proteins (FABPs), cellular chaperones of PUFAs, are involved in PUFA intracellular trafficking, signal transduction, and gene transcription. In this study, we show that FABP3 is strongly expressed in the γ-aminobutyric acid (GABA)-ergic inhibitory interneurons of the male mouse anterior cingulate cortex (ACC), which is a component of the limbic cortex and is important for the coordination of cognitive and emotional behaviors...
October 19, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/30337373/lysine-methyltransferase-2d-regulates-pancreatic-carcinogenesis-through-metabolic-reprogramming
#2
Marina Koutsioumpa, Maria Hatziapostolou, Christos Polytarchou, Ezequiel J Tolosa, Luciana L Almada, Swapna Mahurkar-Joshi, Jennifer Williams, Ana Belen Tirado-Rodriguez, Sara Huerta-Yepez, Dimitrios Karavias, Helen Kourea, George A Poultsides, Kevin Struhl, David W Dawson, Timothy R Donahue, Martín E Fernández-Zapico, Dimitrios Iliopoulos
OBJECTIVE: Despite advances in the identification of epigenetic alterations in pancreatic cancer, their biological roles in the pathobiology of this dismal neoplasm remain elusive. Here, we aimed to characterise the functional significance of histone lysine methyltransferases (KMTs) and demethylases (KDMs) in pancreatic tumourigenesis. DESIGN: DNA methylation sequencing and gene expression microarrays were employed to investigate CpG methylation and expression patterns of KMTs and KDMs in pancreatic cancer tissues versus normal tissues...
October 18, 2018: Gut
https://www.readbyqxmd.com/read/30336352/platform-independent-models-for-age-prediction-using-dna-methylation-data
#3
Sae Rom Hong, Kyoung-Jin Shin, Sang-Eun Jung, Eun Hee Lee, Hwan Young Lee
Age prediction has been in the spotlight recently because it can provide an important information about the contributors of biological evidence left at crime scenes. Specifically, many researchers have actively suggested age-prediction models using DNA methylation at several CpG sites and tested the candidates using platforms such as the HumanMethylation 450 array and pyrosequencing. With DNA methylation data obtained from each platform, age prediction models were constructed using diverse statistical methods typically with multivariate linear regression...
October 9, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/30334356/dna-methylation-of-fkbp5-and-response-to-exposure-based-psychological-therapy
#4
Susanna Roberts, Robert Keers, Gerome Breen, Jonathan R I Coleman, Peter Jöhren, Agnieszka Kepa, Kathryn J Lester, Jürgen Margraf, Silvia Scheider, Tobias Teismann, André Wannemüller, Thalia C Eley, Chloe C Y Wong
Differential DNA methylation of the hypothalamic-pituitary-adrenal axis related gene FKBP5 has recently been shown to be associated with varying response to environmental influences and may play a role in how well people respond to psychological treatments. Participants (n = 111) received exposure-based cognitive behavioural therapy (CBT) for agoraphobia with or without panic disorder, or specific phobias. Percentage DNA methylation levels were measured for the promoter region and intron 7 of FKBP5. The association between percentage reduction in clinical severity and change in DNA methylation was tested using linear mixed models...
October 18, 2018: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/30333755/a-novel-dnmt3a1-transcript-inhibits-adipogenesis
#5
Bahareldin A Abdalla, Zhenhui Li, Hongjia Ouyang, Endashaw Jebessa, Tianhao Sun, Jia-Ao Yu, Bolin Cai, Biao Chen, Qinghua Nie, Xiquan Zhang
DNA (cytosine-5)-methyltransferase 3a ( Dnmt3a ) is an enzyme that catalyzes the transfer of methyl groups to specific CpG forms in DNA. In mammals, two variant transcripts of Dnmt3a have been successfully identified. To the best of our knowledge, no Dnmt3a transcripts in an avian have been successfully identified. This study was performed to detect different transcripts of Dnmt3a in chickens and to examine whether a novel Dnmt3a transcript named Dnmt3a1 may regulate adipogenesis. In addition to cloning, sequencing, transcript detection, and expression studies, a novel Dnmt3a1 transcript overexpression and knockdown were conducted to explore the potential role of Dnmt3a1 in preadipocyte proliferation and the early stage of adipocyte differentiation...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/30332658/integrated-multi-omic-analysis-of-esthesioneuroblastomas-identifies-two-subgroups-linked-to-cell-ontogeny
#6
Marion Classe, Hui Yao, Roger Mouawad, Chad J Creighton, Alice Burgess, Frederick Allanic, Michel Wassef, Xavier Leroy, Benjamin Verillaud, Geoffrey Mortuaire, Franck Bielle, Christophe Le Tourneau, Jean-Emmanuel Kurtz, David Khayat, Xiaoping Su, Gabriel G Malouf
Esthesioneuroblastoma (ENB) is a rare cancer of the olfactory mucosa, with no established molecular stratification to date. We report similarities of ENB with tumors arising in the neural crest and perform integrative analysis of these tumors. We propose a molecular-based subtype classification of ENB as basal or neural, both of which have distinct pathological, transcriptomic, proteomic, and immune features. Among the basal subtype, we uncovered an IDH2 R172 mutant-enriched subgroup (∼35%) harboring a CpG island methylator phenotype reminiscent of IDH2 mutant gliomas...
October 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/30332484/a-methyl-sensitive-element-induces-bidirectional-transcription-in-tata-less-cpg-island-associated-promoters
#7
Amin Mahpour, Benjamin S Scruggs, Dominic Smiraglia, Toru Ouchi, Irwin H Gelman
How TATA-less promoters such as those within CpG islands (CGI) control gene expression is still a subject of active research. Here, we have identified the "CGCG element", a ten-base pair motif with a consensus sequence of TCTCGCGAGA present in a group of promoter-associated CGI-enriched in ribosomal protein and housekeeping genes. This element is evolutionarily conserved in vertebrates, found in DNase-accessible regions and employs RNA Pol II to activate gene expression. Through analysis of capped-nascent transcripts and supporting evidence from reporter assays, we demonstrate that this element activates bidirectional transcription through divergent start sites...
2018: PloS One
https://www.readbyqxmd.com/read/30328613/integrated-genetic-epigenetic-and-gene-set-enrichment-analyses-identify-notch-as-a-potential-mediator-for-ptsd-risk-after-trauma-results-from-two-independent-african-cohorts
#8
Daniela Conrad, Sarah Wilker, Anna Schneider, Alexander Karabatsiakis, Anett Pfeiffer, Stephan Kolassa, Virginie Freytag, Vanja Vukojevic, Christian Vogler, Annette Milnik, Andreas Papassotiropoulos, Dominique J-F de Quervain, Thomas Elbert, Iris-Tatjana Kolassa
The risk of developing posttraumatic stress disorder (PTSD) increases with the number of traumatic event types experienced (trauma load) in interaction with other psychobiological risk factors. The NOTCH (neurogenic locus notch homolog proteins) signaling pathway, consisting of four different trans-membrane receptor proteins (NOTCH1-4), constitutes an evolutionarily well-conserved intercellular communication pathway (involved, e.g., in cell-cell interaction, inflammatory signaling, and learning processes). Its association with fear memory consolidation makes it an interesting candidate for PTSD research...
October 17, 2018: Psychophysiology
https://www.readbyqxmd.com/read/30327826/benzene-metabolite-1-2-4-benzenetriol-changes-dna-methylation-and-histone-acetylation-of-erythroid-specific-genes-in-k562-cells
#9
Chun-Hong Yu, Yang Li, Xiao Zhao, Shui-Qing Yang, Lei Li, Ning-Xuan Cui, Long Rong, Zong-Chun Yi
1,2,4-Benzenetriol (BT) is one of the phenolic metabolites of benzene, a general occupational hazard and ubiquitous environmental air pollutant with leukemogenic potential in humans. Previous studies have revealed that the benzene metabolites phenol and hydroquinone can inhibit hemin-induced erythroid differentiation in K562 cells. We investigated the roles of DNA methylation and histone acetylation in BT-inhibited erythroid differentiation in K562 cells. When K562 cells were treated with 0, 5, 10, 15 or 20 µM BT for 72 h, hemin-induced hemoglobin synthesis decreased in a concentration-dependent manner...
October 16, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/30326963/systematic-evaluation-of-dna-methylation-age-estimation-with-common-preprocessing-methods-and-the-infinium-methylationepic-beadchip-array
#10
Lisa M McEwen, Meaghan J Jones, David Tse Shen Lin, Rachel D Edgar, Lucas T Husquin, Julia L MacIsaac, Katia E Ramadori, Alexander M Morin, Christopher F Rider, Chris Carlsten, Lluís Quintana-Murci, Steve Horvath, Michael S Kobor
BACKGROUND: The capacity of technologies measuring DNA methylation (DNAm) is rapidly evolving, as are the options for applicable bioinformatics methods. The most commonly used DNAm microarray, the Illumina Infinium HumanMethylation450 (450K array), has recently been replaced by the Illumina Infinium HumanMethylationEPIC (EPIC array), nearly doubling the number of targeted CpG sites. Given that a subset of 450K CpG sites is absent on the EPIC array and that several tools for both data normalization and analyses were developed on the 450K array, it is important to assess their utility when applied to EPIC array data...
October 16, 2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/30326341/hypomethylation-of-line-1-elements-in-schizophrenia-and-bipolar-disorder
#11
Shufen Li, Qiong Yang, Yu Hou, Tingyun Jiang, Lu Zong, Zhongju Wang, Xia Luo, Wenquan Liang, Hu Zhao, Yuping Ning, Cunyou Zhao
Schizophrenia (SCZ) and bipolar disorder (BPD) are severe mental illnesses with evidence of significant genetic and environmental etiological elements in their complex etiologies. 5'-Methylcytosine is the main epigenetic DNA modification that mediates the interplay between genetic and environmental components. In humans, most 5'-methylcytosine modifications are observed in CpG-rich regions within the long interspersed nuclear element (LINE-1). LINE-1 is a mobile retrotransposon that comprises ∼17% of the human genome, and its methylation levels are highly correlated with global DNA methylation levels...
October 10, 2018: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/30324808/a-novel-discriminating-colorectal-cancer-model-for-differentiating-normal-and-tumor-tissues
#12
Xiaohui Sun, Yiping Tian, Qianqian Zheng, Ruizhi Zheng, Aifen Lin, Tianhui Chen, Yimin Zhu, Maode Lai
AIM: To construct a model discriminating colorectal cancer (CRC) based on differential DNA methylation. MATERIALS & METHODS: The CRC-related methylation-modulated genes were retrieved from literature. The methylation levels of CpG sites in the promoter regions and the first exons of candidate genes were verified in The Cancer Genome Atlas data. A model for discriminating CRC based on methylation levels was established using least absolute shrinkage and selection operator regression...
October 16, 2018: Epigenomics
https://www.readbyqxmd.com/read/30324719/myc-and-dnmt3a-mediated-dna-methylation-represses-microrna-200b-in-triple-negative-breast-cancer
#13
Yamei Pang, Jian Liu, Xiang Li, Guodong Xiao, Huangzhen Wang, Ganghua Yang, Yanbo Li, Shou-Ching Tang, Sida Qin, Ning Du, Henggang Zhang, Dapeng Liu, Xin Sun, Hong Ren
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with a poor prognosis. The microRNA-200 (miR-200) family has been associated with breast cancer metastasis. However, the epigenetic mechanisms underlying miR-200b repression in TNBC are not fully elucidated. In this study, we found that MYC proto-oncogene, bHLH transcription factor (MYC) and DNA methyltransferase 3A (DNMT3A) were highly expressed in TNBC tissues compared with other breast cancer subtypes, while miR-200b expression was inhibited significantly...
October 16, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/30321476/gestational-vitamin-d-supplementation-leads-to-reduced-perinatal-rxra-dna-methylation-results-from-the-mavidos-trial
#14
Elizabeth M Curtis, Nevena Krstic, Eloïse Cook, Stefania D'Angelo, Sarah R Crozier, Rebecca J Moon, Robert Murray, Emma Garratt, Paula Costello, Jane Cleal, Brogan Ashley, Nicholas J Bishop, Stephen Kennedy, Aris T Papageorghiou, Inez Schoenmakers, Robert Fraser, Saurabh V Gandhi, Ann Prentice, M Kassim Javaid, Hazel M Inskip, Keith M Godfrey, Christopher G Bell, Karen A Lillycrop, Cyrus Cooper, Nicholas C Harvey
We have previously demonstrated inverse associations between maternal 25(OH)-vitamin D status and perinatal DNA methylation at the retinoid-X-receptor-alpha (RXRA) locus and between RXRA methylation and offspring bone mass. We therefore used an existing randomised trial to test the hypothesis that maternal gestational vitamin D supplementation would lead to reduced perinatal RXRA locus DNA methylation. The Maternal Vitamin D Osteoporosis Study (MAVIDOS) was a multicentre, double-blind, randomised, placebo-controlled trial of 1000IU/day cholecalciferol or matched placebo from 14 weeks' gestation until delivery...
October 15, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/30320886/a-whole-methylome-study-of-ethanol-exposure-in-brain-and-blood-an-exploration-of-the-utility-of-peripheral-blood-as-proxy-tissue-for-brain-in-alcohol-methylation-studies
#15
Shaunna L Clark, Blair N Costin, Robin F Chan, Alexander W Johnson, Linying Xie, Jessica L Jurmain, Gaurav Kumar, Andrey A Shabalin, Ashutosh K Pandey, Karolina A Aberg, Michael F Miles, Edwin van den Oord
BACKGROUND: Recent reviews have highlighted the potential use of blood-based methylation biomarkers as diagnostic and prognostic tools of current and future alcohol use and addiction. Due to the substantial overlap that often exists between methylation patterns across different tissues, including blood and brain, blood-based methylation may track methylation changes in brain, however, little work has explored the overlap in alcohol related methylation in these tissues. METHODS: To study the effects of alcohol on the brain methylome and identify possible biomarkers of these changes in blood, we performed a methylome-wide association study in brain and blood from 40 male DBA/2J mice that received either an acute ethanol or saline intraperitoneal injection...
October 15, 2018: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/30318509/phenotype-independent-dna-methylation-changes-in-prostate-cancer
#16
Davide Pellacani, Alastair P Droop, Fiona M Frame, Matthew S Simms, Vincent M Mann, Anne T Collins, Connie J Eaves, Norman J Maitland
BACKGROUND: Human prostate cancers display numerous DNA methylation changes compared to normal tissue samples. However, definitive identification of features related to the cells' malignant status has been compromised by the predominance of cells with luminal features in prostate cancers. METHODS: We generated genome-wide DNA methylation profiles of cell subpopulations with basal or luminal features isolated from matched prostate cancer and normal tissue samples...
October 15, 2018: British Journal of Cancer
https://www.readbyqxmd.com/read/30317605/lin28a-activates-the-transcription-of-nanog-in-dairy-goat-male-germline-stem-cells
#17
REVIEW
Fanglin Ma, Xiaomin Du, Yudong Wei, Zhe Zhou, Daguia Zambe John Clotaire, Na Li, Sha Peng, Guangpeng Li, Jinlian Hua
LIN28A serves as a crucial marker of dairy goat male germline stem cells (GmGSCs). In our previous study, we demonstrated that LIN28A promotes proliferation, self-renewal, and maintains the stemness of GmGSCs. Here, we found that LIN28A could activate the transcription of NANOG in a let-7g independent manner. We cloned the 5' upstream of two NANOG genes which were located on chromosome 15 ( NANOG-ch15) and chromosome 5 ( NANOG-ch5), respectively, and then examined their promoter activities and promoter methylation levels...
October 14, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/30315898/dynamic-alterations-in-methylation-of-global-dna-and-growth-related-genes-in-large-yellow-croaker-larimichthys-crocea-in-response-to-starvation-stress
#18
Yu Zhang, Weiliang Shen, Mingyue Cao, Juan Li, Baoxiao Zheng, Zhengjia Lou, Baoying Qian, Liangyi Xue
DNA methylation is susceptible to various environmental factors such as salinity, temperature and nutritional conditions, and can affect gene function, organ metabolism, body growth and development. In order to explore the effect of starvation on growth-related genes in large yellow croaker (Larimichthys crocea), we studied methylation of the global DNA and growth-related genes (MSTN1,MSTN2,IGF1,IGF2) and the corresponding mRNA expressions, using ELISA-based technique, bisulfite sequencing PCR (BSP) technique and quantitative Real-time PCR (qRT-PCR) respectively...
October 11, 2018: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/30312431/smoking-and-risk-of-colorectal-cancer-sub-classified-by-tumor-infiltrating-t-cells
#19
Tsuyoshi Hamada, Jonathan A Nowak, Yohei Masugi, David A Drew, Mingyang Song, Yin Cao, Keisuke Kosumi, Kosuke Mima, Tyler S Twombly, Li Liu, Yan Shi, Annacarolina da Silva, Mancang Gu, Wanwan Li, Katsuhiko Nosho, NaNa Keum, Marios Giannakis, Jeffrey A Meyerhardt, Kana Wu, Molin Wang, Andrew T Chan, Edward L Giovannucci, Charles S Fuchs, Reiko Nishihara, Xuehong Zhang, Shuji Ogino
Background: Evidence indicates not only carcinogenic effect of cigarette smoking but also its immunosuppressive effect. We hypothesized that the association of smoking with colorectal cancer risk might be stronger for tumors with lower anti-tumor adaptive immune response. Methods: During follow-up of 134 981 participants (3 490 851 person-years) in the Nurses' Health Study and Health Professionals Follow-up Study, we documented 729 rectal and colon cancer cases with available data on T-cell densities in tumor microenvironment...
October 11, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/30310175/bcat1-and-mir-2504-novel-methylome-signature-distinguishes-spindle-desmoplastic-melanoma-from-superficial-malignant-peripheral-nerve-sheath-tumor
#20
George Jour, Varshini Vasudevaraja, Victor G Prieto, Matija Snuderl, Carlos A Torres-Cabala, Rami Al-Rohil, Erik P Sulman, Leomar Y Ballester, Phyu P Aung
Superficial/cutaneous malignant peripheral nerve sheath tumor is a rare soft tissue neoplasm that shares morphological, immunohistochemical, and molecular features with spindle/desmoplastic melanoma. We aimed to identify a methylome signature to distinguish these two entities. We analyzed 15 cases of spindle/desmoplastic melanoma and 15 cases of cutaneous malignant peripheral nerve sheath tumor in 23 men and 7 women. DNA from formalin-fixed, paraffin-embedded tissues was extracted and processed using the Illumina Infinium Methylation EPIC array interrogating 866,562 CpG sites...
October 11, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
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