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https://www.readbyqxmd.com/read/28805248/epigenetics-and-dna-methylomic-profiling-in-alzheimer-s-disease-and-other-neurodegenerative-diseases
#1
REVIEW
Janou A Y Roubroeks, Rebecca G Smith, Daniel L A van den Hove, Katie Lunnon
Recent studies have suggested a role for epigenetic mechanisms in the complex etiology of various neurodegenerative diseases. In this review, we discuss advances that have been made towards understanding the role of epigenetic processes in neurodegenerative disorders, with a particular focus on Alzheimer's disease, where the most extensive studies have been undertaken to date. We provide a brief overview of DNA modifications, followed by a summarization of studies of DNA modifications in Alzheimer's disease and other neurodegenerative diseases...
August 14, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28801915/manganese-and-1-methyl-4-phenylpyridinium-mpp-induced-neurotoxicity-indicate-differences-in-morphological-electrophysiological-and-genome-wide-alterations-implications-for-idiopathic-parkinson-s-disease
#2
Rajeswara Babu Mythri, Narayana Reddy Raghunath, Santosh Chandrakant Narwade, Mirazkar DasharathaRao Pandareesh, Kollarkandi Rajesh Sabitha, Mohamad Aiyaz, Bipin Chand, Manas Sule, Krittika Ghosh, Senthil Kumar, Bhagyalakshmi Shankarappa, Soundarya Soundararajan, Phalguni Anand Alladi, Meera Purushottam, Narayanappa Gayathri, Deepti Dileep Deobagkar, Thenkanidiyoor Rao Laxmi, Srinivas Bharath Muchukunte Mukunda
Idiopathic Parkinson's disease (iPD) and manganese-induced atypical Parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to levodopa distinguish both, differences at the neuronal level are largely unknown. We studied the morphological, neurophysiological and molecular differences in dopaminergic neurons exposed to the PD toxin 1-methyl-4-phenylpyridinium ion (MPP(+) ) and manganese (Mn) followed by validation in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and Mn mouse models...
August 12, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28798132/single-cell-methylomes-identify-neuronal-subtypes-and-regulatory-elements-in-mammalian-cortex
#3
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval, Brian Bui, Terrence J Sejnowski, Timothy T Harkins, Eran A Mukamel, M Margarita Behrens, Joseph R Ecker
The mammalian brain contains diverse neuronal types, yet we lack single-cell epigenomic assays that are able to identify and characterize them. DNA methylation is a stable epigenetic mark that distinguishes cell types and marks regulatory elements. We generated >6000 methylomes from single neuronal nuclei and used them to identify 16 mouse and 21 human neuronal subpopulations in the frontal cortex. CG and non-CG methylation exhibited cell type-specific distributions, and we identified regulatory elements with differential methylation across neuron types...
August 11, 2017: Science
https://www.readbyqxmd.com/read/28796917/single-base-methylome-analysis-reveals-dynamic-epigenomic-differences-associated-with-water-deficit-in-apple
#4
Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan
Cytosine methylation is an essential feature of epigenetic regulation and is involved in various biological processes. Although cytosine methylation has been analyzed at the genomic scale for several plant species, there is a general lack of understanding of the dynamics of global and genic DNA methylation in plants growing in environments challenged with biotic and abiotic stresses. In this study, we mapped cytosine methylation at single-base resolution in the genome of commercial apple (Malus x domestica), and analyzed changes in methylation patterns associated with water deficit in representative drought-sensitive and drought-tolerant cultivars...
August 10, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28781890/self-reported-pregnancy-exposures-and-placental-dna-methylation-in-the-marbles-prospective-autism-sibling-study
#5
Rebecca J Schmidt, Diane I Schroeder, Florence K Crary-Dooley, Jacqueline M Barkoski, Daniel J Tancredi, Cheryl K Walker, Sally Ozonoff, Irva Hertz-Picciotto, Janine M LaSalle
Human placenta is a fetal-derived tissue that offers a unique sample of epigenetic and environmental exposures present in utero. In the MARBLES prospective pregnancy study of high-risk younger siblings of children with autism spectrum disorder (ASD), pregnancy and environmental factors collected by maternal interviews were examined as predictors of placental DNA methylation, including partially methylated domains (PMDs), an embryonic feature of the placental methylome. DNA methylation data from MethylC-seq analysis of 47 placentas of children clinically diagnosed at 3 years with ASD or typical development using standardized assessments were examined in relation to: child's gestational age, birth-weight, and diagnosis; maternal pre-pregnancy body mass index, smoking, education, parity, height, prenatal vitamin and folate intake; home ownership; pesticides professionally applied to lawns or gardens or inside homes, pet flea/tick pouches, collars, or soaps/shampoos used in the 3 months prior to or during pregnancy...
December 2016: Environmental Epigenetics
https://www.readbyqxmd.com/read/28763057/becon-a-tool-for-interpreting-dna-methylation-findings-from-blood-in-the-context-of-brain
#6
R D Edgar, M J Jones, M J Meaney, G Turecki, M S Kobor
Tissue differences are one of the largest contributors to variability in the human DNA methylome. Despite the tissue-specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well-documented...
August 1, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28758879/genome-wide-analysis-of-cytosine-dna-methylation-revealed-salicylic-acid-promotes-defense-pathways-over-seedling-development-in-pearl-millet
#7
Baba Ngom, Ibrahima Sarr, Josphert Kimatu, Edward Mamati, Ndjido Ardo Kane
Cytosine DNA methylation is an epigenetic regulatory system used by plants to control gene expression. Methylation pattern always changes after abiotic stresses, pathogens and pest infections or after a treatment with salicylic acid (SA). The latter is a key player in plant development and defense against insect herbivores, pathogens, and abiotic stresses. The roles of SA on the methylation patterns and the plant development were carried out in four pearl millet (Pennisetum glaucum) varieties. Seedlings of four early-flowering photosensitive genotypes (PMS3, PMI8, PMG, and PMT2) were grown on MS medium supplemented with null or different doses of SA...
July 31, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28756583/phytopathogen-induced-changes-to-plant-methylomes
#8
REVIEW
Tarek Hewezi, Vince Pantalone, Morgan Bennett, C Neal Stewart, Tessa M Burch-Smith
DNA methylation is a dynamic and reversible type of epigenetic mark that contributes to cellular physiology by affecting transcription activity, transposon mobility and genome stability. When plants are infected with pathogens, plant DNA methylation patterns can change, indicating an epigenetic interplay between plant host and pathogen. In most cases methylation can change susceptibility. While DNA hypomethylation appears to be a common phenomenon during the susceptible interaction, the levels and patterns of hypomethylation in transposable elements and genic regions may mediate distinct responses against various plant pathogens...
July 29, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28754676/nsd1-inactivation-and-setd2-mutation-drive-a-convergence-toward-loss-of-function-of-h3k36-writers-in-clear-cell-renal-cell-carcinomas
#9
Xiaoping Su, Jianping Zhang, Roger Mouawad, Eva Compérat, Morgan Roupret, Frederick Allanic, Jérôme Parra, Marc-Olivier Bitker, Erika J Thompson, Banumathy Gowrishankar, Jane Houldsworth, John N Weinstein, Jörg Tost, Bradley M Broom, David Khayat, Jean-Philippe Spano, Nizar M Tannir, Gabriel G Malouf
Extensive dysregulation of chromatin-modifying genes in clear-cell renal cell carcinoma (ccRCC) has been uncovered through next-generation sequencing. However, a scientific understanding of the crosstalk between epigenetic and genomic aberrations remains limited. Here we identify three ccRCC epigenetic clusters, including a clear-cell CpG island methylator phenotype (C-CIMP) subgroup associated with promoter methylation of vascular endothelial growth factor receptor genes (FLT4, FLT1 and KDR). C-CIMP was furthermore characterized by silencing of genes related to vasculature development...
July 28, 2017: Cancer Research
https://www.readbyqxmd.com/read/28751909/simultaneous-methylation-level-assessment-of-hundreds-of-cpg-sites-by-targeted-bisulfite-pcr-sequencing-tbpseq
#10
Kyuheum Jeon, Byungkuk Min, Jung S Park, Yong-Kook Kang
Methylated-DNA sequencing technologies are producing vast amounts of methylome data from cancer samples, from which cancer-associated differentially methylated CpG sites (cDMCs) are continuously identified and filed. The inclusion of as many cDMCs as possible helps improve the accuracy of cancer diagnosis and sometimes identify cancer subtypes. However, the lack of an established method for the analysis of 100s of cDMCs practically impedes their robust use in clinical medicine. Here, we tested the availability of targeted bisulfite-PCR-sequencing (TBPseq) technology for the assessment of methylation levels of a myriad of CpGs scattered over the genome...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28748001/a-long-range-interactive-dna-methylation-marker-panel-for-the-promoters-of-hoxa9-and-hoxa10-predicts-survival-in-breast-cancer-patients
#11
Seong-Min Park, Eun-Young Choi, Mingyun Bae, Jung Kyoon Choi, Youn-Jae Kim
BACKGROUND: Most DNA cancer methylation markers are based on the transcriptional regulation of the promoter-gene relationship. Recently, the importance of long-range interactions between distal CpGs and target genes has been revealed. Here, we attempted to identify methylation markers for breast cancer that interact with distant genes. RESULTS: We performed integrated analysis using chromatin interactome data, methylome data, transcriptome data, and clinical information for breast cancer from public databases...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28747387/molecular-characteristics-of-the-kcnj5-mutated-aldosterone-producing-adenomas
#12
Masanori Murakami, Takanobu Yoshimoto, Kazuhiko Nakabayashi, Yujiro Nakano, Takahiro Fukaishi, Kyoichiro Tsuchiya, Isao Minami, Ryotaro Bouchi, Kohji Okamura, Yasuhisa Fujii, Koshi Hashimoto, Ken-Ichiro Hata, Kazunori Kihara, Yoshihiro Ogawa
The pathophysiology of aldosterone-producing adenomas (APAs) has been investigated via genetic approaches and the pathogenic significance of a series of somatic mutations, including KCNJ5, has been uncovered. However, how the mutational status of an APA is associated with its molecular characteristics, including its transcriptome and methylome, has not been fully understood. This study was undertaken to explore the molecular characteristics of APAs, specifically focusing on APAs with KCNJ5 mutations as opposed to those without KCNJ5 mutations, by comparing their transcriptome and methylome status...
July 26, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28742980/disease-relevant-modifications-of-the-methylome-and-transcriptome-by-particulate-matter-pm2-5-from-biomass-combustion
#13
Katharina Heßelbach, Gwang-Jin Kim, Stephan Flemming, Thomas Häupl, Marc Bonin, Regina Dornhof, Stefan Günther, Irmgard Merfort, Matjaz Humar
Exposure to particulate matter (PM) is recognized as a major health hazard, but molecular responses are still insufficiently described. We analyzed the epigenetic impact of ambient PM2.5 from biomass combustion on the methylome of primary human bronchial epithelial BEAS-2B cells using the Illumina HumanMethylation450 BeadChip. The transcriptome was determined by the Affymetrix HG-U133 Plus 2.0 Array. PM2.5 induced genome wide alterations of the DNA methylation pattern, including differentially methylated CpGs in the promoter region associated with CpG islands...
July 25, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28742579/a-review-of-the-epigenetic-contributions-to-endometriosis
#14
Frances W Grimstad, Alan Decherney
Epigenetic influences have been postulated to affect the course of endometriosis. DNA methyltransferases, estrogen and progesterone receptors, micro-RNAs, and histone deacetylators, have shown differential expression in endometriosis compared with normal endometrium. Others such as aromatase, Steroid Factor-1, COX-2, and Homeobox A10 also have epigenetic modifications in endometriosis. Limitations in this area of research include heterogeneity in study design, patient populations, and methods of analysis. Larger, controlled studies are needed...
September 2017: Clinical Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28740750/herbicide-injury-induces-dna-methylome-alterations-in-arabidopsis
#15
Gunjune Kim, Christopher R Clarke, Hailey Larose, Hong T Tran, David C Haak, Liqing Zhang, Shawn Askew, Jacob Barney, James H Westwood
The emergence of herbicide-resistant weeds is a major threat facing modern agriculture. Over 470 weedy-plant populations have developed resistance to herbicides. Traditional evolutionary mechanisms are not always sufficient to explain the rapidity with which certain weed populations adapt in response to herbicide exposure. Stress-induced epigenetic changes, such as alterations in DNA methylation, are potential additional adaptive mechanisms for herbicide resistance. We performed methylC sequencing of Arabidopsis thaliana leaves that developed after either mock treatment or two different sub-lethal doses of the herbicide glyphosate, the most-used herbicide in the history of agriculture...
2017: PeerJ
https://www.readbyqxmd.com/read/28735485/genome-wide-analysis-of-dna-methylation-in-hematopoietic-cells-dna-methylation-analysis-by-wgbs
#16
Mira Jeong, Anna G Guzman, Margaret A Goodell
DNA methylation is a major epigenetic modification that regulates gene expression, genome imprinting, and development and has a role in diseases including cancer. There are various methods for whole-genome methylation profiling that differ in cost and resolution. Recent advances in high-throughput sequencing technologies coupled with bisulfite treatment enable absolute DNA methylation quantification and genome-wide single-nucleotide resolution analysis. In this chapter, we provide detailed protocols for whole-genome bisulfite sequencing (WGBS), which captures the complete methylome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735349/connecting-the-dots-between-fatty-acids-mitochondrial-function-and-dna-methylation-in-atherosclerosis
#17
REVIEW
Silvio Zaina, Gertrud Lund
PURPOSE OF REVIEW: The quest for factors and mechanisms responsible for aberrant DNA methylation in human disease-including atherosclerosis-is a promising area of research. This review focuses on the role of fatty acids (FAs) as modulators of DNA methylation-in particular the role of mitochondrial beta-oxidation in FA-induced changes in DNA methylation during the progression of atherosclerosis. RECENT FINDINGS: Recent publications have advanced the knowledge in all areas touched by this review: the causal role of lipids in shaping the DNA methylome, the associations between chronic degenerative disease and mitochondrial function, the lipid composition of the atheroma, and the relevance of DNA hypermethylation in atherosclerosis...
September 2017: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/28730820/tryptic-peptides-bearing-c-terminal-dimethyllysine-need-be-considered-during-the-analysis-of-lysine-dimethylation-in-proteomic-study
#18
Ming Chen, Min Zhang, Linhui Zhai, Hao Hu, Ping Liu, Minjia Tan
Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue. In this study, we tested the ability of trypsin to cleave dimethylated lysine residues in synthetic peptides, purified albumin and whole cell lysate, and found that the C-terminal of dimethylated lysine residue could be cleaved in a protein sequence-dependent manner...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28728396/characterization-and-functional-inferences-of-a-genome-wide-dna-methylation-profile-in-the-loin-longissimus-dorsi-muscle-of-swine
#19
Woonsu Kim, Hyesun Park, Kang-Seok Seo, Seongwon Seo
Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates)...
May 14, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28724534/m6aviewer-software-for-the-detection-analysis-and-visualization-of-n6-methyl-adenosine-peaks-from-m6a-seq-me-rip-sequencing-data
#20
Agne Antanaviciute, Belinda Baquero-Perez, Christopher M Watson, Sally M Harrison, Carolina Lascelles, Laura Crinnion, Alexander F Markham, David T Bonthron, Adrian Whitehouse, Ian M Carr
Recent methods for transcriptome-wide N6-methyl-adenosine(m6A) profiling have facilitated investigations into the RNA methylome and established m6A as a dynamic modification that has critical regulatory roles in gene expression and may play a role in human disease. However, bioinformatics resources available for the analysis of m6A sequencing data are still limited. Here, we describe m6aViewer - a cross-platform application for analysis and visualisation of m6A peaks from sequencing data. m6aViewer implements a novel m6A peak-calling algorithm that identifies high-confidence methylated residues with more precision than previously described approaches...
July 19, 2017: RNA
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